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:ribbon: A data mining suite for gene expression data.

Home Page: http://candis.readthedocs.io

License: GNU General Public License v3.0

Python 26.53% JavaScript 46.96% CSS 0.75% HTML 0.72% Jupyter Notebook 22.14% R 0.69% Mako 0.12% Dockerfile 1.22% Shell 0.87%
machine-learning weka r python bioinformatics flask react redux data-mining

candis's Introduction


A data mining suite for gene expression data

Candis is an open source data mining suite (released under the GNU General Public License v3) for gene expression data that consists of a wide collection of tools you require, right from Data Extraction to Model Deployment. candis is built on top of the toolkit - CancerDiscover written by the bioinformaticians at HelikarLab.

Citation: If you use candis please cite our work
Mohammed, A., Biegert, G., Adamec, J., & Helikar, T. (2017). Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. Oncotarget, 8(49), 85692-85715. https://doi.org/10.18632/oncotarget.21127

Or

Mohammed, A., Biegert, G., Adamec, J., & Helikar, T. (2018). CancerDiscover: An integrative pipeline for cancer biomarker and cancer class prediction from high-throughput sequencing data. Oncotarget, 9(2), 2565-2573. https://doi.org/10.18632/oncotarget.23511

WARNING: candis currently is still in dev mode and not production-ready yet. In case if you run across bugs or errors, raise an issue over here.

Table of Contents

Installation

Assuming you've installed dependencies, simply

$ pip install candis

TL;DR

$ curl -sL git.io/install-candis | python # with dependencies

... and launch candis's development server:

$ candis

To install candis right from scratch, check out our exhaustive guides:

Docker Image

You can also attempt to install candis via Docker as follows:

$ docker pull helikarlab/candis

... and simply run the image optionally mapping the port 5000.

$ docker run -p 8888:5000 helikarlab/candis

OR

After cloning the repository, build from the updated Dockerfile and docker-compose.yml:

For development:

$ ./manage up -d --build

For production:

$ CANDIS_ENVIRONMENT=production ./manage up -d --build

Then go to localhost:5000 in your browser to open the app.

Other Commands:

$ ./manage [service] [command]

$ ./manage db backup			 		# Backup the database
$ ./manage db restore /path/to/backup	# Restore a snapshot
$ ./manage db backups 				 	# List all backups

Usage

Launching the RIA (Rich Internet Application)

via CLI

$ candis

OR

$ python -m candis

via Python

>>> import candis
>>> candis.main()

Using the CLI (Command Line Interface)

$ candis --cdata path/to/data.cdata --config path/to/config.json

Using the Jupyter Notebook from inside the docker container

  • Starting the jupyter notebook server inside the candis app container
$ docker-compose exec app jupyter notebook --ip 0.0.0.0 --no-browser --allow-root

Features

  • Converting a CDATA to an ARFF file

     >>> import candis
     >>> cdata = candis.cdata.read('path/to/data.cdata')

    Then, simply use the CData.toARFF API:

     >>> cdata.toARFF('path/to/data.arff')
  • Running a Pipeline.

     >>> pipe = candis.Pipeline()
     >>> pipe.run(cdata)
     >>> while pipe.status == candis.Pipeline.RUNNING:
     ...     # do something while pipeline is running

Dependencies

  • Production Dependencies
    • R
    • WEKA (NOTE: Requires Java)
    • Python 3.6+ and PIP (Python's Package Manager)
    • NumPy
  • Development Dependencies

Team


Dr. Tomas Helikar
[email protected]

Principal Investigator


Dr. Akram Mohammed
[email protected]

Author and Maintainer


Achilles Rasquinha
[email protected]

Author and Maintainer


Rupav Jain
[email protected]

Author and Maintainer

License

This software has been released under the GNU General Public License v3.

candis's People

Contributors

achillesrasquinha avatar akram-mohammed avatar helikarlabpersonal avatar promehul avatar rupav avatar

Stargazers

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candis's Issues

Setup Development from Production and Fixes

Personal ToDo List. Feel free to contribute.

