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ETL configuration for BMEG

Shell 2.85% Python 70.63% Dockerfile 0.72% Go 9.09% R 14.03% Common Workflow Language 0.71% Java 1.97%

bmeg-etl's Introduction

overview

This repository contains nginx and static file setup for:

bmeg public site https://bmeg.io
bmeg data directory https://bmeg.io/bmeg-data
secure access to grip server https://bmeg.io/analyze/access
secure access to recount.bio data https://recount.bio

Additionally, we maintain nginx configurations for:

jupyterhub - for analysis https://bmeg-jupyter.ddns.net
cadvisor - for devops statistics https://bmeg-jupyter.ddns.net/cadvisor
gen3 - example arbitrary other content https://gen3-ohsu.ddns.net

Each site (domain) is backed by a letsencrypt certbot certificate renewal process.

deployment

databases and docker workareas live on : /mnt/data1/...
repositories, etl and configurations live on : /mnt/data2/...

structure

nginx

The nginx service leverages two key technologies:

certbot and a shared volume data/
- provides signed valid certs for multiple sites
cloudflare/nginx-google-oauth
- implements google oauth, implemented for external connections to the grip server
- see secrets/nginx.env for parameters, matched with 'bmeg' gcp

The run.sh script launches nginx within its container

The script will reload the config and certs every 6 hours.
The DEBUG env variable controls parameter logging

  nginx
  ├── Dockerfile
  ├── etc
  │   └── nginx
  │       ├── conf.d
  │       │   ├── default.conf
  │       │   └── protected.conf
  │       ├── grip.conf
  │       ├── http.conf.d
  │       │   └── env.conf
  │       ├── lua
  │       │   └── nginx-google-oauth
  │       ├── nginx.conf
  │       ├── protected.conf
  │       ├── sites-available
  │       │   └── default
  │       └── sites-enabled
  │           ├── bmeg.io
  │           ├── bmegio.ohsu.edu
  │           ├── bmeg-jupyter.ddns.net
  │           └── gen3-ohsu.ddns.net
  └── usr
      └── share
          └── nginx
              ├── default
              └── gen3-ohsu.ddns.net

sites

Each site has a file in etc/nginx/sites-enabled. Ensure that the site is included in etc/nginx/

Content is mapped to usr/share/nginx/.... The bmeg-data/ directory is mounted to /usr/share/nginx/bmeg.io.data

The bmeg-site hugo single page app is generated into nginx/bmeg-site/bmeg.io/public and mounted to /usr/share/nginx/bmeg.io

The makesite.sh script sets the base site in the hugo config and runs the docker image site-builder

├── makesite.sh
├── site-builder
│   └── Dockerfile

To update the content:

DEPLOYMENT_DIR=/mnt/data2/bmeg/deployment
cd $DEPLOYMENT_DIR
alias dc='docker-compose -f docker-compose.yml -f compose-services/docker-compose.yml  -f compose-services/onprem/docker-compose.yml'

cd nginx
./makesite.sh
cd ..
$dc build nginx
$dc stop nginx
$dc rm -f nginx
$dc up -d

certbot

The init-letsencrypt.sh cli tool :

creates temporary self signed certs
requests the letsencrypt certificate
maintains shared convention to data/ with the certbot and nginx services. See volume mapping docker-compose.yml
certbot will check renewal for each domain cert every 12 hours

init-letsencrypt.sh     // cli tool
data                    // letsencrypt data
└── certbot
    ├── conf
    │   ├── accounts
    │   │   └── acme-v02.api.letsencrypt.org
    │   ├── archive
    │   │   ├── bmegio.ohsu.edu
    │   │   ├── bmeg-jupyter.ddns.net
    │   │   └── gen3-ohsu.ddns.net
    │   ├── csr
    │   │   ├── 0000_csr-certbot.pem
    │   │   └── ....
    │   ├── keys
    │   │   ├── 0000_key-certbot.pem
    │   │   └── ...
    │   ├── live
    │   │   ├── bmegio.ohsu.edu
    │   │   ├── bmeg-jupyter.ddns.net
    │   │   ├── gen3-ohsu.ddns.net
    │   │   └── README
    │   ├── options-ssl-nginx.conf
    │   ├── renewal
    │   │   ├── bmegio.ohsu.edu.conf
    │   │   ├── bmeg-jupyter.ddns.net.conf
    │   │   └── gen3-ohsu.ddns.net.conf
    │   ├── renewal-hooks
    │   │   ├── deploy
    │   │   ├── post
    │   │   └── pre
    │   └── ssl-dhparams.pem
    └── www

creating a new host

To create a new host, in this example bmeg.io

First, point the DNS at this host. Once that is verified, ask letsencrypt for new certs.

sudo  ./init-letsencrypt.sh  bmeg.io

This should respond with a "congratulations" message.

updating the bmeg.io website

bash convenience

#  stop, rebuild, start and montitor
alias dc='docker-compose '
rs() {
  dc stop $1; dc rm -f $1; dc build $1; dc up -d $1; dc logs -f $1
}

# in the nginx dir, build the new site.
cd nginx/
export SERVER_NAME=bmeg.io
export BASE_URL=https://bmeg.io
export BMEG_SITE_BRANCH=master
./makesite.sh

# restart nginx
cd ..
rs nginx

mongo

Plain vanilla mongo installation. Data maintained on /mnt/data1/bmeg/mongo-data

grip

See secrets/grip_config.yml for configuration. It's default schema is mapped from bmeg-site/static/meta/schema.json

jupyterhub

The nginx service leverages two key technologies:

dockerspawner==0.11.1
- see secrets/userlist for whitelist of users.
- see secrets/jupyterhub_config.py for parameters:
  - each user's notebook is launched with cpu_limit = 1, mem_limit = '10G' and will be paused after 1 hr of inactivity
oauthenticator==0.8.2
- see secrets/oauth.env for parameters, matched with 'bmeg-jupyter' gcp

The jupyterlab image is used for notebooks. Build via dc build jupyterlab

Please Note: While hub data is maintained in /mnt/data1/bmeg/jupyter-data, the lifecycle of data has NOT been tested. Please back up your work.

├── jupyterhub
│   └── Dockerfile
├── jupyterlab
│   └── Dockerfile
├── secrets
│   ├── jupyter.env
│   ├── jupyterhub_config.py

other services

etl

Note: exec into the grip server to drop & create graph. The mount bmeg-etl directory, is mounted on /bmeg-etl.

├── etl                    // python 3.7 utility
│   ├── Dockerfile
│   ├── docker-start.sh
│   └── README.md

cadvisor

A streaming ui is provided at https://bmeg-jupyter.ddns.net/cadvisor.

Notes:

the data is not persisted
you need to log into jupyterhub before accessing

sync

Notes: to sync from internal services -

This crontab will sync daily at 00:00

0 0 * * * rsync --checksum  <source-directory>/*.*  <user@host>:<target-directory>

gen3 compose-services

setup

# see commons.bmeg.io
cd xxx/deployment
git status
# On branch commons.bmeg.io
git clone [email protected]:ohsu-comp-bio/compose-services.git
checkout compose-services
git checkout commons.bmeg.io
cd ..

alias dc='docker-compose -f docker-compose.yml -f compose-services/docker-compose.yml  -f compose-services/onprem/docker-compose.yml'


# build local services

cd compose-services/onprem/
make

>>>
$ docker images | grep onprem
onprem/tube                     latest              b455e7513b9f        9 minutes ago       2.11GB
onprem/data-portal              latest              552a3d09ca9c        11 minutes ago      1.22GB
onprem/hatchery                 latest              b88a0a5e39da        15 minutes ago      954MB
onprem/s3indexer                latest              1bde3a35f4cf        16 minutes ago      1.16GB
onprem/indexs3client            latest              4658ee3c14dc        17 minutes ago      10.5MB
onprem/fence                    latest              857b63840d4a        18 minutes ago      670MB


# customize gen3 secrets

cd Secrets
grep commons.bmeg.io  *.*
fence-config.yaml:BASE_URL: 'https://commons.bmeg.io/user'
peregrine_creds.json:  "hostname": "commons.bmeg.io"
sheepdog_creds.json:  "hostname": "commons.bmeg.io",


cd ..

# prep for elastic
sysctl -w vm.max_map_count=262144

# install yp needed by creds_setup.sh
# see https://mikefarah.gitbook.io/yq/#on-ubuntu-16-04-or-higher-from-debian-package



# generate local certs
$ bash ./creds_setup.sh  commons.bmeg.io

>>>
The Subject's Distinguished Name is as follows
...
commonName            :ASN.1 12:'<hostname>'
...
Write out database with 1 new entries
Data Base Updated


# configure keys
check `Secrets/fenceJwtKeys/<now() timestamp>/`  fence will use most recent timestamp

# copy fence's public key to elastic  Secrets/elasticsearch-open-distro/config.yml
# see jwt_auth_domain/signing_key  
# see voucher-service in compose-services/onprem/docker-compose.yml

update compose-services/Secrets/.env

# slow start order (use this if you are having problems), otherwise skip to next

dc up -d postgres
dc up -d fence-service
dc up -d arborist-service
dc exec fence-service fence-create migrate
dc exec fence-service fence-create sync --arborist http://arborist-service --yaml user.yaml


# bring up gen3

dc up -d

# apply security config to elastic
### note: compare against top of elastic log file

dc exec esproxy-service \
"/usr/share/elasticsearch/plugins/opendistro_security/tools/securityadmin.sh" -cd "/usr/share/elasticsearch/plugins/opendistro_security/securityconfig" -icl -key "/usr/share/elasticsearch/config/kirk-key.pem" -cert "/usr/share/elasticsearch/config/kirk.pem" -cacert "/usr/share/elasticsearch/config/root-ca.pem" -nhnv

### should produce

>>>
...
Done with success

bmeg-etl's People

Contributors

Stargazers

Watchers

Forkers

ds2643 evergreen700

bmeg-etl's Issues

Variant vertex not linked to CallSet

The chain should be

BioSample -> Callset -> Variant --(VariantAnnotation)--> Gene

TCGA CNA transform issues

CNA Segment IDs don't match edges

Vertex entry:

{"label":"CNASegment","gid":"cnaSegment:e355913a-6e4c-4d63-8a53-8be4c5b003b8:1:915307:3291811","data":{"end":3291811,"callSetId":"e355913a-6e4c-4d63-8a53-8be4c5b003b8","start":915307,"value":-0.33320000767707825,"source":"tcga","referenceName":"1"}}

Edge Entry

{"gid":"(cnaSegment:e355913a-6e4c-4d63-8a53-8be4c5b003b8:1:915307:3291811:-0.33320000767707825)--segmentOf->(gene:ENSG00000279839)","fromLabel":"CNASegment","from":"cnaSegment:e355913a-6e4c-4d63-8a53-8be4c5b003b8:1:915307:3291811:-0.33320000767707825","label":"segmentOf","toLabel":"Gene","to":"gene:ENSG00000279839","data":{}}

The from entry appends the value field gid.

Ratify results: 2/7

@prismofeverything @kellrott @buchanae @adamstruck

Progress

protobuf validation for first 10 in each file works!

$ DATA_DIR=/tmp/SWIFT  SAMPLE_SIZE=10 pytest tests/test_biostream.py
============================================================================================================================ test session starts =============================================================================================================================
platform darwin -- Python 2.7.13, pytest-3.0.6, py-1.4.34, pluggy-0.4.0
rootdir: /Users/walsbr/ratify, inifile:
plugins: flask-0.8.1, catchlog-1.2.2
collected 7 items

tests/test_biostream.py .......

========================================================================================================================== 7 passed in 9.25 seconds ==========================================================================================================================

Needs attention

test_ccle

gids have blanks - protograph/ccle/ccle.Biosample.Vertex.json

test_tcga

swift IO error protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Edge.json
json parse protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNASegment.Vertex.json

test_ensembl

swift IO error protograph/ensembl/ensembl.Gene.Vertex.json

$ DATA_DIR=/tmp/SWIFT  SAMPLE_SIZE=1 pytest tests/test_protograph.py
============================================================================================================================ test session starts =============================================================================================================================
platform darwin -- Python 2.7.13, pytest-3.0.6, py-1.4.34, pluggy-0.4.0
rootdir: /Users/walsbr/ratify, inifile:
plugins: flask-0.8.1, catchlog-1.2.2
collected 9 items

tests/test_protograph.py .F...F..F

================================================================================================================================== FAILURES ==================================================================================================================================
_________________________________________________________________________________________________________________________________ test_ccle __________________________________________________________________________________________________________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...label': 'hasDisease', 'to': 'term:{{disease.term}}'}], 'label': 'Biosample'})})

    def test_ccle(protograph):
        """ assert ccle data is ok """
        project_error_count = _validate_project(protograph, 'ccle')
>       assert project_error_count == 0
E       assert 1 == 0

tests/test_protograph.py:181: AssertionError
----------------------------------------------------------------------------------------------------------------------------- Captured log call ------------------------------------------------------------------------------------------------------------------------------
__init__.py                 54 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/ccle
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json
__init__.py                 45 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error_type": "AssertionError", "error": "gid contains blanks 'biosample::1321N1_CENTRAL_NERVOUS_SYSTEM' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 46 ERROR    gid contains blanks 'biosample::1321N1_CENTRAL_NERVOUS_SYSTEM' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json
assert False
 +  where False = _exists('')
Traceback (most recent call last):
  File "/Users/walsbr/ratify/tests/__init__.py", line 33, in _logging
    yield
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 135, in _validate_vertex_file
    assert _exists(gid_part), "gid contains blanks '{}' in {}".format(vertex.gid, path)  # noqa
AssertionError: gid contains blanks 'biosample::1321N1_CENTRAL_NERVOUS_SYSTEM' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json
assert False
 +  where False = _exists('')
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.CallSet.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.CallSet.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.VariantAnnotation.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.VariantAnnotation.Vertex.json
test_protograph.py         160 INFO     {"project": "ccle", "project_error_count": 1}
________________________________________________________________________________________________________________________________ test_ensembl ________________________________________________________________________________________________________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...label': 'hasDisease', 'to': 'term:{{disease.term}}'}], 'label': 'Biosample'})})

    def test_ensembl(protograph):
        """ assert ensembl data is ok """
        project_error_count = _validate_project(protograph, 'ensembl')
>       assert project_error_count == 0
E       assert 1 == 0

tests/test_protograph.py:207: AssertionError
----------------------------------------------------------------------------------------------------------------------------- Captured log call ------------------------------------------------------------------------------------------------------------------------------
__init__.py                 54 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/ensembl
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Exon.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Exon.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Gene.Vertex.json
__init__.py                 45 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ensembl/ensembl.Gene.Vertex.json", "error_type": "IOError", "error": ""}
__init__.py                 46 ERROR    [Errno 5] Input/output error: '/tmp/SWIFT/biostream/protograph/ensembl/ensembl.Gene.Vertex.json'
Traceback (most recent call last):
  File "/Users/walsbr/ratify/tests/__init__.py", line 33, in _logging
    yield
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 156, in _validate_project
    error_count = _validate_vertex_file(protograph, p)
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 123, in _validate_vertex_file
    for vertex in _load_records(path):
  File "/Users/walsbr/ratify/tests/__init__.py", line 96, in _load_records
    with open(path, 'r') as ins:
IOError: [Errno 5] Input/output error: '/tmp/SWIFT/biostream/protograph/ensembl/ensembl.Gene.Vertex.json'
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Transcript.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Transcript.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ensembl/ensembl.Gene.Edge.json
test_protograph.py         160 INFO     {"project": "ensembl", "project_error_count": 1}
_________________________________________________________________________________________________________________________________ test_tcga __________________________________________________________________________________________________________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...label': 'hasDisease', 'to': 'term:{{disease.term}}'}], 'label': 'Biosample'})})

    def test_tcga(protograph):
        """ assert go data is ok """
        for dir_name in _get_dirs('tcga'):
            project_error_count = _validate_project(protograph,
                                                    'tcga/{}'.format(dir_name))
>           assert project_error_count == 0
E           assert 2 == 0

tests/test_protograph.py:227: AssertionError
----------------------------------------------------------------------------------------------------------------------------- Captured log call ------------------------------------------------------------------------------------------------------------------------------
__init__.py                 61 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/tcga
__init__.py                 54 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.Biosample.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.Biosample.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.CNACallSet.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.CNACallSet.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.CNASegment.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.CNASegment.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.ClinicalFollowup.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.ClinicalFollowup.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.DrugTherapy.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.GeneExpression.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.GeneExpression.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.Individual.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.RadiationTherapy.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.RadiationTherapy.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.Individual.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA/tcga.TCGA-BRCA.DrugTherapy.Vertex.json
test_protograph.py         160 INFO     {"project": "tcga.TCGA-BRCA", "project_error_count": 0}
__init__.py                 54 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.Biosample.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.Biosample.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNACallSet.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNACallSet.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNASegment.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNASegment.Vertex.json
__init__.py                 45 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.CNASegment.Vertex.json", "error_type": "ValueError", "error": "Extra data: line 1 column 4 - line 2 column 1 (char 3 - 202)"}
__init__.py                 46 ERROR    Extra data: line 1 column 4 - line 2 column 1 (char 3 - 202)
Traceback (most recent call last):
  File "/Users/walsbr/ratify/tests/__init__.py", line 33, in _logging
    yield
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 156, in _validate_project
    error_count = _validate_vertex_file(protograph, p)
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 123, in _validate_vertex_file
    for vertex in _load_records(path):
  File "/Users/walsbr/ratify/tests/__init__.py", line 102, in _load_records
    yield AttrDict(json.loads(line))
  File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/json/__init__.py", line 339, in loads
    return _default_decoder.decode(s)
  File "/usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/lib/python2.7/json/decoder.py", line 367, in decode
    raise ValueError(errmsg("Extra data", s, end, len(s)))
ValueError: Extra data: line 1 column 4 - line 2 column 1 (char 3 - 202)
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.ClinicalFollowup.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.ClinicalFollowup.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.DrugTherapy.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Edge.json
__init__.py                 45 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Edge.json", "error_type": "IOError", "error": ""}
__init__.py                 46 ERROR    [Errno 5] Input/output error: '/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Edge.json'
Traceback (most recent call last):
  File "/Users/walsbr/ratify/tests/__init__.py", line 33, in _logging
    yield
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 154, in _validate_project
    error_count = _validate_edge_file(protograph, p)
  File "/Users/walsbr/ratify/tests/test_protograph.py", line 91, in _validate_edge_file
    for edge in _load_records(path):
  File "/Users/walsbr/ratify/tests/__init__.py", line 96, in _load_records
    with open(path, 'r') as ins:
IOError: [Errno 5] Input/output error: '/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Edge.json'
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.GeneExpression.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.Individual.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.RadiationTherapy.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.RadiationTherapy.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.DrugTherapy.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD/tcga.TCGA-LUAD.Individual.Edge.json
test_protograph.py         160 INFO     {"project": "tcga.TCGA-LUAD", "project_error_count": 2}
===================================================================================================================== 3 failed, 6 passed in 7.35 seconds =====================================================================================================================