  • Use pipenv to setup development environment (โœจ ๐Ÿฐ โœจ) Update the Makefile.
  • Setup develop, hotfix and master branch for releases.
  • Delete dev branch. Switch to develop. (@akram-mohammed can I have administration rights on the repository?)
  • Setup administration commands. (Use click?)
  • DB-Driven (ensuring to store states) (SQLite / PostGreSQL?)
  • Serve Static CSS + JS within webpack bundle.
  • Better Deploy with ansible? (Recommended) Currently with get-candis Setup logger for get-candis
  • Setup wergzeug with nginx OTFB.

Create an API endpoint to download data from NCBI - through Download tool of Candis.

This will be used to download data from NCBI into Candis.

Checklist: to implement

  • Add API endpoint to call Entrez module.
  • Add GEO module
  • Implement Esearch
  • Implement Esummary
  • Implement the logic as described in https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html#ExampleIII
  • Use socket.io for download progress.
  • Add test cases
  • Remove time.sleep()
  • Setup logging instead of print statements. - refer #137
  • Start redis server from Procfile (now using honho Manager class) - use different port if initialized. - refer #99
  • ftplib is used for downloading- show progress bar (It shows up with 'wget')
  • Integrate with front-end. - refer issue #110 TODO: Improvements needed as mentioned in the related PRs to #110
  • Add JS test cases for the same.
  • Instead of using requests.Timeout error, use custom error class.

candis not running on docker

Executed the commands from readme, after pulling image from the hub, I can't run candis:
screenshot from 2018-05-12 19-05-06
docker run -p 8888:5000 candis creating error.

Then I tried building the image locally using Dockerfile present in the repository:

rupav@rupav-VirtualBox:~/opensource/submodule/candisCopy/candis$ docker build .
Sending build context to Docker daemon  288.3MB
Step 1/4 : FROM ubuntu
latest: Pulling from library/ubuntu
a48c500ed24e: Pull complete 
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0b4aba487617: Pull complete 
Digest: sha256:c8c275751219dadad8fa56b3ac41ca6cb22219ff117ca98fe82b42f24e1ba64e
Status: Downloaded newer image for ubuntu:latest
 ---> 452a96d81c30
Step 2/4 : RUN apt-get update         && apt-get install -y                 sudo                 bash                 curl                 python3         && curl -sL git.io/install-candis | sudo python3
 ---> Running in ae46c2fe8d8a
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Preparing to unpack .../19-libhcrypto4-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libhcrypto4-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libwind0-heimdal:amd64.
Preparing to unpack .../20-libwind0-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libwind0-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libhx509-5-heimdal:amd64.
Preparing to unpack .../21-libhx509-5-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libhx509-5-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libkrb5-26-heimdal:amd64.
Preparing to unpack .../22-libkrb5-26-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libkrb5-26-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libheimntlm0-heimdal:amd64.
Preparing to unpack .../23-libheimntlm0-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libheimntlm0-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libgssapi3-heimdal:amd64.
Preparing to unpack .../24-libgssapi3-heimdal_7.5.0+dfsg-1_amd64.deb ...
Unpacking libgssapi3-heimdal:amd64 (7.5.0+dfsg-1) ...
Selecting previously unselected package libsasl2-modules-db:amd64.
Preparing to unpack .../25-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2_amd64.deb ...
Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Selecting previously unselected package libsasl2-2:amd64.
Preparing to unpack .../26-libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2_amd64.deb ...
Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Selecting previously unselected package libldap-common.
Preparing to unpack .../27-libldap-common_2.4.45+dfsg-1ubuntu1_all.deb ...
Unpacking libldap-common (2.4.45+dfsg-1ubuntu1) ...
Selecting previously unselected package libldap-2.4-2:amd64.
Preparing to unpack .../28-libldap-2.4-2_2.4.45+dfsg-1ubuntu1_amd64.deb ...
Unpacking libldap-2.4-2:amd64 (2.4.45+dfsg-1ubuntu1) ...
Selecting previously unselected package libnghttp2-14:amd64.
Preparing to unpack .../29-libnghttp2-14_1.30.0-1ubuntu1_amd64.deb ...
Unpacking libnghttp2-14:amd64 (1.30.0-1ubuntu1) ...
Selecting previously unselected package librtmp1:amd64.
Preparing to unpack .../30-librtmp1_2.4+20151223.gitfa8646d.1-1_amd64.deb ...
Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libcurl4:amd64.
Preparing to unpack .../31-libcurl4_7.58.0-2ubuntu3_amd64.deb ...
Unpacking libcurl4:amd64 (7.58.0-2ubuntu3) ...
Selecting previously unselected package curl.
Preparing to unpack .../32-curl_7.58.0-2ubuntu3_amd64.deb ...
Unpacking curl (7.58.0-2ubuntu3) ...
Selecting previously unselected package libsasl2-modules:amd64.
Preparing to unpack .../33-libsasl2-modules_2.1.27~101-g0780600+dfsg-3ubuntu2_amd64.deb ...
Unpacking libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up readline-common (7.0-3) ...
Setting up libnghttp2-14:amd64 (1.30.0-1ubuntu1) ...
Setting up mime-support (3.60ubuntu1) ...
Setting up sudo (1.8.21p2-3ubuntu1) ...
Setting up libldap-common (2.4.45+dfsg-1ubuntu1) ...
Setting up libreadline7:amd64 (7.0-3) ...
Setting up libpsl5:amd64 (0.19.1-5build1) ...
Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ...
Setting up libkrb5support0:amd64 (1.16-2build1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:amd64 (1:5.32-2) ...
Setting up krb5-locales (1.16-2build1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Setting up publicsuffix (20180223.1310-1) ...
Setting up xz-utils (5.2.2-1.3) ...
update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/lzma.1.gz because associated file /usr/share/man/man1/xz.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/unlzma.1.gz because associated file /usr/share/man/man1/unxz.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzcat.1.gz because associated file /usr/share/man/man1/xzcat.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzmore.1.gz because associated file /usr/share/man/man1/xzmore.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzless.1.gz because associated file /usr/share/man/man1/xzless.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzdiff.1.gz because associated file /usr/share/man/man1/xzdiff.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzcmp.1.gz because associated file /usr/share/man/man1/xzcmp.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzgrep.1.gz because associated file /usr/share/man/man1/xzgrep.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzegrep.1.gz because associated file /usr/share/man/man1/xzegrep.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzfgrep.1.gz because associated file /usr/share/man/man1/xzfgrep.1.gz (of link group lzma) doesn't exist
Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up openssl (1.1.0g-2ubuntu4) ...
Setting up libsqlite3-0:amd64 (3.22.0-1) ...
Setting up libkeyutils1:amd64 (1.5.9-9.2ubuntu2) ...
Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up ca-certificates (20180409) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
debconf: unable to initialize frontend: Readline
debconf: (Can't locate Term/ReadLine.pm in @INC (you may need to install the Term::ReadLine module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Debconf/FrontEnd/Readline.pm line 7.)
debconf: falling back to frontend: Teletype
Updating certificates in /etc/ssl/certs...
133 added, 0 removed; done.
Setting up libmpdec2:amd64 (2.4.2-1ubuntu1) ...
Setting up libpython3.6-stdlib:amd64 (3.6.5-3) ...
Setting up libk5crypto3:amd64 (1.16-2build1) ...
Setting up python3.6 (3.6.5-3) ...
Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up file (1:5.32-2) ...
Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libkrb5-3:amd64 (1.16-2build1) ...
Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libpython3-stdlib:amd64 (3.6.5-3) ...
Setting up python3 (3.6.5-3) ...
running python rtupdate hooks for python3.6...
running python post-rtupdate hooks for python3.6...
Setting up libgssapi-krb5-2:amd64 (1.16-2build1) ...
Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1ubuntu1) ...
Setting up libcurl4:amd64 (7.58.0-2ubuntu3) ...
Setting up curl (7.58.0-2ubuntu3) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for ca-certificates (20180409) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Traceback (most recent call last):
  File "<stdin>", line 12, in <module>
ModuleNotFoundError: No module named 'distutils.spawn'
The command '/bin/sh -c apt-get update         && apt-get install -y                 sudo                 bash                 curl                 python3         && curl -sL git.io/install-candis | sudo python3' returned a non-zero code: 1

screenshot from 2018-05-12 19-12-34

@achillesrasquinha

Change sign from "minimize" to "downward arrow" after ToolBox is minimized.

Expected Behaviour

After ToolBox is minimized, its icon should be changed to v downward arrow, indicating to expand the ToolBox.

Actual Behaviour

Currently after minimizing ToolBox (localted in left side of UI), option to open it again is to click minimize option.

Steps to Reproduce:

  • Run Candis, then click on ToolBox minimize option.

Error in setup on Ubuntu

I am having a problem when I click on create a dataset.
The rows are not getting added immediately when I am clicking on the add rows button.
This is the console output of the event.
Can someone please help me out?
jserror

NOTE: Add a GIF/Screenshot if required.

Add React Components documentation

Expected Behaviour

Currently, there are many components which make it difficult for a newcomer to parse through, having a documentation of such components will make it easy to know about the components. Hence, I will be using an open-source library to generate documentation of components: react-docgen.

This will be the modified docs directory then.

|-- docs
| ____ |-- Client
| ___________ |-- componentsDocs.json # generated documentation.
| ____ |-- source

@achillesrasquinha

Make React developer tools work in Candis

Expected Behaviour

React developers should work in development mode.

Actual Behaviour

Currently React-dev-tool plugin dont work because Candis is Preact based not React.

Allow editing of pipeline which is read from the file.

Expected Behaviour

After opening a pipeline, the user can edit the pipeline. - add stages, change values of existing ones.

Actual Behaviour

After opening a file, values of stages cant be edited (no action on clicking those stages).
Also, adding more stages is not get reflected in the UI, although gets written back to the file.

Steps to Reproduce:

NOTE: Add a GIF/Screenshot if required.

Candis on Ubuntu using pip3 install

I am getting the following errors while installing candis using pip3 install.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting pandas (from candis)
Using cached pandas-0.21.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting numpy (from candis)
Using cached numpy-1.13.3-cp35-cp35m-manylinux1_x86_64.whl
Collecting pygraphviz (from candis)
Using cached pygraphviz-1.3.1.zip
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting django-htmlmin (from candis)
Using cached django_htmlmin-0.10.0-py2.py3-none-any.whl
Collecting PyYAML (from candis)
Downloading PyYAML-3.12.tar.gz (253kB)
100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 256kB 707kB/s
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting numpy (from candis)
Using cached numpy-1.13.3-cp35-cp35m-manylinux1_x86_64.whl
Collecting scipy (from candis)
Using cached scipy-1.0.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting liac-arff (from candis)
Using cached liac-arff-2.1.1.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting addict (from candis)
Using cached addict-2.1.1.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting Pillow (from candis)
Downloading Pillow-4.3.0-cp35-cp35m-manylinux1_x86_64.whl (5.8MB)
100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 5.8MB 129kB/s
Collecting javabridge (from candis)
Using cached javabridge-1.0.15.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting Flask-SocketIO (from candis)
Using cached Flask_SocketIO-2.9.3-py2.py3-none-any.whl
Collecting pandas (from candis)
Using cached pandas-0.21.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting gunicorn (from candis)
Using cached gunicorn-19.7.1-py2.py3-none-any.whl
Collecting python-weka-wrapper3 (from candis)
Using cached python-weka-wrapper3-0.1.3.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting rpy2 (from candis)
Using cached rpy2-2.9.1.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting scipy (from candis)
Using cached scipy-1.0.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting pandas (from candis)
Using cached pandas-0.21.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting javabridge (from candis)
Using cached javabridge-1.0.15.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

amohammed@Akram:~$ pip3 install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Collecting PyYAML (from candis)
Using cached PyYAML-3.12.tar.gz
Could not import setuptools which is required to install from a source distribution.
Please install setuptools.