Pubchem Compound Transform

https://github.com/biostream/pubchem-transform/blob/master/pubchem-extract-compound.cwl

ccle.Variant.Vertex.json contains CallSet data?

biostream/protograph/ccle/ccle.Variant.Vertex.json

head -10 /Users/walsbr/CCC2/biostream/protograph/ccle/ccle.Variant.Vertex.json
{"label":"CallSet","gid":"callSet:ccle:variant:22RV1_PROSTATE","data":{"biosampleId":"ccle:biosample:22RV1_PROSTATE","attributes":{"center":null},"id":"ccle:variant:22RV1_PROSTATE","name":"22RV1_PROSTATE","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:253J_URINARY_TRACT","data":{"biosampleId":"ccle:biosample:253J_URINARY_TRACT","attributes":{"center":null},"id":"ccle:variant:253J_URINARY_TRACT","name":"253J_URINARY_TRACT","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:253JBV_URINARY_TRACT","data":{"biosampleId":"ccle:biosample:253JBV_URINARY_TRACT","attributes":{"center":null},"id":"ccle:variant:253JBV_URINARY_TRACT","name":"253JBV_URINARY_TRACT","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:ACCMESO1_PLEURA","data":{"biosampleId":"ccle:biosample:ACCMESO1_PLEURA","attributes":{"center":null},"id":"ccle:variant:ACCMESO1_PLEURA","name":"ACCMESO1_PLEURA","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","data":{"biosampleId":"ccle:biosample:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","attributes":{"center":null},"id":"ccle:variant:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","name":"ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","data":{"biosampleId":"ccle:biosample:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","attributes":{"center":null},"id":"ccle:variant:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","name":"AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","data":{"biosampleId":"ccle:biosample:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","attributes":{"center":null},"id":"ccle:variant:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","name":"AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","data":{"biosampleId":"ccle:biosample:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","attributes":{"center":null},"id":"ccle:variant:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","name":"BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:BICR16_UPPER_AERODIGESTIVE_TRACT","data":{"biosampleId":"ccle:biosample:BICR16_UPPER_AERODIGESTIVE_TRACT","attributes":{"center":null},"id":"ccle:variant:BICR16_UPPER_AERODIGESTIVE_TRACT","name":"BICR16_UPPER_AERODIGESTIVE_TRACT","_label":"CallSet"}}
{"label":"CallSet","gid":"callSet:ccle:variant:BICR18_UPPER_AERODIGESTIVE_TRACT","data":{"biosampleId":"ccle:biosample:BICR18_UPPER_AERODIGESTIVE_TRACT","attributes":{"center":null},"id":"ccle:variant:BICR18_UPPER_AERODIGESTIVE_TRACT","name":"BICR18_UPPER_AERODIGESTIVE_TRACT","_label":"CallSet"}}

ratify joins errors

DATA_DIR=/tmp/SWIFT pytest -s tests/test_joins.py

__init__.py                 44 ERROR    {"path": "ensembl_Transcript_Vertex", "error": "transcript toGene not in gene gene:ENSG00000232860\nassert 'gene:ENSG00000232860' in ['gene:ENSG00000186092', 'gene:ENSG00000284733', 'gene:ENSG00000284662', 'gene:ENSG00000187634', 'gene:ENSG00000188976', 'gene:ENSG00000187961', ...]\n +  where 'gene:ENSG00000232860' = AttrDict({u'to': u'gene:ENSG00000232860', u'fromLabel': u'Transcript', u'from'...For->(gene:ENSG00000232860)', u'toLabel': u'Gene', u'label': u'transcriptFor'}).to"}

TCGA-BRCA.CNASegment.Vertex.json issues

First line broken/truncated?

start":"167325607","referenceName":"6","_label":"CNASegment"}}

The locations are quoted:

"data":{"start":"126406822","end":"126421379",

Refactor ResponseCurve from Edge to Vertex

We talked about moving ResponseCurve data to be on a vertex

GDSC Transform

https://github.com/biostream/gdsc-transform/blob/master/gdsc-transform.cwl

Ensure Gaia reads keys from data store each time it determines new jobs to run

PubMed Transform

https://github.com/biostream/pubmed-transform/blob/master/pubmed-transform.cwl

First line in ccle.GeneExpression.Edge.json has empty fields

{"gid":"(geneExpression::GeneExpression)--expressionFor->()","fromLabel":"GeneExpression","from":"geneExpression::GeneExpression","label":"expressionFor","toLabel":"Biosample","to":"","data":{}}

GeneExpression.Edge has `level.float`

https://github.com/biostream/bmeg-etl/blob/master/bmeg.protograph.yaml#L239

yaml defines field name as level.float

but data record has level.

Should the record be flagged as an error, or should the config yaml be changed?

{"gid":"()--expressionLevel->(gene:ENSG00000215811.3)","fromLabel":"Biosample","from":"","label":"expressionLevel","toLabel":"Gene","to":"gene:ENSG00000215811.3","data":{"gene":"ENSG00000215811.3","level":0.106453105807304,"sample":""}}

BioSample shouldn't create ontology terms

BioSamples should link to ontology terms, but they shouldn't create them.

TCGA Biosamples uses barcode rather then uuid

BioSamples need to be coded with TCGA uuid.

BioSample file:

"gid":"biosample:TCGA-LUAD:TCGA-97-7553-01A",

"from":"biosample:TCGA-LUAD:TCGA-97-7553-01A","label":"sampleOf","toLabel":"Individual","to":"tcga:37c8d73a-45ae-40fc-ba9a-721b755c1160",

G2P.Features expressed as BMEG.Variants

@kellrott @prismofeverything

This was confusing - "Multiple alternate alleles are possible." - Shouldn't those be separate variants?
https://github.com/biostream/schemas/blob/master/proto/bmeg/variants.proto#L190-L196

This code & test now ensures that ref and alt are transformed correctly.

However, we should clarify/refactor BMEG.Variants

Pubchem BioAssay and Gene Link extractor

bioschemas inconsistent file naming

The files within biostream/biostream are inconsistent in that the expected pattern is xxx.[LABEL].json where xxx is the project

For example see ccle

https://github.com/biostream/bmeg-etl/blob/master/bmeg.processes.yaml#L53-L55

G2P GID construction

The GID created for the the biostream G2P records doesn't seem to reflect where the evidence comes from

{"label":"Evidence","gid":"evidence:A,HLA-A:Lymphoreticular tumour",

Seems to be a combo of the genotype and the disease. But there could be multiple pieces of evidence connected with association in this disease context.

Pathway Commons SIF convert

https://github.com/biostream/pathway-commons-transform/blob/master/sif_convert.py

CCLE Transform Process

Variants
Cell lines
Drug Response
Expression

TCGA Individual files need to be coded with UUID

Need to use uuid, rather then barcode

"gid":"individual:TCGA-LUAD:TCGA-78-7146",

Remove _label from data block?

This seems redundant, given it is in the label block. Is there a technical reason that all messages have a _label in the data section?

G2P needs to link to Ensembl gene ID

In g2p.Evidence.Edge.json

{
	"gid": "(evidence:A,HLA-A:Lymphoreticular tumour)--genotypeOf->(gene:HLA-A)",
	"fromLabel": "Evidence",
	"from": "evidence:A,HLA-A:Lymphoreticular tumour",
	"label": "genotypeOf",
	"toLabel": "Gene",
	"to": "gene:HLA-A",
	"data": {
		"geneSymbol": "HLA-A"
	}
}

Rather then "to: "gene:HLA-A" it should be "to" : "gene:ENSG00000206503"

remove all `repo` keys from commands

GraphViz schema output

To make debugging build easier, emit the schema in GraphViz format ( https://graphviz.gitlab.io/ ) so it can be rendered and reviewed.

TCGA CNACallSet files are empty

TCGA-BRCA.CNACallSet.Vertex.json and TCGA-BRCA.CNACallSet.Edge.json are empty

empty from field in ccle.GeneExpression.Edge.json

{"gid":"()--expressionLevel->(gene:ENSG00000252876.1)","fromLabel":"Biosample","from":"","label":"expressionLevel","toLabel":"Gene","to":"gene:ENSG00000252876.1","data":{"gene":"ENSG00000252876.1","level":0.0,"sample":""}}

Ensembl Exon and Transcripts need a field containing the ensembl id without a prefix

GTEX Transform

https://github.com/biostream/gtex-transform

rewrite ccle biosample transformer and protograph to match tcga

Weird whitespace in TCGA-*.Individual.Vertex.json

In the JSON

"patient_withdrawal":"\n            \n        ",

Rebuild 2018.01

protograph/ccle/ccle.Biosample.Vertex.json BioSamples have wrong gid (u'vertex': {u'gid': u'biosample::', u'data': {u'_label': u'Biosample', u'source': u'ATCC', ...)
New schema has ResponseCurve being created a vertex, rather then edge
Inconsistent ids used in different response curve records. In protograph/ctdd/ctdd.ResponseCurve.Edge.json it is "from":"ccle:CAKI2_KIDNEY" and in protograph/ccle/ccle.ResponseCurve.Edge.json it is biosample:CCLE:CAKI2_KIDNEY
protograph/mc3/mc3.VariantAnnotation.Edge.json has nothing by "to":"gene:0"
No edge connecting Variant to Callset
MC3 Convert Incorrect #19

Missing Elements:

CTDD Fix

Response Curve moving from edge to vector. The to field is empty, because the compounds data is now an array. Note in this example that the experiment is based on two compounds:

{
	"gid": "(ccle:TUHR4TKB_KIDNEY)--responseTo->()",
	"fromLabel": "Biosample",
	"from": "ccle:TUHR4TKB_KIDNEY",
	"label": "responseTo",
	"toLabel": "Compound",
	"to": "",
	"data": {
		"responseType": "ACTIVITY",
		"compounds": [{
			"ratio": 0.5,
			"compound": "pubchem:24978538"
		}, {
			"ratio": 0.5,
			"compound": "pubchem:216239"
		}],
		"summary": [{
			"type": "EC50",
			"value": 1.3319999999999999,
			"unit": "uM"
		}, {
			"type": "AUC",
			"value": 10.021,
			"unit": "uM"
		}],
		"sample": "ccle:TUHR4TKB_KIDNEY",
		"gid": "ccle-response:TUHR4TKB_KIDNEY/navitoclax:sorafenib (1:1 mol/mol)",
		"values": [{
			"response": 0.1961,
			"dose": 0.0015
		}, {
			"response": -3.637E-4,
			"dose": 0.003
		}, {
			"response": 0.129,
			"dose": 0.0061
		}, {
			"response": 0.09207,
			"dose": 0.012
		}, {
			"response": -0.241,
			"dose": 0.024
		}, {
			"response": 0.1883,
			"dose": 0.049
		}, {
			"response": -0.020069999999999998,
			"dose": 0.09699999999999999
		}, {
			"response": 0.011290000000000001,
			"dose": 0.19
		}, {
			"response": -0.5448,
			"dose": 0.39
		}, {
			"response": -0.2828,
			"dose": 0.78
		}, {
			"response": -1.246,
			"dose": 1.6
		}, {
			"response": -1.827,
			"dose": 3.1
		}, {
			"response": -3.074,
			"dose": 6.2
		}, {
			"response": -2.6430000000000002,
			"dose": 12.0
		}, {
			"response": -4.47,
			"dose": 25.0
		}, {
			"response": -4.846,
			"dose": 50.0
		}],
		"_label": "ResponseCurve"
	}
}

ratify biostream errors

DATA_DIR=/tmp/SWIFT SAMPLE_SIZE=10 pytest -s tests/test_biostream.py

============================= test session starts ==============================
platform darwin -- Python 2.7.13, pytest-3.0.6, py-1.4.34, pluggy-0.4.0
rootdir: /Users/walsbr/ratify, inifile: 
plugins: flask-0.8.1, catchlog-1.2.2
collected 6 items

tests/test_biostream.py FF..FF

=================================== FAILURES ===================================
__________________________________ test_ccle ___________________________________

    def test_ccle():
        """ assert ccle data is ok """
        project_error_count = _validate_project('ccle')
>       assert project_error_count == 0
E       assert 30 == 0

tests/test_biostream.py:90: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/biostream/ccle
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"astrocytoma\", \"gid\": \"ccle:1321N1_CENTRAL_NERVOUS_SYSTEM\", \"histology\": \"glioma\", \"tissue\": \"central_nervous_system\", \"alias\": \"1321N1\", \"source\": \"ECACC\", \"notes\": \"Identical lines: U-118 MG, U-138 MG and 1321N1 share high SNP identity\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"NS\", \"gid\": \"ccle:143B_BONE\", \"histology\": \"osteosarcoma\", \"tissue\": \"bone\", \"alias\": \"143B\", \"source\": \"ATCC\", \"notes\": \"Identical lines: HTK-, HOS and 143B share high SNP identity and are very likely to be osteosarcoma\", \"type\": \"Sample\", \"sex\": \"F\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"NS\", \"gid\": \"ccle:22RV1_PROSTATE\", \"histology\": \"carcinoma\", \"tissue\": \"prostate\", \"alias\": \"22Rv1\", \"source\": \"ATCC\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"adenocarcinoma\", \"gid\": \"ccle:2313287_STOMACH\", \"histology\": \"carcinoma\", \"tissue\": \"stomach\", \"alias\": \"23132/87\", \"source\": \"DSMZ\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"transitional_cell_carcinoma\", \"gid\": \"ccle:253JBV_URINARY_TRACT\", \"histology\": \"carcinoma\", \"tissue\": \"urinary_tract\", \"alias\": \"253J-BV\", \"source\": \"KCLB\", \"notes\": \"Identical lines: 253J and 253J-BV share high SNP identity\", \"type\": \"Sample\", \"sex\": \"U\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"transitional_cell_carcinoma\", \"gid\": \"ccle:253J_URINARY_TRACT\", \"histology\": \"carcinoma\", \"tissue\": \"urinary_tract\", \"alias\": \"253J\", \"source\": \"KCLB\", \"notes\": \"Identical lines: 253J and 253J-BV share high SNP identity\", \"type\": \"Sample\", \"sex\": \"\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"astrocytoma_Grade_IV\", \"gid\": \"ccle:42MGBA_CENTRAL_NERVOUS_SYSTEM\", \"histology\": \"glioma\", \"tissue\": \"central_nervous_system\", \"alias\": \"42-MG-BA\", \"source\": \"DSMZ\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"NS\", \"gid\": \"ccle:5637_URINARY_TRACT\", \"histology\": \"carcinoma\", \"tissue\": \"urinary_tract\", \"alias\": \"5637\", \"source\": \"ATCC\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"NS\", \"gid\": \"ccle:59M_OVARY\", \"histology\": \"carcinoma\", \"tissue\": \"ovary\", \"alias\": \"59M\", \"source\": \"ECACC\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"F\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.Biosample.json", "error": "pb parse e:Message type \"ga4gh.Biosample\" has no field named \"alias\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a075910>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075950>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075990>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a0759d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a50>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075a90>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075ad0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b10>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a075b50>] cls:Biosample {\"subtype\": \"transitional_cell_carcinoma\", \"gid\": \"ccle:639V_URINARY_TRACT\", \"histology\": \"carcinoma\", \"tissue\": \"urinary_tract\", \"alias\": \"639-V\", \"source\": \"DSMZ\", \"notes\": \"\", \"type\": \"Sample\", \"sex\": \"M\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:22RV1_PROSTATE\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:22RV1_PROSTATE\", \"name\": \"22RV1_PROSTATE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:253J_URINARY_TRACT\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:253J_URINARY_TRACT\", \"name\": \"253J_URINARY_TRACT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:253JBV_URINARY_TRACT\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:253JBV_URINARY_TRACT\", \"name\": \"253JBV_URINARY_TRACT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:ACCMESO1_PLEURA\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:ACCMESO1_PLEURA\", \"name\": \"ACCMESO1_PLEURA\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"name\": \"ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"name\": \"AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"name\": \"AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"name\": \"BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:BICR16_UPPER_AERODIGESTIVE_TRACT\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:BICR16_UPPER_AERODIGESTIVE_TRACT\", \"name\": \"BICR16_UPPER_AERODIGESTIVE_TRACT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"ccle:biosample:BICR18_UPPER_AERODIGESTIVE_TRACT\", \"attributes\": {\"center\": null}, \"id\": \"ccle:variant:BICR18_UPPER_AERODIGESTIVE_TRACT\", \"name\": \"BICR18_UPPER_AERODIGESTIVE_TRACT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 8.717773588, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 8.0, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -42.55801392}, {\"type\": \"ACTIVITY_AREA\", \"value\": 0.7124}], \"sample\": \"biosample:CCLE:1321N1_CENTRAL_NERVOUS_SYSTEM\", \"gid\": \"responseCurve:1321N1_CENTRAL_NERVOUS_SYSTEM:AEW541\", \"values\": [{\"response\": 8.67, \"dose\": 0.0025}, {\"response\": 11.0, \"dose\": 0.008}, {\"response\": 2.16, \"dose\": 0.025}, {\"response\": 0.27, \"dose\": 0.08}, {\"response\": -10.0, \"dose\": 0.25}, {\"response\": -13.0, \"dose\": 0.8}, {\"response\": -26.0, \"dose\": 2.53}, {\"response\": -43.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 8.165163646, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 2.329924107, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -71.58934021}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.6723}], \"sample\": \"biosample:CCLE:22RV1_PROSTATE\", \"gid\": \"responseCurve:22RV1_PROSTATE:AEW541\", \"values\": [{\"response\": 0.94, \"dose\": 0.0025}, {\"response\": 12.5, \"dose\": 0.008}, {\"response\": -14.0, \"dose\": 0.025}, {\"response\": 4.16, \"dose\": 0.08}, {\"response\": -25.0, \"dose\": 0.25}, {\"response\": -32.0, \"dose\": 0.8}, {\"response\": -52.0, \"dose\": 2.53}, {\"response\": -71.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 1.514508486, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 2.68212986, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -63.49137115}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.1852}], \"sample\": \"biosample:CCLE:42MGBA_CENTRAL_NERVOUS_SYSTEM\", \"gid\": \"responseCurve:42MGBA_CENTRAL_NERVOUS_SYSTEM:AEW541\", \"values\": [{\"response\": 8.91, \"dose\": 0.0025}, {\"response\": 8.39, \"dose\": 0.008}, {\"response\": -3.5, \"dose\": 0.025}, {\"response\": 12.4, \"dose\": 0.08}, {\"response\": -0.55, \"dose\": 0.25}, {\"response\": -6.2, \"dose\": 0.8}, {\"response\": -48.0, \"dose\": 2.53}, {\"response\": -63.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 8.006595166, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 5.002314091, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -62.35277557}, {\"type\": \"ACTIVITY_AREA\", \"value\": 0.9948}], \"sample\": \"biosample:CCLE:5637_URINARY_TRACT\", \"gid\": \"responseCurve:5637_URINARY_TRACT:AEW541\", \"values\": [{\"response\": 2.15, \"dose\": 0.0025}, {\"response\": 9.91, \"dose\": 0.008}, {\"response\": -3.5, \"dose\": 0.025}, {\"response\": 0.056, \"dose\": 0.08}, {\"response\": -2.1, \"dose\": 0.25}, {\"response\": -14.0, \"dose\": 0.8}, {\"response\": -30.0, \"dose\": 2.53}, {\"response\": -62.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 0.931195736, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 1.736181378, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -51.95980835}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.5436}], \"sample\": \"biosample:CCLE:639V_URINARY_TRACT\", \"gid\": \"responseCurve:639V_URINARY_TRACT:AEW541\", \"values\": [{\"response\": 11.8, \"dose\": 0.0025}, {\"response\": -7.3, \"dose\": 0.008}, {\"response\": -9.4, \"dose\": 0.025}, {\"response\": -15.0, \"dose\": 0.08}, {\"response\": -11.0, \"dose\": 0.25}, {\"response\": -21.0, \"dose\": 0.8}, {\"response\": -53.0, \"dose\": 2.53}, {\"response\": -50.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 8.700654505, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 4.260821819, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -73.33378601}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.7665}], \"sample\": \"biosample:CCLE:697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE\", \"gid\": \"responseCurve:697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE:AEW541\", \"values\": [{\"response\": 18.4, \"dose\": 0.0025}, {\"response\": 4.65, \"dose\": 0.008}, {\"response\": 8.64, \"dose\": 0.025}, {\"response\": 19.3, \"dose\": 0.08}, {\"response\": -19.0, \"dose\": 0.25}, {\"response\": -20.0, \"dose\": 0.8}, {\"response\": -21.0, \"dose\": 2.53}, {\"response\": -78.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 0.306242794, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 8.0, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -39.68809509}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.4376}], \"sample\": \"biosample:CCLE:769P_KIDNEY\", \"gid\": \"responseCurve:769P_KIDNEY:AEW541\", \"values\": [{\"response\": 2.58, \"dose\": 0.0025}, {\"response\": -4.1, \"dose\": 0.008}, {\"response\": 6.18, \"dose\": 0.025}, {\"response\": -7.0, \"dose\": 0.08}, {\"response\": -13.0, \"dose\": 0.25}, {\"response\": -40.0, \"dose\": 0.8}, {\"response\": -28.0, \"dose\": 2.53}, {\"response\": -47.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 5.267667294, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 7.613147736, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -51.68631744}, {\"type\": \"ACTIVITY_AREA\", \"value\": 0.5954}], \"sample\": \"biosample:CCLE:786O_KIDNEY\", \"gid\": \"responseCurve:786O_KIDNEY:AEW541\", \"values\": [{\"response\": -1.2, \"dose\": 0.0025}, {\"response\": -0.53, \"dose\": 0.008}, {\"response\": 0.55, \"dose\": 0.025}, {\"response\": -4.1, \"dose\": 0.08}, {\"response\": 2.41, \"dose\": 0.25}, {\"response\": -11.0, \"dose\": 0.8}, {\"response\": -8.8, \"dose\": 2.53}, {\"response\": -52.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 8.520771485, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 4.95063591, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -66.22883606}, {\"type\": \"ACTIVITY_AREA\", \"value\": 1.2929}], \"sample\": \"biosample:CCLE:8305C_THYROID\", \"gid\": \"responseCurve:8305C_THYROID:AEW541\", \"values\": [{\"response\": 1.0, \"dose\": 0.0025}, {\"response\": -1.9, \"dose\": 0.008}, {\"response\": 8.83, \"dose\": 0.025}, {\"response\": 9.38, \"dose\": 0.08}, {\"response\": -18.0, \"dose\": 0.25}, {\"response\": -17.0, \"dose\": 0.8}, {\"response\": -28.0, \"dose\": 2.53}, {\"response\": -68.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ccle/ccle.ResponseCurve.json", "error": "pb parse e:Message type \"bmeg.ResponseCurve\" has no field named \"compound\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a1e42d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4310>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4350>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4390>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e43d0>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4410>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4450>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e4490>, <google.protobuf.descriptor.FieldDescriptor object at 0x10a1e44d0>] cls:ResponseCurve {\"responseType\": \"ACTIVITY\", \"summary\": [{\"type\": \"EC50\", \"value\": 1.846689939, \"unit\": \"uM\"}, {\"type\": \"IC50\", \"value\": 8.0, \"unit\": \"uM\"}, {\"type\": \"AMAX\", \"value\": -22.26882553}, {\"type\": \"ACTIVITY_AREA\", \"value\": 0.3189}], \"sample\": \"biosample:CCLE:8505C_THYROID\", \"gid\": \"responseCurve:8505C_THYROID:AEW541\", \"values\": [{\"response\": -6.0, \"dose\": 0.0025}, {\"response\": -0.21, \"dose\": 0.008}, {\"response\": -2.4, \"dose\": 0.025}, {\"response\": 6.8, \"dose\": 0.08}, {\"response\": -6.3, \"dose\": 0.25}, {\"response\": 1.35, \"dose\": 0.8}, {\"response\": -19.0, \"dose\": 2.53}, {\"response\": -22.0, \"dose\": 8.0}], \"compound\": \"pubchem:11476171\"}\n"}
__________________________________ test_ctdd ___________________________________

    def test_ctdd():
        """ assert ctdd data is ok """
        project_error_count = _validate_project('ctdd')
>       assert project_error_count == 0
E       assert 1 == 0

tests/test_biostream.py:96: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/biostream/ctdd
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/ctdd/ctdd.ResponseCurve.json", "error": "pb parse e:Failed to load JSON: Extra data: line 1 column 2 - line 2 column 1 (char 1 - 344). cls:ResponseCurve 005, \"dose\": 0.19}, {\"response\": -0.6924, \"dose\": 0.39}, {\"response\": -0.4604, \"dose\": 0.78}, {\"response\": -1.595, \"dose\": 1.6}, {\"response\": -5.257999999999999, \"dose\": 3.1}, {\"response\": -5.696000000000001, \"dose\": 6.2}, {\"response\": -5.681, \"dose\": 12.0}, {\"response\": -6.082000000000001, \"dose\": 25.0}, {\"response\": -6.187, \"dose\": 50.0}]}\n"}
___________________________________ test_mc3 ___________________________________

    def test_mc3():
        """ assert go data is ok """
        project_error_count = _validate_project('mc3')
>       assert project_error_count == 0
E       assert 10 == 0

tests/test_biostream.py:114: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/biostream/mc3
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0003-01A-01D-1490-08\", \"attributes\": {\"center\": \"MUTECT\"}, \"id\": \"mc3:variant:TCGA-02-0003-01A-01D-1490-08:MUTECT\", \"name\": \"TCGA-02-0003-01A-01D-1490-08:MUTECT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0003-01A-01D-1490-08\", \"attributes\": {\"center\": \"RADIA\"}, \"id\": \"mc3:variant:TCGA-02-0003-01A-01D-1490-08:RADIA\", \"name\": \"TCGA-02-0003-01A-01D-1490-08:RADIA\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0003-01A-01D-1490-08\", \"attributes\": {\"center\": \"SOMATICSNIPER\"}, \"id\": \"mc3:variant:TCGA-02-0003-01A-01D-1490-08:SOMATICSNIPER\", \"name\": \"TCGA-02-0003-01A-01D-1490-08:SOMATICSNIPER\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0003-01A-01D-1490-08\", \"attributes\": {\"center\": \"MUSE\"}, \"id\": \"mc3:variant:TCGA-02-0003-01A-01D-1490-08:MUSE\", \"name\": \"TCGA-02-0003-01A-01D-1490-08:MUSE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0003-01A-01D-1490-08\", \"attributes\": {\"center\": \"VARSCANS\"}, \"id\": \"mc3:variant:TCGA-02-0003-01A-01D-1490-08:VARSCANS\", \"name\": \"TCGA-02-0003-01A-01D-1490-08:VARSCANS\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0033-01A-01D-1490-08\", \"attributes\": {\"center\": \"MUTECT\"}, \"id\": \"mc3:variant:TCGA-02-0033-01A-01D-1490-08:MUTECT\", \"name\": \"TCGA-02-0033-01A-01D-1490-08:MUTECT\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0033-01A-01D-1490-08\", \"attributes\": {\"center\": \"RADIA\"}, \"id\": \"mc3:variant:TCGA-02-0033-01A-01D-1490-08:RADIA\", \"name\": \"TCGA-02-0033-01A-01D-1490-08:RADIA\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0033-01A-01D-1490-08\", \"attributes\": {\"center\": \"SOMATICSNIPER\"}, \"id\": \"mc3:variant:TCGA-02-0033-01A-01D-1490-08:SOMATICSNIPER\", \"name\": \"TCGA-02-0033-01A-01D-1490-08:SOMATICSNIPER\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0033-01A-01D-1490-08\", \"attributes\": {\"center\": \"MUSE\"}, \"id\": \"mc3:variant:TCGA-02-0033-01A-01D-1490-08:MUSE\", \"name\": \"TCGA-02-0033-01A-01D-1490-08:MUSE\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/mc3/mc3.CallSet.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"center\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a178c50>] cls:CallSet {\"biosampleId\": \"mc3:biosample:TCGA-02-0033-01A-01D-1490-08\", \"attributes\": {\"center\": \"VARSCANS\"}, \"id\": \"mc3:variant:TCGA-02-0033-01A-01D-1490-08:VARSCANS\", \"name\": \"TCGA-02-0033-01A-01D-1490-08:VARSCANS\"}\n"}
__________________________________ test_tcga ___________________________________

    def test_tcga():
        """ assert go data is ok """
        project_error_count = _validate_project('tcga')
>       assert project_error_count == 0
E       assert 40 == 0