After deleting a pipeline, enchance UI.

Expected Behaviour

After deleting a pipeline, activePipeline should be set to a one of the pipelines in document list (i.e. opened by the user). And if only one pipeline was present before deleting it, clicking on delete again (after deleting it) should indicate error.

get-candis on Ubuntu 17.04

I'm getting the following error in Ubuntu 17.04 while installing candis.

$ curl -sL bit.do/get-candis | python

#!/System/Library/Frameworks/Ruby.framework/Versions/Current/usr/bin/ruby
#This script installs to /usr/local only. To install elsewhere you can just
#untar https://github.com/Homebrew/brew/tarball/master anywhere you like or
#change the value of HOMEBREW_PREFIX.
HOMEBREW_PREFIX = "/usr/local".freeze
HOMEBREW_REPOSITORY = "/usr/local/Homebrew".freeze
HOMEBREW_CACHE = "#{ENV["HOME"]}/Library/Caches/Homebrew".freeze
HOMEBREW_OLD_CACHE = "/Library/Caches/Homebrew".freeze
BREW_REPO = "https://github.com/Homebrew/brew".freeze
CORE_TAP_REPO = "https://github.com/Homebrew/homebrew-core".freeze

#no analytics during installation
ENV["HOMEBREW_NO_ANALYTICS_THIS_RUN"] = "1"
ENV["HOMEBREW_NO_ANALYTICS_MESSAGE_OUTPUT"] = "1"

module Tty
module_function

def blue
bold 34
end

def red
bold 31
end

def reset
escape 0
end

def bold(n = 39)
escape "1;#{n}"
end

def underline
escape "4;39"
end

def escape(n)
"\033[#{n}m" if STDOUT.tty?
end
end

class Array
def shell_s
cp = dup
first = cp.shift
cp.map { |arg| arg.gsub " ", "\ " }.unshift(first).join(" ")
end
end

def ohai(*args)
puts "#{Tty.blue}==>#{Tty.bold} #{args.shell_s}#{Tty.reset}"
end

def warn(warning)
puts "#{Tty.red}Warning#{Tty.reset}: #{warning.chomp}"
end

def system(*args)
abort "Failed during: #{args.shell_s}" unless Kernel.system(*args)
end

def sudo(*args)
args.unshift("-A") unless ENV["SUDO_ASKPASS"].nil?
ohai "/usr/bin/sudo", *args
system "/usr/bin/sudo", *args
end

def getc # NOTE only tested on OS X
system "/bin/stty raw -echo"
if STDIN.respond_to?(:getbyte)
STDIN.getbyte
else
STDIN.getc
end
ensure
system "/bin/stty -raw echo"
end

def wait_for_user
puts
puts "Press RETURN to continue or any other key to abort"
c = getc
#we test for \r and \n because some stuff does \r instead
abort unless (c == 13) || (c == 10)
end

class Version
include Comparable
attr_reader :parts

def initialize(str)
@Parts = str.split(".").map { |p| p.to_i }
end

def <=>(other)
parts <=> self.class.new(other).parts
end
end

def force_curl?
ARGV.include?("--force-curl")
end

def macos_version
@macos_version ||= Version.new(/usr/bin/sw_vers -productVersion.chomp[/10.\d+/])
end

def should_install_command_line_tools?
return false if force_curl?
return false if macos_version < "10.9"
developer_dir = /usr/bin/xcode-select -print-path 2>/dev/null.chomp
developer_dir.empty? || !File.exist?("#{developer_dir}/usr/bin/git")
end

def git
return false if force_curl?