tests/test_biostream.py:120: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/biostream/tcga
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"days_to_collection\": \"1407\", \"bcr_sample_uuid\": \"66CBC8DF-FF46-45F0-A2B4-2A5F4E6A3A2A\", \"bcr_patient_uuid\": \"4E509F73-99C7-48EB-A3A4-D34E3BFACE33\", \"days_to_index\": \"0\", \"sample_type\": \"Blood Derived Normal\", \"bcr_patient_barcode\": \"TCGA-OL-A5DA\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"gender\": \"FEMALE\", \"batch_number\": \"288.54.0\", \"patient_id\": \"A5DA\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"0967F358-424A-418E-866B-C9374397DC4C\", \"bcr_sample_barcode\": \"TCGA-OL-A5DA-10A\", \"tissue_source_site\": \"OL\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:4e509f73-99c7-48eb-a3a4-d34e3bface33\", \"id\": \"tcga:66cbc8df-ff46-45f0-a2b4-2a5f4e6a3a2a\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-OL-A5DA-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"11\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"year_of_dcc_upload\": \"2016\", \"bcr_sample_uuid\": \"065663ea-1f4d-4b94-9083-9199f696f09a\", \"bcr_patient_uuid\": \"3558dec7-eae3-4a41-a217-266c6a4535fb\", \"days_to_index\": \"0\", \"sample_type\": \"Solid Tissue Normal\", \"bcr_sample_barcode\": \"TCGA-E2-A1LI-11A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"batch_number\": \"136.76.0\", \"patient_id\": \"A1LI\", \"days_to_collection\": \"2815\", \"file_uuid\": \"CF09155C-41DC-4A04-BE79-B64C934B0C46\", \"bcr_patient_barcode\": \"TCGA-E2-A1LI\", \"initial_weight\": \"190\", \"tissue_source_site\": \"E2\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:3558dec7-eae3-4a41-a217-266c6a4535fb\", \"id\": \"tcga:065663ea-1f4d-4b94-9083-9199f696f09a\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-E2-A1LI-11A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-A8-A06Q.8FE77EF7-C83A-431F-B3BA-D93B5ECC70AF.pdf\", \"days_to_collection\": \"1184\", \"bcr_sample_uuid\": \"a03cd506-47aa-4333-a9a4-fa1a6815ac75\", \"bcr_patient_uuid\": \"281f70c5-876f-44b3-84fb-f2302f85e74c\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_sample_barcode\": \"TCGA-A8-A06Q-01A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"pathology_report_uuid\": \"8FE77EF7-C83A-431F-B3BA-D93B5ECC70AF\", \"batch_number\": \"56.90.0\", \"patient_id\": \"A06Q\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"C72BCFE0-CF56-494E-9283-47E7F114365B\", \"bcr_patient_barcode\": \"TCGA-A8-A06Q\", \"initial_weight\": \"50\", \"tissue_source_site\": \"A8\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:281f70c5-876f-44b3-84fb-f2302f85e74c\", \"id\": \"tcga:a03cd506-47aa-4333-a9a4-fa1a6815ac75\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-A8-A06Q-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"year_of_dcc_upload\": \"2016\", \"bcr_sample_uuid\": \"F0385728-4DBF-4D3E-9AB0-2217EC993F1A\", \"bcr_patient_uuid\": \"91B09291-5944-4691-A0D8-7D1CCC649B9B\", \"days_to_index\": \"0\", \"sample_type\": \"Blood Derived Normal\", \"bcr_sample_barcode\": \"TCGA-BH-A6R8-10A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"gender\": \"FEMALE\", \"batch_number\": \"338.45.0\", \"patient_id\": \"A6R8\", \"days_to_collection\": \"260\", \"file_uuid\": \"73F36D22-67AB-4AAC-9F05-581A3B3EBDC0\", \"bcr_patient_barcode\": \"TCGA-BH-A6R8\", \"tissue_source_site\": \"BH\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:91b09291-5944-4691-a0d8-7d1ccc649b9b\", \"id\": \"tcga:f0385728-4dbf-4d3e-9ab0-2217ec993f1a\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-BH-A6R8-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"year_of_dcc_upload\": \"2016\", \"bcr_sample_uuid\": \"06a3d2e0-d0d4-4c80-9a74-bbba9997e928\", \"bcr_patient_uuid\": \"408cb583-6dc3-4698-8bd2-e284042bd5ef\", \"days_to_index\": \"0\", \"sample_type\": \"Blood Derived Normal\", \"bcr_sample_barcode\": \"TCGA-E9-A1RH-10A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"gender\": \"FEMALE\", \"batch_number\": \"142.78.0\", \"patient_id\": \"A1RH\", \"days_to_collection\": \"32\", \"file_uuid\": \"E9BD4DC5-AC8F-4AA7-8F91-A88F1A3FE060\", \"bcr_patient_barcode\": \"TCGA-E9-A1RH\", \"tissue_source_site\": \"E9\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:408cb583-6dc3-4698-8bd2-e284042bd5ef\", \"id\": \"tcga:06a3d2e0-d0d4-4c80-9a74-bbba9997e928\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-E9-A1RH-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"bcr_sample_barcode\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"day_of_dcc_upload\": \"31\", \"bcr_sample_uuid\": \"6ae136b4-1bd8-4567-bcdf-a3b96809674a\", \"is_ffpe\": \"NO\", \"bcr_patient_uuid\": \"3f834fa7-6d7b-4b85-98c0-5c55d55b6c95\", \"month_of_dcc_upload\": \"3\", \"days_to_index\": \"0\", \"batch_number\": \"56.90.0\", \"sample_type\": \"Blood Derived Normal\", \"patient_id\": \"A0IE\", \"days_to_collection\": \"5557\", \"file_uuid\": \"9586B897-C353-4371-A1BF-98F8700E91CD\", \"disease_code\": \"BRCA\", \"oct_embedded\": \"false\", \"year_of_dcc_upload\": \"2016\", \"tissue_source_site\": \"B6\", \"bcr_patient_barcode\": \"TCGA-B6-A0IE\", \"vial_number\": \"A\", \"project_code\": \"TCGA\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_sample_barcode\": \"TCGA-B6-A0IE-10A\"}, \"individualId\": \"tcga:3f834fa7-6d7b-4b85-98c0-5c55d55b6c95\", \"id\": \"tcga:6ae136b4-1bd8-4567-bcdf-a3b96809674a\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-B6-A0IE-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"day_of_dcc_upload\": \"31\", \"oct_embedded\": \"false\", \"is_ffpe\": \"NO\", \"bcr_patient_uuid\": \"13b860c3-8048-4dc9-9eb0-7480bc660837\", \"project_code\": \"TCGA\", \"month_of_dcc_upload\": \"3\", \"days_to_index\": \"0\", \"batch_number\": \"56.90.0\", \"sample_type\": \"Blood Derived Normal\", \"vial_number\": \"A\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"08F725BB-0508-4A10-BB55-7BE92E887C4D\", \"disease_code\": \"BRCA\", \"bcr_sample_uuid\": \"a0e5f6e4-6f66-4fed-83cc-f63bbb9d5ba6\", \"bcr_sample_barcode\": \"TCGA-AN-A0FX-10A\", \"days_to_collection\": \"34\", \"patient_id\": \"A0FX\", \"tissue_source_site\": \"AN\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_patient_barcode\": \"TCGA-AN-A0FX\"}, \"individualId\": \"tcga:13b860c3-8048-4dc9-9eb0-7480bc660837\", \"id\": \"tcga:a0e5f6e4-6f66-4fed-83cc-f63bbb9d5ba6\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-AN-A0FX-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"10\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"days_to_collection\": \"32\", \"bcr_sample_uuid\": \"FD4C2168-F05E-4286-9ECD-647BF1BA9CE6\", \"bcr_patient_uuid\": \"00B11CA8-8540-4A3D-B602-EC754B00230B\", \"days_to_index\": \"0\", \"sample_type\": \"Blood Derived Normal\", \"bcr_patient_barcode\": \"TCGA-LL-A440\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"gender\": \"FEMALE\", \"batch_number\": \"255.56.0\", \"patient_id\": \"A440\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"BB20ADFF-D98D-4B47-8B96-01D5A69433CA\", \"bcr_sample_barcode\": \"TCGA-LL-A440-10A\", \"tissue_source_site\": \"LL\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:00b11ca8-8540-4a3d-b602-ec754b00230b\", \"id\": \"tcga:fd4c2168-f05e-4286-9ecd-647bf1ba9ce6\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-LL-A440-10A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"oct_embedded\": \"false\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-A8-A09T.C616E97C-8352-4FED-9E83-558318216FB6.pdf\", \"days_to_collection\": \"394\", \"pathology_report_uuid\": \"C616E97C-8352-4FED-9E83-558318216FB6\", \"bcr_patient_uuid\": \"0adf59c6-581a-475d-a2f4-40aa40060b5b\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_patient_barcode\": \"TCGA-A8-A09T\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"bcr_sample_uuid\": \"8df411bb-1d82-4470-84ff-e2d335698d42\", \"batch_number\": \"47.97.0\", \"patient_id\": \"A09T\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"B8F4D30B-CE2F-463B-8349-6FDABA79928D\", \"bcr_sample_barcode\": \"TCGA-A8-A09T-01A\", \"initial_weight\": \"100\", \"tissue_source_site\": \"A8\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:0adf59c6-581a-475d-a2f4-40aa40060b5b\", \"id\": \"tcga:8df411bb-1d82-4470-84ff-e2d335698d42\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-A8-A09T-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"oct_embedded\": \"true\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"BRCA\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-AR-A0TT.E9231B33-E1CE-4396-9F9E-03DBF049919A.pdf\", \"days_to_collection\": \"1567\", \"pathology_report_uuid\": \"E9231B33-E1CE-4396-9F9E-03DBF049919A\", \"bcr_patient_uuid\": \"13ca97a1-75bb-4a49-b8c3-181e5b2c9e86\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_patient_barcode\": \"TCGA-AR-A0TT\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"bcr_sample_uuid\": \"8b5c92b7-52d5-4859-926f-f1264e9c1650\", \"batch_number\": \"72.90.0\", \"patient_id\": \"A0TT\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"FF25B74A-2480-4714-96B3-32F34E09979E\", \"bcr_sample_barcode\": \"TCGA-AR-A0TT-01A\", \"initial_weight\": \"310\", \"tissue_source_site\": \"AR\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:13ca97a1-75bb-4a49-b8c3-181e5b2c9e86\", \"id\": \"tcga:8b5c92b7-52d5-4859-926f-f1264e9c1650\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-AR-A0TT-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-19030\", \"axillary_staging_method\": \"Sentinel lymph node biopsy plus axillary dissection\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Positive\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"micromet_detection_by_ihc\": \"YES\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Alive\", \"margin_status\": \"Negative\", \"project_code\": \"TCGA\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"491d5ebb-e9ab-4b17-acb8-630ff9fef0f2\", \"ajcc_staging_edition\": \"6th\", \"surgical_procedure_first\": \"Simple Mastectomy\", \"histologic_diagnosis\": \"Mixed Histology (please specify)\", \"menopause_status\": \"Pre (<6 months since LMP AND no prior bilateral ovariectomy AND not on estrogen replacement)\", \"pr_status_by_ihc\": \"Positive\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2006\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"lymph_nodes_examined_count\": \"7\", \"her2_fish_status\": \"Negative\", \"icd_o_3_histology\": \"8522/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"er_status_ihc_Percent_Positive\": \"80-89%\", \"her2_ihc_score\": \"2+\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"submitted_tumor_site\": \"Breast\", \"her2_status_by_ihc\": \"Equivocal\", \"form_completion_month\": \"8\", \"pr_status_ihc_percent_positive\": \"90-99%\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"lymph_nodes_examined\": \"YES\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"52\", \"batch_number\": \"142.78.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A24X\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"C36D7A39-09C9-4BE7-A420-F17C5A882277\", \"initial_pathologic_dx_days_to\": \"0\", \"bcr_patient_barcode\": \"TCGA-AR-A24X\", \"last_contact_days_to\": \"1465\", \"histologic_diagnosis_other\": \"Mixed invasive ductal and invasive lobular\", \"method_initial_path_dx\": \"Core needle biopsy\", \"lymph_nodes_examined_he_count\": \"0\", \"form_completion_day\": \"30\", \"tissue_source_site\": \"AR\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:491d5ebb-e9ab-4b17-acb8-630ff9fef0f2\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-AR-A24X\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-20346\", \"first_surgical_procedure_other\": \"Patey's Surgery\", \"tumor_status\": \"TUMOR FREE\", \"vital_status\": \"Alive\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Negative\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"axillary_staging_method\": \"Axillary lymph node dissection alone\", \"metastatic_tumor_indicator\": \"NO\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"7e1673f8-5758-4963-8804-d5e39f06205b\", \"ajcc_staging_edition\": \"6th\", \"surgical_procedure_first\": \"Other\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"pr_status_by_ihc\": \"Negative\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2010\", \"lymph_nodes_examined_he_count\": \"0\", \"lymph_nodes_examined_count\": \"5\", \"icd_o_3_histology\": \"8500/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"submitted_tumor_site\": \"Breast\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"her2_status_by_ihc\": \"Negative\", \"form_completion_month\": \"3\", \"method_initial_path_dx_other\": \"Patey's Surgery\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"NO\", \"lymph_nodes_examined\": \"YES\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"55\", \"batch_number\": \"85.85.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A12V\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"0CE0D14A-8E68-4DBA-8C70-1FAF55337D3D\", \"bcr_patient_barcode\": \"TCGA-C8-A12V\", \"last_contact_days_to\": \"0\", \"method_initial_path_dx\": \"Other method, specify:\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"form_completion_day\": \"22\", \"tissue_source_site\": \"C8\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:7e1673f8-5758-4963-8804-d5e39f06205b\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-C8-A12V\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-30339\", \"first_surgical_procedure_other\": \"Right segmental mastectomy\", \"death_days_to\": \"1286\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"7\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Positive\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Dead\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T1\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"a1093598-d3a8-4ffe-83fc-bc7d1faff7e5\", \"ajcc_staging_edition\": \"5th\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"pr_status_by_ihc\": \"Positive\", \"initial_pathologic_dx_year\": \"1999\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8500/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"submitted_tumor_site\": \"Breast\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage I\", \"her2_status_by_ihc\": \"Negative\", \"form_completion_month\": \"9\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"lymph_nodes_examined\": \"NO\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"83\", \"batch_number\": \"103.78.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A1EU\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"A4F0AC75-A279-4F45-8363-09088950501A\", \"bcr_patient_barcode\": \"TCGA-BH-A1EU\", \"method_initial_path_dx\": \"Fine needle aspiration biopsy\", \"tissue_source_site\": \"BH\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:a1093598-d3a8-4ffe-83fc-bc7d1faff7e5\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-BH-A1EU\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-21949\", \"her2_ihc_percent_positive\": \"<10%\", \"first_surgical_procedure_other\": \"Segmental mastectomy\", \"tumor_status\": \"TUMOR FREE\", \"vital_status\": \"Alive\", \"month_of_dcc_upload\": \"3\", \"age_at_initial_pathologic_diagnosis\": \"60\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"micromet_detection_by_ihc\": \"NO\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"axillary_staging_method\": \"Sentinel lymph node biopsy plus axillary dissection\", \"project_code\": \"TCGA\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2010\", \"pr_positivity_ihc_intensity_score\": \"1+\", \"bcr_patient_uuid\": \"327a2395-85c8-42e1-9638-8e037a1723ed\", \"er_status_ihc_Percent_Positive\": \"90-99%\", \"surgical_procedure_first\": \"Other\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"pr_status_by_ihc\": \"Positive\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2007\", \"lymph_nodes_examined_he_count\": \"12\", \"lymph_nodes_examined_count\": \"18\", \"icd_o_3_histology\": \"8500/3\", \"er_status_by_ihc\": \"Positive\", \"er_ihc_score\": \"3+\", \"her2_ihc_score\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIIC\", \"submitted_tumor_site\": \"Breast\", \"her2_status_by_ihc\": \"Negative\", \"form_completion_month\": \"11\", \"pr_status_ihc_percent_positive\": \"30-39%\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"gender\": \"FEMALE\", \"margin_status\": \"Negative\", \"batch_number\": \"72.90.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A0BC\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"F9C6E7A3-F0B5-4C5C-8C36-A6B79658B067\", \"initial_pathologic_dx_days_to\": \"0\", \"bcr_patient_barcode\": \"TCGA-BH-A0BC\", \"last_contact_days_to\": \"974\", \"method_initial_path_dx\": \"Core needle biopsy\", \"ajcc_nodes_pathologic_pn\": \"N3\", \"form_completion_day\": \"4\", \"tissue_source_site\": \"BH\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:327a2395-85c8-42e1-9638-8e037a1723ed\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-BH-A0BC\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-22798\", \"pr_positivity_define_method\": \"IHC\", \"death_days_to\": \"362\", \"tumor_status\": \"WITH TUMOR\", \"form_completion_day\": \"2\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Indeterminate\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"micromet_detection_by_ihc\": \"NO\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Dead\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T3\", \"axillary_staging_method\": \"No axillary staging\", \"form_completion_year\": \"2010\", \"bcr_patient_uuid\": \"44954053-0b93-4577-a436-42777e442300\", \"ajcc_staging_edition\": \"3rd\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Indeterminate (neither Pre or Postmenopausal)\", \"pr_status_by_ihc\": \"Positive\", \"initial_pathologic_dx_year\": \"1992\", \"ajcc_nodes_pathologic_pn\": \"NX\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8500/3\", \"submitted_tumor_site\": \"Breast\", \"initial_pathologic_dx_days_to\": \"0\", \"er_positivity_method\": \"IHC\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IV\", \"form_completion_month\": \"11\", \"method_initial_path_dx_other\": \"Biopsy, NOS\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"ajcc_metastasis_pathologic_pm\": \"M1\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"62\", \"batch_number\": \"56.90.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A0I9\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"55E98AA1-A2F9-4E7A-A4EF-0723107D34D7\", \"bcr_patient_barcode\": \"TCGA-B6-A0I9\", \"method_initial_path_dx\": \"Other method, specify:\", \"tissue_source_site\": \"B6\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:44954053-0b93-4577-a436-42777e442300\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-B6-A0I9\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-27287\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"26\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Positive\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"micromet_detection_by_ihc\": \"YES\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Alive\", \"metastatic_tumor_indicator\": \"NO\", \"margin_status\": \"Negative\", \"file_uuid\": \"73D88F72-4C32-4DF8-9D15-777818D59E95\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T3\", \"axillary_staging_method\": \"Sentinel node biopsy alone\", \"er_positivity_scale_other\": \"Strong\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"cd0c96a4-6414-4efb-879b-7408b62ed5b6\", \"ajcc_staging_edition\": \"7th\", \"surgical_procedure_first\": \"Simple Mastectomy\", \"histologic_diagnosis\": \"Infiltrating Lobular Carcinoma\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"pr_status_by_ihc\": \"Positive\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2010\", \"ajcc_nodes_pathologic_pn\": \"N0 (i+)\", \"lymph_nodes_examined_count\": \"2\", \"her2_fish_status\": \"Negative\", \"icd_o_3_histology\": \"8520/3\", \"her2_cent17_ratio\": \"0.92\", \"er_status_ihc_Percent_Positive\": \"90-99%\", \"her2_ihc_score\": \"1+\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIB\", \"submitted_tumor_site\": \"Breast\", \"her2_status_by_ihc\": \"Negative\", \"form_completion_month\": \"5\", \"pr_positivity_scale_other\": \"Strong\", \"pr_status_ihc_percent_positive\": \"<10%\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"NO\", \"lymph_nodes_examined\": \"YES\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"74\", \"batch_number\": \"109.88.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A1FV\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"initial_pathologic_dx_days_to\": \"0\", \"lymph_nodes_examined_ihc_count\": \"1\", \"bcr_patient_barcode\": \"TCGA-A2-A1FV\", \"last_contact_days_to\": \"461\", \"method_initial_path_dx\": \"Core needle biopsy\", \"lymph_nodes_examined_he_count\": \"0\", \"tissue_source_site\": \"A2\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:cd0c96a4-6414-4efb-879b-7408b62ed5b6\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-A2-A1FV\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-22844\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"12\", \"month_of_dcc_upload\": \"3\", \"lymph_nodes_examined_ihc_count\": \"0\", \"history_neoadjuvant_treatment\": \"No\", \"her2_status_by_ihc\": \"Negative\", \"micromet_detection_by_ihc\": \"YES\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Alive\", \"radiation_treatment_adjuvant\": \"YES\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"axillary_staging_method\": \"Sentinel node biopsy alone\", \"form_completion_year\": \"2015\", \"bcr_patient_uuid\": \"5C59028F-B8FA-4811-8314-BE3EAED5F364\", \"ajcc_staging_edition\": \"7th\", \"surgical_procedure_first\": \"Modified Radical Mastectomy\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"pr_status_by_ihc\": \"Negative\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2012\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"lymph_nodes_examined_count\": \"8\", \"icd_o_3_histology\": \"8500/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"er_status_by_ihc\": \"Negative\", \"initial_pathologic_dx_days_to\": \"0\", \"pharmaceutical_tx_adjuvant\": \"YES\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage II\", \"submitted_tumor_site\": \"Breast\", \"form_completion_month\": \"3\", \"margin_status\": \"Negative\", \"history_other_malignancy\": \"No\", \"lymph_nodes_examined\": \"YES\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"62\", \"batch_number\": \"334.45.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A6SB\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"D0F636EE-B8B7-4AEC-9361-3D66C83332F8\", \"bcr_patient_barcode\": \"TCGA-EW-A6SB\", \"last_contact_days_to\": \"760\", \"method_initial_path_dx\": \"Core needle biopsy\", \"lymph_nodes_examined_he_count\": \"0\", \"tissue_source_site\": \"EW\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:5c59028f-b8fa-4811-8314-be3eaed5f364\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-EW-A6SB\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-22708\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"10\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Negative\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"icd_o_3_site\": \"C50.9\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"vital_status\": \"Alive\", \"margin_status\": \"Negative\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"axillary_staging_method\": \"Sentinel lymph node biopsy plus axillary dissection\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"3afa1e93-1df8-4e4c-aaa4-557463f4bb77\", \"surgical_procedure_first\": \"Lumpectomy\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"pr_status_by_ihc\": \"Negative\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2009\", \"ajcc_nodes_pathologic_pn\": \"N0 (i-)\", \"lymph_nodes_examined_count\": \"1\", \"icd_o_3_histology\": \"8500/3\", \"submitted_tumor_site\": \"Breast\", \"her2_ihc_score\": \"1+\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"her2_status_by_ihc\": \"Negative\", \"form_completion_month\": \"1\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"NO\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"62\", \"batch_number\": \"85.85.0\", \"disease_code\": \"BRCA\", \"patient_id\": \"A0DA\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"06D5DF5C-1E14-41F3-9012-D94CBCC409C8\", \"initial_pathologic_dx_days_to\": \"0\", \"bcr_patient_barcode\": \"TCGA-A7-A0DA\", \"last_contact_days_to\": \"373\", \"method_initial_path_dx\": \"Core needle biopsy\", \"lymph_nodes_examined_he_count\": \"0\", \"tissue_source_site\": \"A7\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:3afa1e93-1df8-4e4c-aaa4-557463f4bb77\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-A7-A0DA\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-17490\", \"first_surgical_procedure_other\": \"Wide local excision\", \"age_at_initial_pathologic_diagnosis\": \"47\", \"her2_fish_status\": \"Negative\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Positive\", \"history_neoadjuvant_treatment\": \"No\", \"her2_status_by_ihc\": \"Equivocal\", \"micromet_detection_by_ihc\": \"YES\", \"disease_code\": \"BRCA\", \"tumorSite\": \"Breast\", \"icd_10\": \"C50.9\", \"form_completion_day\": \"16\", \"file_uuid\": \"4AFA0D70-566B-444A-B446-57D8F9707702\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T1\", \"axillary_staging_method\": \"Sentinel lymph node biopsy plus axillary dissection\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"d1fd8ed2-be13-4272-b31e-df86911db3b1\", \"ajcc_staging_edition\": \"6th\", \"surgical_procedure_first\": \"Other\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"vital_status\": \"Alive\", \"pr_status_by_ihc\": \"Positive\", \"initial_pathologic_dx_year\": \"2005\", \"lymph_nodes_examined_he_count\": \"0\", \"tissue_source_site\": \"AR\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8500/3\", \"submitted_tumor_site\": \"Breast\", \"menopause_status\": \"Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage I\", \"prospective_collection\": \"NO\", \"form_completion_month\": \"8\", \"pr_status_ihc_percent_positive\": \"10-19%\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"lymph_nodes_examined\": \"YES\", \"gender\": \"FEMALE\", \"margin_status\": \"Negative\", \"batch_number\": \"142.78.0\", \"icd_o_3_site\": \"C50.9\", \"patient_id\": \"A24P\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"her2_ihc_score\": \"2+\", \"bcr_patient_barcode\": \"TCGA-AR-A24P\", \"last_contact_days_to\": \"26\", \"lymph_nodes_examined_count\": \"3\", \"method_initial_path_dx\": \"Core needle biopsy\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"er_status_ihc_Percent_Positive\": \"10-19%\", \"bcr\": \"Nationwide Children's Hospital\", \"patient_withdrawal\": \"\\n            \\n        \"}, \"id\": \"tcga:d1fd8ed2-be13-4272-b31e-df86911db3b1\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-AR-A24P\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-BRCA.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-12642\", \"tumor_status\": \"TUMOR FREE\", \"her2_fish_status\": \"Positive\", \"month_of_dcc_upload\": \"3\", \"er_status_by_ihc\": \"Positive\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"micromet_detection_by_ihc\": \"YES\", \"disease_code\": \"BRCA\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C50.9\", \"form_completion_day\": \"9\", \"margin_status\": \"Negative\", \"patient_id\": \"A04X\", \"project_code\": \"TCGA\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"axillary_staging_method\": \"Sentinel node biopsy alone\", \"er_positivity_scale_other\": \"STRONG\", \"form_completion_year\": \"2010\", \"bcr_patient_uuid\": \"733a2a0f-b37a-4b81-b49e-3c0f30d1eb37\", \"ajcc_staging_edition\": \"6th\", \"surgical_procedure_first\": \"Simple Mastectomy\", \"histologic_diagnosis\": \"Infiltrating Ductal Carcinoma\", \"menopause_status\": \"Pre (<6 months since LMP AND no prior bilateral ovariectomy AND not on estrogen replacement)\", \"pr_status_by_ihc\": \"Positive\", \"day_of_dcc_upload\": \"31\", \"initial_pathologic_dx_year\": \"2006\", \"ajcc_nodes_pathologic_pn\": \"N0 (i-)\", \"lymph_nodes_examined_count\": \"3\", \"vital_status\": \"Alive\", \"icd_o_3_histology\": \"8500/3\", \"her2_cent17_ratio\": \"3.2\", \"submitted_tumor_site\": \"Breast\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"her2_status_by_ihc\": \"Positive\", \"form_completion_month\": \"8\", \"pr_positivity_scale_other\": \"MODERATE\", \"pr_status_ihc_percent_positive\": \"50-59%\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"34\", \"batch_number\": \"56.90.0\", \"icd_o_3_site\": \"C50.9\", \"tissue_source_site\": \"A2\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"7E1208C1-5C2E-4F60-9F1A-C38D6510A218\", \"her2_ihc_score\": \"3+\", \"lymph_nodes_examined_ihc_count\": \"0\", \"bcr_patient_barcode\": \"TCGA-A2-A04X\", \"last_contact_days_to\": \"1349\", \"method_initial_path_dx\": \"Core needle biopsy\", \"lymph_nodes_examined_he_count\": \"0\", \"er_status_ihc_Percent_Positive\": \"80-89%\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Breast\"}, \"id\": \"tcga:733a2a0f-b37a-4b81-b49e-3c0f30d1eb37\", \"datasetId\": \"TCGA-BRCA\", \"name\": \"TCGA-A2-A04X\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"1\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-97-7553.85eedad8-21be-4b10-910b-5b71802ae52f.pdf\", \"pathology_report_uuid\": \"85eedad8-21be-4b10-910b-5b71802ae52f\", \"bcr_patient_uuid\": \"37c8d73a-45ae-40fc-ba9a-721b755c1160\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_sample_barcode\": \"TCGA-97-7553-01A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.4\", \"vial_number\": \"A\", \"bcr_sample_uuid\": \"d23900e0-0335-429c-b9b6-16fa06740f92\", \"batch_number\": \"166.66.0\", \"patient_id\": \"7553\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"3BF2CD21-B7C4-4326-9BBD-CADB523A5C03\", \"bcr_patient_barcode\": \"TCGA-97-7553\", \"tissue_source_site\": \"97\", \"longest_dimension\": \"1.5\"}, \"individualId\": \"tcga:37c8d73a-45ae-40fc-ba9a-721b755c1160\", \"id\": \"tcga:d23900e0-0335-429c-b9b6-16fa06740f92\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-97-7553-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"0.4\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-55-8090.8f75f207-fe12-44ba-86b2-444ab5578d45.pdf\", \"bcr_sample_uuid\": \"53a420fd-6e31-46ee-8ac6-b383f4305cd2\", \"bcr_patient_uuid\": \"4d51ee44-e6f4-4bcb-be28-e9df54b39a8d\", \"longest_dimension\": \"1\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_patient_barcode\": \"TCGA-55-8090\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.2\", \"vial_number\": \"A\", \"pathology_report_uuid\": \"8f75f207-fe12-44ba-86b2-444ab5578d45\", \"gender\": \"MALE\", \"batch_number\": \"213.59.0\", \"patient_id\": \"8090\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"5E7B9F7D-9374-4617-AAB0-6E5873E899FA\", \"bcr_sample_barcode\": \"TCGA-55-8090-01A\", \"tissue_source_site\": \"55\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:4d51ee44-e6f4-4bcb-be28-e9df54b39a8d\", \"id\": \"tcga:53a420fd-6e31-46ee-8ac6-b383f4305cd2\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-55-8090-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"day_of_dcc_upload\": \"11\", \"bcr_sample_uuid\": \"72972ebc-3153-4803-a5b4-e03e00f277db\", \"is_ffpe\": \"NO\", \"bcr_patient_uuid\": \"fddc4d29-1ae8-451d-a13e-8ef6492be201\", \"project_code\": \"TCGA\", \"month_of_dcc_upload\": \"12\", \"batch_number\": \"34.10.0\", \"sample_type\": \"Primary Tumor\", \"vial_number\": \"A\", \"year_of_dcc_upload\": \"2015\", \"file_uuid\": \"062C75CA-5132-4AD2-BA97-0F712A93FB81\", \"disease_code\": \"LUAD\", \"bcr_sample_barcode\": \"TCGA-17-Z030-01A\", \"patient_id\": \"Z030\", \"tissue_source_site\": \"17\", \"bcr\": \"Washington University\", \"bcr_patient_barcode\": \"TCGA-17-Z030\"}, \"individualId\": \"tcga:fddc4d29-1ae8-451d-a13e-8ef6492be201\", \"id\": \"tcga:72972ebc-3153-4803-a5b4-e03e00f277db\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-17-Z030-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"1.2\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-69-7980.a4a32cf5-43b8-4387-9873-d90f7000b134.pdf\", \"bcr_sample_uuid\": \"e54ef0f0-38a5-4226-9a6a-c76aa12de589\", \"bcr_patient_uuid\": \"aee86a89-0377-4080-b16c-408bfbe78687\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_patient_barcode\": \"TCGA-69-7980\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.4\", \"vial_number\": \"A\", \"pathology_report_uuid\": \"a4a32cf5-43b8-4387-9873-d90f7000b134\", \"longest_dimension\": \"1.6\", \"batch_number\": \"204.61.0\", \"patient_id\": \"7980\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"E72BE069-7AF2-4432-A6F9-06F2FC873929\", \"bcr_sample_barcode\": \"TCGA-69-7980-01A\", \"gender\": \"FEMALE\", \"tissue_source_site\": \"69\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:aee86a89-0377-4080-b16c-408bfbe78687\", \"id\": \"tcga:e54ef0f0-38a5-4226-9a6a-c76aa12de589\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-69-7980-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"0.3\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-55-7907.233ef961-8050-47e5-bb53-260a7de4174d.pdf\", \"bcr_sample_uuid\": \"88c65791-1a9c-4121-955a-9bd5ed1b0bba\", \"bcr_patient_uuid\": \"bf755bc2-b7aa-4c3c-8b3c-58b089b5cab6\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_patient_barcode\": \"TCGA-55-7907\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.1\", \"vial_number\": \"A\", \"pathology_report_uuid\": \"233ef961-8050-47e5-bb53-260a7de4174d\", \"gender\": \"MALE\", \"batch_number\": \"196.63.0\", \"patient_id\": \"7907\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"20C7AC42-5417-4FF8-8CA3-70B381570AFF\", \"bcr_sample_barcode\": \"TCGA-55-7907-01A\", \"tissue_source_site\": \"55\", \"longest_dimension\": \"0.3\"}, \"individualId\": \"tcga:bf755bc2-b7aa-4c3c-8b3c-58b089b5cab6\", \"id\": \"tcga:88c65791-1a9c-4121-955a-9bd5ed1b0bba\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-55-7907-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"0.7\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-49-4487.c67031fc-f601-4bd2-b8fd-429a0664cc65.pdf\", \"pathology_report_uuid\": \"c67031fc-f601-4bd2-b8fd-429a0664cc65\", \"bcr_patient_uuid\": \"bd4e9a9f-17f3-4d33-92fc-fcc45dd0e7b4\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_patient_barcode\": \"TCGA-49-4487\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.3\", \"vial_number\": \"A\", \"bcr_sample_uuid\": \"3e88613e-9b97-4dbc-a052-b6dfe8c09956\", \"batch_number\": \"144.69.0\", \"patient_id\": \"4487\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"FB23ED63-9A5A-4A39-82EC-287300C025AB\", \"bcr_sample_barcode\": \"TCGA-49-4487-01A\", \"tissue_source_site\": \"49\", \"longest_dimension\": \"0.9\"}, \"individualId\": \"tcga:bd4e9a9f-17f3-4d33-92fc-fcc45dd0e7b4\", \"id\": \"tcga:3e88613e-9b97-4dbc-a052-b6dfe8c09956\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-49-4487-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"11\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"0.5\", \"project_code\": \"TCGA\", \"bcr_sample_uuid\": \"7bd574da-43aa-40f4-9b95-e50682aed48f\", \"bcr_patient_uuid\": \"199386c2-bb53-4fad-a1b6-59ab216a4a50\", \"days_to_index\": \"0\", \"sample_type\": \"Solid Tissue Normal\", \"bcr\": \"Nationwide Children's Hospital\", \"bcr_patient_barcode\": \"TCGA-55-1596\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.2\", \"vial_number\": \"A\", \"batch_number\": \"37.76.0\", \"patient_id\": \"1596\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"043FA784-4D8A-4AEA-B65D-900666EF2207\", \"bcr_sample_barcode\": \"TCGA-55-1596-11A\", \"tissue_source_site\": \"55\", \"longest_dimension\": \"1\"}, \"individualId\": \"tcga:199386c2-bb53-4fad-a1b6-59ab216a4a50\", \"id\": \"tcga:7bd574da-43aa-40f4-9b95-e50682aed48f\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-55-1596-11A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"intermediate_dimension\": \"1\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-44-4112.9f214c90-f9a8-458c-8a53-ca8e8b09a2b2.pdf\", \"pathology_report_uuid\": \"9f214c90-f9a8-458c-8a53-ca8e8b09a2b2\", \"bcr_patient_uuid\": \"68b86559-38b2-41f2-b66e-c3c2b628b14d\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_sample_barcode\": \"TCGA-44-4112-01A\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"shortest_dimension\": \"0.4\", \"vial_number\": \"A\", \"bcr_sample_uuid\": \"6c206676-e511-4281-91f5-bfe91b3279a4\", \"bcr_patient_barcode\": \"TCGA-44-4112\", \"batch_number\": \"52.73.0\", \"patient_id\": \"4112\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"DCEB95B6-51E5-4C03-A602-963727412846\", \"bcr\": \"Nationwide Children's Hospital\", \"initial_weight\": \"220\", \"tissue_source_site\": \"44\", \"longest_dimension\": \"2\"}, \"individualId\": \"tcga:68b86559-38b2-41f2-b66e-c3c2b628b14d\", \"id\": \"tcga:6c206676-e511-4281-91f5-bfe91b3279a4\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-44-4112-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"day_of_dcc_upload\": \"11\", \"bcr_sample_uuid\": \"815de84c-9fdf-4fcd-94f6-ae66eff41456\", \"is_ffpe\": \"NO\", \"bcr_patient_uuid\": \"392ca7f3-d52e-4aa7-a9ba-4c7d9aa6401c\", \"project_code\": \"TCGA\", \"batch_number\": \"34.10.0\", \"month_of_dcc_upload\": \"12\", \"sample_type\": \"Primary Tumor\", \"vial_number\": \"A\", \"year_of_dcc_upload\": \"2015\", \"file_uuid\": \"97A99889-11F4-439A-985B-3DAB2DBBB93A\", \"disease_code\": \"LUAD\", \"bcr_sample_barcode\": \"TCGA-17-Z056-01A\", \"patient_id\": \"Z056\", \"tissue_source_site\": \"17\", \"bcr\": \"Washington University\", \"bcr_patient_barcode\": \"TCGA-17-Z056\"}, \"individualId\": \"tcga:392ca7f3-d52e-4aa7-a9ba-4c7d9aa6401c\", \"id\": \"tcga:815de84c-9fdf-4fcd-94f6-ae66eff41456\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-17-Z056-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Biosample.