@git ||= if ENV["GIT"] && File.executable?(ENV["GIT"])
ENV["GIT"]
elsif Kernel.system "/usr/bin/which -s git"
"git"
else
exe = xcrun -find git 2>/dev/null.chomp
exe if $? &amp;&amp; $?.success? && !exe.empty? && File.executable?(exe)
end

return unless @git
#Github only supports HTTPS fetches on 1.7.10 or later:
#https://help.github.com/articles/https-cloning-errors
#{@git} --version =~ /git version (\d.\d+.\d+)/
return if $1.nil?
return if Version.new($1) < "1.7.10"

@git
end

def user_only_chmod?(d)
return false unless File.directory?(d)
mode = File.stat(d).mode & 0777
#u = (mode >> 6) & 07
#g = (mode >> 3) & 07
#o = (mode >> 0) & 07
mode != 0755
end

def chmod?(d)
File.exist?(d) && !(File.readable?(d) && File.writable?(d) && File.executable?(d))
end

def chown?(d)
!File.owned?(d)
end

def chgrp?(d)
!File.grpowned?(d)
end

#Invalidate sudo timestamp before exiting (if it wasn't active before).
Kernel.system "/usr/bin/sudo -n -v 2>/dev/null"
at_exit { Kernel.system "/usr/bin/sudo", "-k" } unless $?.success?

#The block form of Dir.chdir fails later if Dir.CWD doesn't exist which I
#guess is fair enough. Also sudo prints a warning message for no good reason
Dir.chdir "/usr"

####################################################################### script
abort "See Linuxbrew: http://linuxbrew.sh/" if RUBY_PLATFORM.to_s.downcase.include?("linux")
abort "Mac OS X too old, see: https://github.com/mistydemeo/tigerbrew" if macos_version < "10.5"
abort "Don't run this as root!" if Process.uid.zero?
abort <<-EOABORT unless dsmemberutil checkmembership -U "#{ENV["USER"]}" -G admin.include? "user is a member"
This script requires the user #{ENV["USER"]} to be an Administrator.
EOABORT
#Tests will fail if the prefix exists, but we don't have execution
#permissions. Abort in this case.
abort <<-EOABORT if File.directory?(HOMEBREW_PREFIX) && (!File.executable? HOMEBREW_PREFIX)
The Homebrew prefix, #{HOMEBREW_PREFIX}, exists but is not searchable. If this is
not intentional, please restore the default permissions and try running the
installer again:
sudo chmod 775 #{HOMEBREW_PREFIX}
EOABORT

ohai "This script will install:"
puts "#{HOMEBREW_PREFIX}/bin/brew"
puts "#{HOMEBREW_PREFIX}/share/doc/homebrew"
puts "#{HOMEBREW_PREFIX}/share/man/man1/brew.1"
puts "#{HOMEBREW_PREFIX}/share/zsh/site-functions/_brew"
puts "#{HOMEBREW_PREFIX}/etc/bash_completion.d/brew"
puts HOMEBREW_REPOSITORY.to_s

group_chmods = %w[ bin bin/brew etc Frameworks include lib sbin share var
etc/bash_completion.d lib/pkgconfig var/log
share/aclocal share/doc share/info share/locale share/man
share/man/man1 share/man/man2 share/man/man3 share/man/man4
share/man/man5 share/man/man6 share/man/man7 share/man/man8].
map { |d| File.join(HOMEBREW_PREFIX, d) }.
select { |d| chmod?(d) }
#zsh refuses to read from these directories if group writable
zsh_dirs = %w[share/zsh share/zsh/site-functions].
map { |d| File.join(HOMEBREW_PREFIX, d) }
user_chmods = zsh_dirs.select { |d| user_only_chmod?(d) }
chmods = group_chmods + user_chmods
chowns = chmods.select { |d| chown?(d) }
chgrps = chmods.select { |d| chgrp?(d) }
mkdirs = %w[Cellar Homebrew Frameworks bin etc include lib opt sbin share share/zsh share/zsh/site-functions var].
map { |d| File.join(HOMEBREW_PREFIX, d) }.
reject { |d| File.directory?(d) }