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"sample_type_id\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Biosample {\"attributes\": {\"sample_type_id\": \"01\", \"oct_embedded\": \"true\", \"month_of_dcc_upload\": \"3\", \"disease_code\": \"LUAD\", \"project_code\": \"TCGA\", \"pathology_report_file_name\": \"TCGA-49-AAR4.8982CE18-FA5A-4882-AAC4-F2AC6ED60C49.pdf\", \"days_to_collection\": \"2842\", \"bcr_sample_uuid\": \"3BCE57D8-32D5-4F56-B0A4-544C3FEE778F\", \"bcr_patient_uuid\": \"765AD5A5-134B-4680-A6D4-1DD113DC47CC\", \"days_to_index\": \"0\", \"sample_type\": \"Primary Tumor\", \"bcr_patient_barcode\": \"TCGA-49-AAR4\", \"day_of_dcc_upload\": \"31\", \"is_ffpe\": \"NO\", \"vial_number\": \"A\", \"pathology_report_uuid\": \"8982CE18-FA5A-4882-AAC4-F2AC6ED60C49\", \"gender\": \"MALE\", \"batch_number\": \"423.35.0\", \"patient_id\": \"AAR4\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"B1C57D4E-D404-4B2B-872D-0389C9DD91DA\", \"bcr_sample_barcode\": \"TCGA-49-AAR4-01A\", \"initial_weight\": \"200\", \"tissue_source_site\": \"49\", \"bcr\": \"Nationwide Children's Hospital\"}, \"individualId\": \"tcga:765ad5a5-134b-4680-a6d4-1dd113dc47cc\", \"id\": \"tcga:3bce57d8-32d5-4f56-b0a4-544c3fee778f\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-49-AAR4-01A\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-26272\", \"tobacco_smoking_pack_years_smoked\": \"6\", \"death_days_to\": \"173\", \"residual_tumor\": \"R0\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"anatomic_organ_subdivision\": \"L-Lower\", \"disease_code\": \"LUAD\", \"tumorSite\": \"Lung\", \"icd_10\": \"C34.3\", \"form_completion_day\": \"28\", \"project_code\": \"TCGA\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"ff9def3d-17e5-4ef6-b74e-933f11ed6f00\", \"ajcc_staging_edition\": \"6th\", \"egfr_mutation_status\": \"NO\", \"performance_status_timing\": \"Preoperative\", \"tobacco_smoking_history_indicator\": \"4\", \"kras_gene_analysis_indicator\": \"NO\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"vital_status\": \"Dead\", \"location_lung_parenchyma\": \"Peripheral Lung\", \"initial_pathologic_dx_year\": \"1999\", \"ajcc_nodes_pathologic_pn\": \"N2\", \"day_of_dcc_upload\": \"31\", \"ecog_score\": \"1\", \"icd_o_3_histology\": \"8255/3\", \"submitted_tumor_site\": \"Lung\", \"initial_pathologic_dx_days_to\": \"0\", \"tobacco_smoking_year_stopped\": \"1998\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIIA\", \"eml4_alk_translocation_status\": \"NO\", \"form_completion_month\": \"9\", \"history_other_malignancy\": \"No\", \"tobacco_smoking_year_started\": \"1988\", \"retrospective_collection\": \"YES\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"71\", \"batch_number\": \"166.66.0\", \"icd_o_3_site\": \"C34.3\", \"patient_id\": \"7146\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"E29B5F35-128E-4630-BD0E-5EE71487B9C0\", \"bcr_patient_barcode\": \"TCGA-78-7146\", \"tissue_source_site\": \"78\", \"bcr\": \"Nationwide Children's Hospital\", \"patient_withdrawal\": \"\\n            \\n        \"}, \"id\": \"tcga:ff9def3d-17e5-4ef6-b74e-933f11ed6f00\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-78-7146\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-29989\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"3\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"anatomic_organ_subdivision\": \"R-Upper\", \"disease_code\": \"LUAD\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"vital_status\": \"Alive\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"673493f6-975c-49e8-934c-001e9a0fff90\", \"ajcc_staging_edition\": \"6th\", \"egfr_mutation_status\": \"NO\", \"icd_o_3_histology\": \"8140/3\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"initial_pathologic_dx_year\": \"2009\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"kras_gene_analysis_indicator\": \"NO\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"submitted_tumor_site\": \"Lung\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IB\", \"eml4_alk_translocation_status\": \"NO\", \"form_completion_month\": \"3\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"NO\", \"tobacco_smoking_history_indicator\": \"1\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"82\", \"batch_number\": \"37.76.0\", \"icd_o_3_site\": \"C34.1\", \"patient_id\": \"3772\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"E3F790AC-CFB5-4DDC-8FAB-7AD23A35064D\", \"bcr_patient_barcode\": \"TCGA-67-3772\", \"last_contact_days_to\": \"573\", \"tissue_source_site\": \"67\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:673493f6-975c-49e8-934c-001e9a0fff90\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-67-3772\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-20219\", \"tobacco_smoking_pack_years_smoked\": \"25\", \"pulmonary_function_test_indicator\": \"YES\", \"residual_tumor\": \"R0\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"anatomic_organ_subdivision\": \"R-Upper\", \"disease_code\": \"LUAD\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"form_completion_day\": \"3\", \"file_uuid\": \"6447EDCB-2FC5-4374-B69D-0680A241AC81\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"41c4c704-825e-49f5-9d54-dbd7d30725e0\", \"ajcc_staging_edition\": \"6th\", \"fev1_percent_ref_prebroncholiator\": \"77\", \"performance_status_timing\": \"Post-Adjuvant Therapy\", \"carbon_monoxide_diffusion_dlco\": \"73\", \"vital_status\": \"Alive\", \"location_lung_parenchyma\": \"Central Lung\", \"tumor_status\": \"TUMOR FREE\", \"initial_pathologic_dx_year\": \"2007\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"ecog_score\": \"0\", \"icd_o_3_histology\": \"8255/3\", \"submitted_tumor_site\": \"Lung\", \"initial_pathologic_dx_days_to\": \"0\", \"tobacco_smoking_year_stopped\": \"2007\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IB\", \"form_completion_month\": \"5\", \"history_other_malignancy\": \"No\", \"tobacco_smoking_year_started\": \"1982\", \"retrospective_collection\": \"YES\", \"tobacco_smoking_history_indicator\": \"4\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"55\", \"fev1_fvc_ratio_prebroncholiator\": \"61\", \"batch_number\": \"84.72.0\", \"icd_o_3_site\": \"C34.1\", \"patient_id\": \"5781\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"bcr_patient_barcode\": \"TCGA-64-5781\", \"last_contact_days_to\": \"1202\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"tissue_source_site\": \"64\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:41c4c704-825e-49f5-9d54-dbd7d30725e0\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-64-5781\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-24725\", \"carbon_monoxide_diffusion_dlco\": \"90\", \"eml4_alk_analysis_type\": \"FISH\", \"tobacco_smoking_pack_years_smoked\": \"40\", \"pharmaceutical_therapy_adjuvant\": \"YES\", \"death_days_to\": \"164\", \"pulmonary_function_test_indicator\": \"YES\", \"vital_status\": \"Dead\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"anatomic_organ_subdivision\": \"R-Upper\", \"egfr_mutation_status\": \"YES\", \"disease_code\": \"LUAD\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"form_completion_day\": \"13\", \"radiation_treatment_adjuvant\": \"NO\", \"file_uuid\": \"3CC3F939-7924-4A03-8489-E95F433F6955\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2b\", \"form_completion_year\": \"2012\", \"bcr_patient_uuid\": \"8c695c24-e7f9-449a-9258-a1bc8a33bf9a\", \"ajcc_staging_edition\": \"7th\", \"fev1_percent_ref_prebroncholiator\": \"91\", \"performance_status_timing\": \"Preoperative\", \"icd_o_3_histology\": \"8260/3\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"initial_pathologic_dx_year\": \"2011\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"ecog_score\": \"0\", \"kras_gene_analysis_indicator\": \"YES\", \"eml4_alk_translocation_status\": \"YES\", \"submitted_tumor_site\": \"Lung\", \"fev1_percent_ref_postbroncholiator\": \"99\", \"initial_pathologic_dx_days_to\": \"0\", \"tobacco_smoking_year_stopped\": \"1985\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"kras_mutation_found\": \"NO\", \"form_completion_month\": \"6\", \"history_other_malignancy\": \"No\", \"tobacco_smoking_year_started\": \"1965\", \"fev1_fvc_ratio_postbroncholiator\": \"86\", \"retrospective_collection\": \"NO\", \"tobacco_smoking_history_indicator\": \"3\", \"gender\": \"MALE\", \"age_at_initial_pathologic_diagnosis\": \"67\", \"fev1_fvc_ratio_prebroncholiator\": \"81\", \"batch_number\": \"222.59.0\", \"icd_o_3_site\": \"C34.1\", \"patient_id\": \"8174\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"bcr_patient_barcode\": \"TCGA-97-8174\", \"tissue_source_site\": \"97\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:8c695c24-e7f9-449a-9258-a1bc8a33bf9a\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-97-8174\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-21565\", \"tobacco_smoking_pack_years_smoked\": \"30\", \"pulmonary_function_test_indicator\": \"YES\", \"vital_status\": \"Alive\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"anatomic_organ_subdivision\": \"R-Upper\", \"icd_o_3_site\": \"C34.1\", \"tumorSite\": \"Lung\", \"icd_10\": \"C34.1\", \"form_completion_day\": \"5\", \"project_code\": \"TCGA\", \"carbon_monoxide_diffusion_dlco\": \"44\", \"ajcc_tumor_pathologic_pt\": \"T2b\", \"form_completion_year\": \"2013\", \"bcr_patient_uuid\": \"EA0B9461-0D4D-4ADE-A255-1B03DD85E30E\", \"ajcc_staging_edition\": \"7th\", \"egfr_mutation_status\": \"NO\", \"kras_gene_analysis_indicator\": \"NO\", \"tobacco_smoking_history_indicator\": \"4\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"initial_pathologic_dx_year\": \"2012\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8140/3\", \"submitted_tumor_site\": \"Lung\", \"fev1_percent_ref_postbroncholiator\": \"69\", \"initial_pathologic_dx_days_to\": \"0\", \"tobacco_smoking_year_stopped\": \"2001\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIA\", \"form_completion_month\": \"2\", \"history_other_malignancy\": \"Yes, History of Synchronous/Bilateral Malignancy\", \"tobacco_smoking_year_started\": \"1976\", \"retrospective_collection\": \"NO\", \"ajcc_metastasis_pathologic_pm\": \"MX\", \"gender\": \"MALE\", \"age_at_initial_pathologic_diagnosis\": \"59\", \"batch_number\": \"258.58.0\", \"disease_code\": \"LUAD\", \"patient_id\": \"A4BC\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"E82437A1-5FFE-40DF-9A42-061E0A8F7883\", \"bcr_patient_barcode\": \"TCGA-91-A4BC\", \"last_contact_days_to\": \"44\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"tissue_source_site\": \"91\", \"bcr\": \"Nationwide Children's Hospital\", \"patient_withdrawal\": \"\\n            \\n        \"}, \"id\": \"tcga:ea0b9461-0d4d-4ade-a255-1b03dd85e30e\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-91-A4BC\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-19216\", \"carbon_monoxide_diffusion_dlco\": \"97\", \"tobacco_smoking_pack_years_smoked\": \"50\", \"tumor_status\": \"TUMOR FREE\", \"form_completion_day\": \"20\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"anatomic_organ_subdivision\": \"R-Upper\", \"icd_o_3_site\": \"C34.1\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"vital_status\": \"Alive\", \"egfr_mutation_status\": \"NO\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"0b31dbdf-0623-48e4-a0ec-017650dceda7\", \"ajcc_staging_edition\": \"7th\", \"fev1_percent_ref_prebroncholiator\": \"108\", \"icd_o_3_histology\": \"8140/3\", \"file_uuid\": \"F16503A4-395E-4C0B-81A7-A37C0C8BB7A7\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"pulmonary_function_test_indicator\": \"YES\", \"initial_pathologic_dx_year\": \"2010\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"kras_gene_analysis_indicator\": \"NO\", \"submitted_tumor_site\": \"Lung\", \"fev1_percent_ref_postbroncholiator\": \"109\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IB\", \"form_completion_month\": \"7\", \"history_other_malignancy\": \"Yes\", \"tobacco_smoking_year_started\": \"1973\", \"fev1_fvc_ratio_postbroncholiator\": \"101\", \"retrospective_collection\": \"YES\", \"tobacco_smoking_history_indicator\": \"2\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"52\", \"batch_number\": \"144.69.0\", \"disease_code\": \"LUAD\", \"patient_id\": \"6836\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"MX\", \"bcr_patient_barcode\": \"TCGA-91-6836\", \"last_contact_days_to\": \"11\", \"tissue_source_site\": \"91\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:0b31dbdf-0623-48e4-a0ec-017650dceda7\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-91-6836\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-19497\", \"death_days_to\": \"1379\", \"tumor_status\": \"TUMOR FREE\", \"residual_tumor\": \"R0\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"anatomic_organ_subdivision\": \"L-Upper\", \"icd_o_3_site\": \"C34.1\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"vital_status\": \"Dead\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T1\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"0a45f302-5748-48f3-9dc9-66c01843a68e\", \"ajcc_staging_edition\": \"6th\", \"egfr_mutation_status\": \"NO\", \"kras_gene_analysis_indicator\": \"NO\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"initial_pathologic_dx_year\": \"2005\", \"ajcc_nodes_pathologic_pn\": \"N2\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8140/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"submitted_tumor_site\": \"Lung\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIIA\", \"eml4_alk_translocation_status\": \"NO\", \"form_completion_month\": \"7\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"tobacco_smoking_history_indicator\": \"3\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"53\", \"batch_number\": \"160.68.0\", \"disease_code\": \"LUAD\", \"patient_id\": \"6981\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"B0FA6140-7C85-46AA-A5C4-AD724C25077A\", \"bcr_patient_barcode\": \"TCGA-55-6981\", \"form_completion_day\": \"27\", \"tissue_source_site\": \"55\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:0a45f302-5748-48f3-9dc9-66c01843a68e\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-55-6981\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-22260\", \"tobacco_smoking_pack_years_smoked\": \"35\", \"tumor_status\": \"TUMOR FREE\", \"residual_tumor\": \"R0\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"anatomic_organ_subdivision\": \"R-Upper\", \"icd_o_3_site\": \"C34.1\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"vital_status\": \"Alive\", \"egfr_mutation_status\": \"NO\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T1a\", \"form_completion_year\": \"2012\", \"bcr_patient_uuid\": \"afe83af5-af22-49c0-88b4-f1d0dfcbe238\", \"ajcc_staging_edition\": \"7th\", \"fev1_percent_ref_prebroncholiator\": \"79\", \"icd_o_3_histology\": \"8140/3\", \"file_uuid\": \"5E6E2847-FCF3-4225-8DD4-F40653B5222E\", \"treatment_outcome_first_course\": \"Complete Remission/Response\", \"carbon_monoxide_diffusion_dlco\": \"74\", \"pulmonary_function_test_indicator\": \"YES\", \"initial_pathologic_dx_year\": \"2012\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"day_of_dcc_upload\": \"31\", \"kras_gene_analysis_indicator\": \"NO\", \"submitted_tumor_site\": \"Lung\", \"fev1_percent_ref_postbroncholiator\": \"87\", \"initial_pathologic_dx_days_to\": \"0\", \"tobacco_smoking_year_stopped\": \"2008\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IA\", \"eml4_alk_translocation_status\": \"NO\", \"form_completion_month\": \"6\", \"history_other_malignancy\": \"No\", \"tobacco_smoking_year_started\": \"1973\", \"retrospective_collection\": \"NO\", \"tobacco_smoking_history_indicator\": \"4\", \"gender\": \"FEMALE\", \"age_at_initial_pathologic_diagnosis\": \"60\", \"batch_number\": \"213.59.0\", \"disease_code\": \"LUAD\", \"patient_id\": \"8097\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"MX\", \"bcr_patient_barcode\": \"TCGA-55-8097\", \"last_contact_days_to\": \"15\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"form_completion_day\": \"15\", \"tissue_source_site\": \"55\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:afe83af5-af22-49c0-88b4-f1d0dfcbe238\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-55-8097\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-24350\", \"tobacco_smoking_pack_years_smoked\": \"58\", \"tumor_status\": \"TUMOR FREE\", \"residual_tumor\": \"R0\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"NO\", \"anatomic_organ_subdivision\": \"R-Upper\", \"disease_code\": \"LUAD\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"vital_status\": \"Alive\", \"project_code\": \"TCGA\", \"ajcc_tumor_pathologic_pt\": \"T2\", \"form_completion_year\": \"2010\", \"bcr_patient_uuid\": \"e737f650-b72d-44e7-b750-558a56716803\", \"ajcc_staging_edition\": \"6th\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"initial_pathologic_dx_year\": \"2008\", \"ajcc_nodes_pathologic_pn\": \"N1\", \"day_of_dcc_upload\": \"31\", \"icd_o_3_histology\": \"8255/3\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"submitted_tumor_site\": \"Lung\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IIB\", \"form_completion_month\": \"7\", \"history_other_malignancy\": \"No\", \"retrospective_collection\": \"YES\", \"tobacco_smoking_history_indicator\": \"2\", \"gender\": \"MALE\", \"age_at_initial_pathologic_diagnosis\": \"66\", \"batch_number\": \"58.76.0\", \"icd_o_3_site\": \"C34.1\", \"patient_id\": \"4432\", \"year_of_dcc_upload\": \"2016\", \"file_uuid\": \"9EE09A77-F18D-4B83-8ED3-0E959B5E6410\", \"bcr_patient_barcode\": \"TCGA-05-4432\", \"last_contact_days_to\": \"761\", \"form_completion_day\": \"22\", \"tissue_source_site\": \"05\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:e737f650-b72d-44e7-b750-558a56716803\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-05-4432\"}\n"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/biostream/tcga/TCGA-LUAD.Individual.json", "error": "pb parse e:Failed to parse attributes field: Message type \"ga4gh.Attributes\" has no field named \"birth_days_to\".\n Available Fields(except extensions): [<google.protobuf.descriptor.FieldDescriptor object at 0x10a11da90>] cls:Individual {\"attributes\": {\"birth_days_to\": \"-21283\", \"tobacco_smoking_pack_years_smoked\": \"67.5\", \"days_to_last_known_alive\": \"9\", \"pulmonary_function_test_indicator\": \"YES\", \"residual_tumor\": \"RX\", \"month_of_dcc_upload\": \"3\", \"history_neoadjuvant_treatment\": \"No\", \"prospective_collection\": \"YES\", \"anatomic_organ_subdivision\": \"R-Upper\", \"disease_code\": \"LUAD\", \"patient_withdrawal\": \"\\n            \\n        \", \"icd_10\": \"C34.1\", \"form_completion_day\": \"7\", \"file_uuid\": \"AC9D1D72-B83B-46E8-830C-5AB31ED60549\", \"project_code\": \"TCGA\", \"ethnicity\": \"NOT HISPANIC OR LATINO\", \"ajcc_tumor_pathologic_pt\": \"T1a\", \"form_completion_year\": \"2011\", \"bcr_patient_uuid\": \"22302e92-fdfa-462a-9249-efdaa26ee5ed\", \"ajcc_staging_edition\": \"7th\", \"fev1_percent_ref_prebroncholiator\": \"63\", \"performance_status_timing\": \"Preoperative\", \"carbon_monoxide_diffusion_dlco\": \"82\", \"vital_status\": \"Alive\", \"tumor_status\": \"TUMOR FREE\", \"initial_pathologic_dx_year\": \"2011\", \"histologic_diagnosis\": \"Lung Adenocarcinoma\", \"day_of_dcc_upload\": \"31\", \"ecog_score\": \"0\", \"icd_o_3_histology\": \"8140/3\", \"submitted_tumor_site\": \"Lung\", \"fev1_percent_ref_postbroncholiator\": \"77\", \"initial_pathologic_dx_days_to\": \"0\", \"patient_consent_status\": \"YES\", \"ajcc_pathologic_tumor_stage\": \"Stage IA\", \"form_completion_month\": \"6\", \"history_other_malignancy\": \"No\", \"tobacco_smoking_year_started\": \"1968\", \"fev1_fvc_ratio_postbroncholiator\": \"97\", \"retrospective_collection\": \"NO\", \"tobacco_smoking_history_indicator\": \"2\", \"gender\": \"MALE\", \"age_at_initial_pathologic_diagnosis\": \"58\", \"fev1_fvc_ratio_prebroncholiator\": \"87\", \"batch_number\": \"119.75.0\", \"icd_o_3_site\": \"C34.1\", \"patient_id\": \"6144\", \"year_of_dcc_upload\": \"2016\", \"ajcc_metastasis_pathologic_pm\": \"M0\", \"bcr_patient_barcode\": \"TCGA-44-6144\", \"last_contact_days_to\": \"9\", \"ajcc_nodes_pathologic_pn\": \"N0\", \"tissue_source_site\": \"44\", \"bcr\": \"Nationwide Children's Hospital\", \"tumorSite\": \"Lung\"}, \"id\": \"tcga:22302e92-fdfa-462a-9249-efdaa26ee5ed\", \"datasetId\": \"TCGA-LUAD\", \"name\": \"TCGA-44-6144\"}\n"}
===================== 4 failed, 2 passed in 23.37 seconds ======================

TCGA drug therapy, clinical followup and radiation need protograph

ratify protograph

We ran ratify w/ the following parameters, please see ERROR log messages below.

$ DATA_DIR=/tmp/SWIFT SAMPLE_SIZE=10 pytest -s tests/test_protograph.py

============================= test session starts ==============================
platform darwin -- Python 2.7.13, pytest-3.0.6, py-1.4.34, pluggy-0.4.0
rootdir: /Users/walsbr/ratify, inifile: 
plugins: flask-0.8.1, catchlog-1.2.2
collected 9 items

tests/test_protograph.py .F..F.FFF

=================================== FAILURES ===================================
__________________________________ test_ccle ___________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...'}, 'toLabel': 'Gene', 'label': 'variantIn'}], 'label': 'VariantAnnotation'})})

    def test_ccle(protograph):
        """ assert ccle data is ok """
        project_error_count = _validate_project(protograph, 'ccle')
>       assert project_error_count == 0
E       assert 36 == 0

tests/test_protograph.py:193: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/ccle
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.VariantAnnotation.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.GeneExpression.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'biosample::', u'data': {}, u'gid': u'(biosample::)--sampleOf->()', u'toLabel': u'Individual', u'label': u'sampleOf'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'biosample::', u'data': {}, u'gid': u'(biosample::)--sampleOf->()', u'toLabel': u'Individual', u'label': u'sampleOf'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'biosample::', u'data': {}, u'gid': u'(biosample::)--sampleOf->()', u'toLabel': u'Individual', u'label': u'sampleOf'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'biosample::', u'data': {}, u'gid': u'(biosample::)--sampleOf->()', u'toLabel': u'Individual', u'label': u'sampleOf'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'biosample::', u'data': {}, u'gid': u'(biosample::)--sampleOf->()', u'toLabel': u'Individual', u'label': u'sampleOf'})\nassert False\n +  where False = _exists('')"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.ResponseCurve.Edge.json", "error": "ratio"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Edge.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Edge.json", "error": "callSetOf"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Edge.json", "error": "callSetOf"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.GeneExpression.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json", "error": "gid contains blanks 'biosample::' in /tmp/SWIFT/biostream/protograph/ccle/ccle.Biosample.Vertex.json\nassert False\n +  where False = _exists('')"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:22RV1_PROSTATE', u'data': {u'biosampl...le:variant:22RV1_PROSTATE', u'name': u'22RV1_PROSTATE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:253J_URINARY_TRACT', u'data': {u'bios...nt:253J_URINARY_TRACT', u'name': u'253J_URINARY_TRACT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:253JBV_URINARY_TRACT', u'data': {u'bi...53JBV_URINARY_TRACT', u'name': u'253JBV_URINARY_TRACT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:ACCMESO1_PLEURA', u'data': {u'biosamp...:variant:ACCMESO1_PLEURA', u'name': u'ACCMESO1_PLEURA'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TI... u'name': u'ALLSIL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:AML193_HAEMATOPOIETIC_AND_LYMPHOID_TI... u'name': u'AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISS...', u'name': u'AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISS...', u'name': u'BDCM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:BICR16_UPPER_AERODIGESTIVE_TRACT', u'...E_TRACT', u'name': u'BICR16_UPPER_AERODIGESTIVE_TRACT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ccle/ccle.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:ccle:variant:BICR18_UPPER_AERODIGESTIVE_TRACT', u'...E_TRACT', u'name': u'BICR18_UPPER_AERODIGESTIVE_TRACT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x1046eb178>()\n +    where <built-in method keys of AttrDict object at 0x1046eb178> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ccle/ccle.VariantAnnotation.Edge.json
test_protograph.py         172 INFO     {"project": "ccle", "project_error_count": 36}
__________________________________ test_ctdd ___________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...'}, 'toLabel': 'Gene', 'label': 'variantIn'}], 'label': 'VariantAnnotation'})})

    def test_ctdd(protograph):
        """ assert ctdd data is ok """
        project_error_count = _validate_project(protograph, 'ctdd')
>       assert project_error_count == 0
E       assert 20 == 0

tests/test_protograph.py:213: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/ctdd
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 0.6666666666666666, u'compound': u'pubchem:24771867'}, {u'ratio': 0.3333333333333333, u'compound': u'pubchem:24978538'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.2736}, {u'type': u'AUC', u'unit': u'uM', u'value': 7.9258}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/alisertib:navitoclax (2:1 mol/mol)', u'values': [{u'response': 0.2007, u'dose': 0.0015}, {u'response': -0.07458, u'dose': 0.003}, {u'response': -0.5947, u'dose': 0.0061}, {u'response': -0.01165, u'dose': 0.012}, {u'response': 0.03235, u'dose': 0.024}, {u'response': -0.08011, u'dose': 0.049}, {u'response': -0.6276, u'dose': 0.09699999999999999}, {u'response': -0.922, u'dose': 0.19}, {u'response': -1.266, u'dose': 0.39}, {u'response': -1.501, u'dose': 0.78}, {u'response': -1.454, u'dose': 1.6}, {u'response': -3.056, u'dose': 3.1}, {u'response': -3.397, u'dose': 6.2}, {u'response': -3.49, u'dose': 12.0}, {u'response': -3.62, u'dose': 25.0}, {u'response': -4.0280000000000005, u'dose': 50.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 0.5, u'compound': u'pubchem:24978538'}, {u'ratio': 0.5, u'compound': u'pubchem:216239'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 1.3319999999999999}, {u'type': u'AUC', u'unit': u'uM', u'value': 10.021}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/navitoclax:sorafenib (1:1 mol/mol)', u'values': [{u'response': 0.1961, u'dose': 0.0015}, {u'response': -0.0003637, u'dose': 0.003}, {u'response': 0.129, u'dose': 0.0061}, {u'response': 0.09207, u'dose': 0.012}, {u'response': -0.241, u'dose': 0.024}, {u'response': 0.1883, u'dose': 0.049}, {u'response': -0.020069999999999998, u'dose': 0.09699999999999999}, {u'response': 0.011290000000000001, u'dose': 0.19}, {u'response': -0.5448, u'dose': 0.39}, {u'response': -0.2828, u'dose': 0.78}, {u'response': -1.246, u'dose': 1.6}, {u'response': -1.827, u'dose': 3.1}, {u'response': -3.074, u'dose': 6.2}, {u'response': -2.6430000000000002, u'dose': 12.0}, {u'response': -4.47, u'dose': 25.0}, {u'response': -4.846, u'dose': 50.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 0.5, u'compound': u'pubchem:24978538'}, {u'ratio': 0.5, u'compound': u'pubchem:637858'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.9687}, {u'type': u'AUC', u'unit': u'uM', u'value': 10.331}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/navitoclax:piperlongumine (1:1 mol/mol)', u'values': [{u'response': -1.044, u'dose': 0.001}, {u'response': -0.061989999999999996, u'dose': 0.002}, {u'response': -0.0024460000000000003, u'dose': 0.0041}, {u'response': 0.08653, u'dose': 0.0081}, {u'response': -0.03174, u'dose': 0.016}, {u'response': -0.03232, u'dose': 0.032}, {u'response': 0.04825, u'dose': 0.065}, {u'response': -0.04052, u'dose': 0.13}, {u'response': -0.06175, u'dose': 0.26}, {u'response': -0.2726, u'dose': 0.52}, {u'response': -1.163, u'dose': 1.0}, {u'response': -1.6869999999999998, u'dose': 2.1}, {u'response': -3.18, u'dose': 4.2}, {u'response': -2.91, u'dose': 8.3}, {u'response': -4.0569999999999995, u'dose': 17.0}, {u'response': -3.9419999999999997, u'dose': 33.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:568763'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 4.47}, {u'type': u'AUC', u'unit': u'uM', u'value': 12.324}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/SMER-3', u'values': [{u'response': 0.04269, u'dose': 0.002}, {u'response': 0.031689999999999996, u'dose': 0.0041}, {u'response': 0.009276000000000001, u'dose': 0.0081}, {u'response': -0.008859, u'dose': 0.016}, {u'response': 0.002274, u'dose': 0.032}, {u'response': 0.1136, u'dose': 0.065}, {u'response': 0.044410000000000005, u'dose': 0.13}, {u'response': 0.009303, u'dose': 0.26}, {u'response': 0.09386, u'dose': 0.52}, {u'response': 0.06253, u'dose': 1.0}, {u'response': -0.08666, u'dose': 2.1}, {u'response': -0.9538, u'dose': 4.2}, {u'response': -2.8480000000000003, u'dose': 8.3}, {u'response': -2.8310000000000004, u'dose': 17.0}, {u'response': -0.3727, u'dose': 33.0}, {u'response': -1.217, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:119182'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.1058}, {u'type': u'AUC', u'unit': u'uM', u'value': 8.8058}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/clofarabine', u'values': [{u'response': 0.1249, u'dose': 0.002}, {u'response': 0.07028999999999999, u'dose': 0.0041}, {u'response': -0.7451, u'dose': 0.0081}, {u'response': -0.01061, u'dose': 0.016}, {u'response': -0.07529, u'dose': 0.032}, {u'response': -0.02767, u'dose': 0.065}, {u'response': -1.136, u'dose': 0.13}, {u'response': -1.787, u'dose': 0.26}, {u'response': -1.238, u'dose': 0.52}, {u'response': -1.3969999999999998, u'dose': 1.0}, {u'response': -1.357, u'dose': 2.1}, {u'response': -1.5930000000000002, u'dose': 4.2}, {u'response': -1.7819999999999998, u'dose': 8.3}, {u'response': -1.5759999999999998, u'dose': 17.0}, {u'response': -1.6369999999999998, u'dose': 33.0}, {u'response': -2.104, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 0.8, u'compound': u'pubchem:5311'}, {u'ratio': 0.2, u'compound': u'pubchem:24978538'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 1.128}, {u'type': u'AUC', u'unit': u'uM', u'value': 10.017}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/vorinostat:navitoclax (4:1 mol/mol)', u'values': [{u'response': -0.03573, u'dose': 0.001}, {u'response': -0.0399, u'dose': 0.002}, {u'response': -0.04513, u'dose': 0.0041}, {u'response': 0.031160000000000004, u'dose': 0.0081}, {u'response': -0.0524, u'dose': 0.016}, {u'response': -0.02814, u'dose': 0.032}, {u'response': -0.5619, u'dose': 0.065}, {u'response': -0.012209999999999999, u'dose': 0.13}, {u'response': -0.2488, u'dose': 0.26}, {u'response': -0.58, u'dose': 0.52}, {u'response': -0.7504, u'dose': 1.0}, {u'response': -1.485, u'dose': 2.1}, {u'response': -3.792, u'dose': 4.2}, {u'response': -4.018, u'dose': 8.3}, {u'response': -3.951, u'dose': 17.0}, {u'response': -4.104, u'dose': 33.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:49867926'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.8768}, {u'type': u'AUC', u'unit': u'uM', u'value': 13.941}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/XL765', u'values': [{u'response': 0.1919, u'dose': 0.002}, {u'response': 0.03658, u'dose': 0.0041}, {u'response': 0.07169, u'dose': 0.0081}, {u'response': 0.1118, u'dose': 0.016}, {u'response': 0.2408, u'dose': 0.032}, {u'response': -0.0533, u'dose': 0.065}, {u'response': 0.1392, u'dose': 0.13}, {u'response': 0.1842, u'dose': 0.26}, {u'response': 0.0193, u'dose': 0.52}, {u'response': -0.1525, u'dose': 1.0}, {u'response': -0.5424, u'dose': 2.1}, {u'response': 0.01891, u'dose': 4.2}, {u'response': -0.553, u'dose': 8.3}, {u'response': -0.5139, u'dose': 17.0}, {u'response': 0.00645, u'dose': 33.0}, {u'response': -0.2407, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:53301938'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 1.11}, {u'type': u'AUC', u'unit': u'uM', u'value': 16.409}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/ML258', u'values': [{u'response': 0.07468, u'dose': 0.002}, {u'response': -0.3932, u'dose': 0.0041}, {u'response': 0.1303, u'dose': 0.0081}, {u'response': 0.1859, u'dose': 0.016}, {u'response': 0.07153999999999999, u'dose': 0.032}, {u'response': 0.1737, u'dose': 0.065}, {u'response': -0.1329, u'dose': 0.13}, {u'response': 0.1472, u'dose': 0.26}, {u'response': 0.2489, u'dose': 0.52}, {u'response': 0.01346, u'dose': 1.0}, {u'response': 0.209, u'dose': 2.1}, {u'response': 0.2695, u'dose': 4.2}, {u'response': 0.1287, u'dose': 8.3}, {u'response': 0.2449, u'dose': 17.0}, {u'response': 0.2284, u'dose': 33.0}, {u'response': 0.2867, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:44241473'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.5053}, {u'type': u'AUC', u'unit': u'uM', u'value': 13.825}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/SR1001', u'values': [{u'response': 0.08559, u'dose': 0.002}, {u'response': 0.1308, u'dose': 0.0041}, {u'response': -0.4168, u'dose': 0.0081}, {u'response': 0.033710000000000004, u'dose': 0.016}, {u'response': 0.1404, u'dose': 0.032}, {u'response': 0.1775, u'dose': 0.065}, {u'response': 0.1135, u'dose': 0.13}, {u'response': 0.049530000000000005, u'dose': 0.26}, {u'response': -0.2004, u'dose': 0.52}, {u'response': -0.2995, u'dose': 1.0}, {u'response': -0.5728, u'dose': 2.1}, {u'response': -0.09107, u'dose': 4.2}, {u'response': -0.5243, u'dose': 8.3}, {u'response': -0.4473, u'dose': 17.0}, {u'response': 0.00916, u'dose': 33.0}, {u'response': -0.04193, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "missing 'to' in /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json AttrDict({u'to': u'', u'fromLabel': u'Biosample', u'from': u'ccle:TUHR4TKB_KIDNEY', u'data': {u'responseType': u'ACTIVITY', u'compounds': [{u'ratio': 1.0, u'compound': u'pubchem:400769'}], u'_label': u'ResponseCurve', u'summary': [{u'type': u'EC50', u'unit': u'uM', u'value': 0.8052}, {u'type': u'AUC', u'unit': u'uM', u'value': 8.9512}], u'sample': u'ccle:TUHR4TKB_KIDNEY', u'gid': u'ccle-response:TUHR4TKB_KIDNEY/bardoxolone methyl', u'values': [{u'response': 0.2978, u'dose': 0.002}, {u'response': 0.0689, u'dose': 0.0041}, {u'response': 0.0071189999999999995, u'dose': 0.0081}, {u'response': -0.02263, u'dose': 0.016}, {u'response': -0.05786, u'dose': 0.032}, {u'response': 0.08782000000000001, u'dose': 0.065}, {u'response': 0.026619999999999998, u'dose': 0.13}, {u'response': -0.0394, u'dose': 0.26}, {u'response': -0.09788999999999999, u'dose': 0.52}, {u'response': -2.166, u'dose': 1.0}, {u'response': -3.537, u'dose': 2.1}, {u'response': -3.6460000000000004, u'dose': 4.2}, {u'response': -5.008, u'dose': 8.3}, {u'response': -5.471, u'dose': 17.0}, {u'response': -4.332, u'dose': 33.0}, {u'response': -5.206, u'dose': 66.0}]}, u'gid': u'(ccle:TUHR4TKB_KIDNEY)--responseTo->()', u'toLabel': u'Compound', u'label': u'responseTo'})\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Edge.json", "error": "ratio"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/ctdd/ctdd.ResponseCurve.Vertex.json
test_protograph.py         172 INFO     {"project": "ctdd", "project_error_count": 20}
___________________________________ test_go ____________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...'}, 'toLabel': 'Gene', 'label': 'variantIn'}], 'label': 'VariantAnnotation'})})