unless group_chmods.empty?
ohai "The following existing directories will be made group writable:"
puts(*group_chmods)
end
unless user_chmods.empty?
ohai "The following existing directories will be made writable by user only:"
puts(*user_chmods)
end
unless chowns.empty?
ohai "The following existing directories will have their owner set to #{Tty.underline}#{ENV["USER"]}#{Tty.reset}:"
puts(*chowns)
end
unless chgrps.empty?
ohai "The following existing directories will have their group set to #{Tty.underline}admin#{Tty.reset}:"
puts(*chgrps)
end
unless mkdirs.empty?
ohai "The following new directories will be created:"
puts(*mkdirs)
end

wait_for_user if STDIN.tty? && !ENV["TRAVIS"]

if File.directory? HOMEBREW_PREFIX
sudo "/bin/chmod", "u+rwx", *chmods unless chmods.empty?
sudo "/bin/chmod", "g+rwx", *group_chmods unless group_chmods.empty?
sudo "/bin/chmod", "755", *user_chmods unless user_chmods.empty?
sudo "/usr/sbin/chown", ENV["USER"], *chowns unless chowns.empty?
sudo "/usr/bin/chgrp", "admin", *chgrps unless chgrps.empty?
else
sudo "/bin/mkdir", "-p", HOMEBREW_PREFIX
sudo "/usr/sbin/chown", "root:wheel", HOMEBREW_PREFIX
end

unless mkdirs.empty?
sudo "/bin/mkdir", "-p", *mkdirs
sudo "/bin/chmod", "g+rwx", *mkdirs
sudo "/bin/chmod", "755", *zsh_dirs
sudo "/usr/sbin/chown", ENV["USER"], *mkdirs
sudo "/usr/bin/chgrp", "admin", *mkdirs
end

[HOMEBREW_CACHE, HOMEBREW_OLD_CACHE].each do |cache|
sudo "/bin/mkdir", "-p", cache unless File.directory? cache
sudo "/bin/chmod", "g+rwx", cache if chmod? cache
sudo "/usr/sbin/chown", ENV["USER"], cache if chown? cache
sudo "/usr/bin/chgrp", "admin", cache if chgrp? cache
end

if should_install_command_line_tools?
ohai "Searching online for the Command Line Tools"
#This temporary file prompts the 'softwareupdate' utility to list the Command Line Tools
clt_placeholder = "/tmp/.com.apple.dt.CommandLineTools.installondemand.in-progress"
sudo "/usr/bin/touch", clt_placeholder
clt_label = softwareupdate -l | grep -B 1 -E "Command Line (Developer|Tools)" | awk -F"*" '/^ +\\*/ {print $2}' | sed 's/^ *//' | tail -n1.chomp
ohai "Installing #{clt_label}"
sudo "/usr/sbin/softwareupdate", "-i", clt_label
sudo "/bin/rm", "-f", clt_placeholder
sudo "/usr/bin/xcode-select", "--switch", "/Library/Developer/CommandLineTools"
end

#Headless install may have failed, so fallback to original 'xcode-select' method
if should_install_command_line_tools? && STDIN.tty?
ohai "Installing the Command Line Tools (expect a GUI popup):"
sudo "/usr/bin/xcode-select", "--install"
puts "Press any key when the installation has completed."
getc
sudo "/usr/bin/xcode-select", "--switch", "/Library/Developer/CommandLineTools"
end

abort <<-EOABORT if /usr/bin/xcrun clang 2>&1 =~ /license/ && !$?.success?
You have not agreed to the Xcode license.
Before running the installer again please agree to the license by opening
Xcode.app or running:
sudo xcodebuild -license
EOABORT

ohai "Downloading and installing Homebrew..."
Dir.chdir HOMEBREW_REPOSITORY do
if git
#we do it in four steps to avoid merge errors when reinstalling
system git, "init", "-q"