    def test_go(protograph):
        """ assert go data is ok """
        project_error_count = _validate_project(protograph, 'go')
>       assert project_error_count == 0
E       assert 1 == 0

tests/test_protograph.py:225: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/go
__init__.py                 44 ERROR    {"path": "go", "error": ""}
test_protograph.py         172 INFO     {"project": "go", "project_error_count": 1}
___________________________________ test_mc3 ___________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...'}, 'toLabel': 'Gene', 'label': 'variantIn'}], 'label': 'VariantAnnotation'})})

    def test_mc3(protograph):
        """ assert go data is ok """
        project_error_count = _validate_project(protograph, 'mc3')
>       assert project_error_count == 0
E       assert 11 == 0

tests/test_protograph.py:231: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/mc3
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Edge.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Edge.json", "error": "callSetOf"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Edge.json", "error": "callSetOf"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0003-01A-01D-1490-08:MUTECT', ...TECT', u'name': u'TCGA-02-0003-01A-01D-1490-08:MUTECT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0003-01A-01D-1490-08:RADIA', u...RADIA', u'name': u'TCGA-02-0003-01A-01D-1490-08:RADIA'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0003-01A-01D-1490-08:SOMATICSN...u'name': u'TCGA-02-0003-01A-01D-1490-08:SOMATICSNIPER'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0003-01A-01D-1490-08:MUSE', u'...8:MUSE', u'name': u'TCGA-02-0003-01A-01D-1490-08:MUSE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0003-01A-01D-1490-08:VARSCANS'...NS', u'name': u'TCGA-02-0003-01A-01D-1490-08:VARSCANS'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0033-01A-01D-1490-08:MUTECT', ...TECT', u'name': u'TCGA-02-0033-01A-01D-1490-08:MUTECT'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0033-01A-01D-1490-08:RADIA', u...RADIA', u'name': u'TCGA-02-0033-01A-01D-1490-08:RADIA'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0033-01A-01D-1490-08:SOMATICSN...u'name': u'TCGA-02-0033-01A-01D-1490-08:SOMATICSNIPER'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0033-01A-01D-1490-08:MUSE', u'...8:MUSE', u'name': u'TCGA-02-0033-01A-01D-1490-08:MUSE'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/mc3/mc3.Variant.Vertex.json", "error": "vertex.label 'CallSet' does not match yaml vertexes ['Variant']\nassert 'CallSet' in ['Variant']\n +  where 'CallSet' = AttrDict({u'gid': u'callSet:mc3:variant:TCGA-02-0033-01A-01D-1490-08:VARSCANS'...NS', u'name': u'TCGA-02-0033-01A-01D-1490-08:VARSCANS'}, u'label': u'CallSet'}).label\n +  and   ['Variant'] = <built-in method keys of AttrDict object at 0x104785050>()\n +    where <built-in method keys of AttrDict object at 0x104785050> = AttrDict({'Variant': AttrDict({'filter': ['calls'], 'merge': True, 'gid': 'var...nateBases|join:,}}', 'chromosome': '{{referenceName}}'}, 'label': 'Variant'})}).keys"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/mc3/mc3.VariantAnnotation.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/mc3/mc3.VariantAnnotation.Vertex.json
test_protograph.py         172 INFO     {"project": "mc3", "project_error_count": 11}
__________________________________ test_tcga ___________________________________

protograph = AttrDict({'Cohort': AttrDict({'vertexes': [{'filter': ['hasMember'], 'merge': ...'}, 'toLabel': 'Gene', 'label': 'variantIn'}], 'label': 'VariantAnnotation'})})

    def test_tcga(protograph):
        """ assert go data is ok """
        project_error_count = _validate_project(protograph, 'tcga')
>       assert project_error_count == 0
E       assert 20 == 0

tests/test_protograph.py:237: AssertionError
------------------------------ Captured log call -------------------------------
__init__.py                 53 DEBUG    loading paths from /tmp/SWIFT/biostream/protograph/tcga
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:ed940a3c-39ed-4127-9174-03ffcf448505:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:f65c895f-cfea-46a3-b3a0-7c8a98d7522a:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:493205f9-34b7-483b-885a-ace1e4894250:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:7d0017c2-db42-4758-8dc4-0250ec5fd83c:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:228443d4-e892-4ae7-88b4-a47463d4094c:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:3ba5f6b9-6458-44e2-a0aa-b5c7e5fcd632:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:90dd1872-3a13-4dd9-b470-962a22663e8d:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:2ea3d6eb-8e72-45f2-bbcc-5561df4e7e37:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:15321297-7110-4e79-8d6f-94c95bc83c94:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:c78b35b2-7299-4fd3-88df-a40b087455e0:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.Biosample.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.CNASegment.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.GeneExpression.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.CNASegment.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.Individual.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.Biosample.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.CNACallSet.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.CNACallSet.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:d91ec6e8-cdea-41b8-a88e-252586d3b9ae:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:d32e480b-d1ee-4bae-af15-8b5b94c1cc8a:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:03eb5ba8-0307-49b0-aa05-003007d79107:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:02ec11f4-1d26-4d2f-babe-d576ebfff1c7:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:0fc347ae-7ad9-4987-887a-d37fe871d6c2:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:2a5f4696-6e02-4fe9-b66d-8c2ae93b7c2f:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:fe23a254-a0a4-452c-a2ba-685f66738a86:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:ef8c35b3-bdab-4a7e-b5ab-a0a99f4db803:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:00f81e98-e5c3-43b2-9757-f769ec17f3f8:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
__init__.py                 44 ERROR    {"path": "/tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json", "error": "gid contains blanks 'geneExpression:tcga:92b16015-e552-48e3-a095-0197b99b52a8:' in /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Vertex.json\nassert False\n +  where False = _exists('')"}
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.Individual.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.Individual.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.Biosample.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.CNACallSet.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.GeneExpression.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.CNACallSet.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.Individual.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.CNASegment.Edge.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-BRCA.CNASegment.Vertex.json
test_protograph.py          58 DEBUG    /tmp/SWIFT/biostream/protograph/tcga/TCGA-LUAD.Biosample.Vertex.json
test_protograph.py         172 INFO     {"project": "TCGA-LUAD", "project_error_count": 20}
====================== 5 failed, 4 passed in 8.27 seconds ======================

Kallisto: Add Transcipt-Level TCGA RNAseq

available here: https://xenabrowser.net/datapages/?dataset=tcga_Kallisto_tpm&host=https://toil.xenahubs.net

useful since we are using the same Kallisto platform to get RNAseq from SMMART patients, so if we want to train models on TCGA to apply to these patients this is the data we'll want to use

Vertex:
{"label":"CNACallSet","gid":"cnaCallSet:tcga-cna:8efb4f70-fc31-42d6-8e99-b95069c771a4","data":{"bioSampleId":"tcga:8efb4f70-fc31-42d6-8e99-b95069c771a4","id":"tcga-cna:8efb4f70-fc31-42d6-8e99-b95069c771a4"}}
Edge:
{"gid":"(cnaCallSet:tcga-cna:8efb4f70-fc31-42d6-8e99-b95069c771a4)--cnaCallSetOf->(biosample:)","fromLabel":"CNACallSet","from":"cnaCallSet:tcga-cna:8efb4f70-fc31-42d6-8e99-b95069c771a4","label":"cnaCallSetOf","toLabel":"Biosample","to":"biosample:","data":{}}

CNASegment has spurious prefixes, also the value should not be in the GID:
{"label":"CNASegment","gid":"cnaSegment:tcga-cna:68f80d6b-1e4c-47e6-bcde-aace6305c555:X:251810:152846040:0.0020000000949949026","data":{"end":152846040,"callSetId":"tcga-cna:68f80d6b-1e4c-47e6-bcde-aace6305c555","value":0.0020000000949949026,"start":251810,"referenceName":"X"}}

MC3 Convert

Example variant ( 10:123810032 C -> T )

biostream/mc3/Variant.json

{"end": "123810032", "calls": [{"callSetId": "mc3:variant:TCGA-02-0003-01A-01D-1490-08"}], "referenceBases": "C", "start": "123810032", "alternateBases": ["C", "T"], "referenceName": "10", "attributes": {"attr": {"center": {"values": [{"stringValue": "."}]}}}, "id": "grch37:10:123810032:123810032:C:C,T"}
{"end": "123810032", "calls": [{"callSetId": "mc3:variant:TCGA-B2-4101-01A-02D-1458-08"}], "referenceBases": "C", "start": "123810032", "alternateBases": ["C", "T"], "referenceName": "10", "attributes": {"attr": {"center": {"values": [{"stringValue": "."}]}}}, "id": "grch37:10:123810032:123810032:C:C,T"}
{"end": "123810032", "calls": [{"callSetId": "mc3:variant:TCGA-QR-A6H4-01A-11D-A35D-08"}], "referenceBases": "C", "start": "123810032", "alternateBases": ["C", "T"], "referenceName": "10", "attributes": {"attr": {"center": {"values": [{"stringValue": "."}]}}}, "id": "grch37:10:123810032:123810032:C:C,T"}

biostream/mc3/VariantAnnotation.json

{"id": "grch37:10:123810032:123810032:C:C,T:", "variantId": "grch37:10:123810032:123810032:C:C,T", "transcriptEffects": [{"featureId": "gene:0", "id": "grch37:0:10:123810032:123810032:C:C,T::C,T", "alternateBases": "C,T", "effects": [{"term": "SNP"}]}]}
{"id": "grch37:10:123810032:123810032:C:C,T:", "variantId": "grch37:10:123810032:123810032:C:C,T", "transcriptEffects": [{"featureId": "gene:0", "id": "grch37:0:10:123810032:123810032:C:C,T::C,T", "alternateBases": "C,T", "effects": [{"term": "SNP"}]}]}
{"id": "grch37:10:123810032:123810032:C:C,T:", "variantId": "grch37:10:123810032:123810032:C:C,T", "transcriptEffects": [{"featureId": "gene:0", "id": "grch37:0:10:123810032:123810032:C:C,T::C,T", "alternateBases": "C,T", "effects": [{"term": "SNP"}]}]}

Produces protograph/mc3/mc3.Variant.Vertex.json

{"label":"Variant","gid":"variant:10:123810032:123810032:C:C,T","data":{"chromosome":"10","referenceBases":"C","start":"123810032","_label":"Variant","id":"grch37:10:123810032:123810032:C:C,T","referenceName":"10","end":"123810032","alternateBases":"C,T","attributes":{"attr":{"center":{"values":[{"stringValue":"."}]}}}}}
{"label":"Variant","gid":"variant:10:123810032:123810032:C:C,T","data":{"chromosome":"10","referenceBases":"C","start":"123810032","_label":"Variant","id":"grch37:10:123810032:123810032:C:C,T","referenceName":"10","end":"123810032","alternateBases":"C,T","attributes":{"attr":{"center":{"values":[{"stringValue":"."}]}}}}}

And protograph/mc3/mc3.VariantAnnotation.Edge.json

{"gid":"(grch37:10:123810032:123810032:C:C,T)--variantIn->(gene:0)","fromLabel":"Variant","from":"grch37:10:123810032:123810032:C:C,T","label":"variantIn","toLabel":"Gene","to":"gene:0","data":{"effects":"SNP","gene":"gene:0","bases":"C,T"}}
{"gid":"(grch37:10:123810032:123810032:C:C,T)--variantIn->(gene:0)","fromLabel":"Variant","from":"grch37:10:123810032:123810032:C:C,T","label":"variantIn","toLabel":"Gene","to":"gene:0","data":{"effects":"SNP","gene":"gene:0","bases":"C,T"}}
{"gid":"(grch37:10:123810032:123810032:C:C,T)--variantIn->(gene:0)","fromLabel":"Variant","from":"grch37:10:123810032:123810032:C:C,T","label":"variantIn","toLabel":"Gene","to":"gene:0","data":{"effects":"SNP","gene":"gene:0","bases":"C,T"}}

Issues:

Call center and Gene fields are empty, the invocation of the program needs to be ./ga4gh-variant.py --maf mc3.v0.2.8.PUBLIC.maf.gz --multi test --callSetPrefix mc3 --bioPrefix tcga --center CENTERS --gene Gene
No edges created to connect the Variant to the callset.
The attributes field in Variant needs to be recast as a google.protobuf.Struct to avoid ugly serialization

Gene Ontology Transform

G2P Ontology vertices

Ontology vertices should probably be associated with an actual ontology
Example

{"label":"OntologyTerm","gid":"term:Lymphoreticular tumour","data":{"term":"Lymphoreticular tumour"}}

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