#"git remote add" will fail if the remote is defined in the global config
system git, "config", "remote.origin.url", BREW_REPO
system git, "config", "remote.origin.fetch", "+refs/heads/*:refs/remotes/origin/*"

#ensure we don't munge line endings on checkout
system git, "config", "core.autocrlf", "false"

args = git, "fetch", "origin", "master:refs/remotes/origin/master",
       "--tags", "--force"
system(*args)

system git, "reset", "--hard", "origin/master"

system "ln", "-sf", "#{HOMEBREW_REPOSITORY}/bin/brew", "#{HOMEBREW_PREFIX}/bin/brew"

system "#{HOMEBREW_PREFIX}/bin/brew", "update", "--force"

else
# -m to stop tar erroring out if it can't modify the mtime for root owned directories
# pipefail to cause the exit status from curl to propagate if it fails
curl_flags = "fsSL"
curl_flags += "k" if macos_version < "10.6"
core_tap = "#{HOMEBREW_PREFIX}/Homebrew/Library/Taps/homebrew/homebrew-core"
system "/bin/bash -o pipefail -c '/usr/bin/curl -#{curl_flags} #{BREW_REPO}/tarball/master | /usr/bin/tar xz -m --strip 1'"

system "ln", "-sf", "#{HOMEBREW_REPOSITORY}/bin/brew", "#{HOMEBREW_PREFIX}/bin/brew"

system "/bin/mkdir", "-p", core_tap
Dir.chdir core_tap do
  system "/bin/bash -o pipefail -c '/usr/bin/curl -#{curl_flags} #{CORE_TAP_REPO}/tarball/master | /usr/bin/tar xz -m --strip 1'"
end

end
end

warn "#{HOMEBREW_PREFIX}/bin is not in your PATH." unless ENV["PATH"].split(":").include? "#{HOMEBREW_PREFIX}/bin"

ohai "Installation successful!"
puts

#Use the shell's audible bell.
print "\a"

#Use an extra newline and bold to avoid this being missed.
ohai "Homebrew has enabled anonymous aggregate user behaviour analytics."
puts <<-EOS
#{Tty.bold}Read the analytics documentation (and how to opt-out) here:
#{Tty.underline}https://docs.brew.sh/Analytics.html#{Tty.reset}

EOS

if git
Dir.chdir HOMEBREW_REPOSITORY do
system git, "config", "--local", "--replace-all", "homebrew.analyticsmessage", "true"
end
end

ohai "Next steps:"

if macos_version < "10.9" && macos_version > "10.6"
/usr/bin/cc --version 2> /dev/null =~ /clang-(\d{2,})/
version = $1.to_i
if version < 425
puts "- Install the #{Tty.bold}Command Line Tools for Xcode:"
puts " #{Tty.underline}https://developer.apple.com/downloads#{Tty.reset}"
end
elsif !File.exist? "/usr/bin/cc"
puts "- Install #{Tty.bold}Xcode:"
puts " #{Tty.underline}https://developer.apple.com/xcode#{Tty.reset}"
end

unless git
puts "- Run brew update --force to complete installation by installing:"
puts " #{HOMEBREW_PREFIX}/share/doc/homebrew"
puts " #{HOMEBREW_PREFIX}/share/man/man1/brew.1"
puts " #{HOMEBREW_PREFIX}/share/zsh/site-functions/_brew"
puts " #{HOMEBREW_PREFIX}/etc/bash_completion.d/brew"
puts " #{HOMEBREW_REPOSITORY}/.git"
end

puts "- Run brew help to get started"
puts "- Further documentation: "
puts " #{Tty.underline}https://docs.brew.sh#{Tty.reset}"
Traceback (most recent call last):
File "", line 131, in
File "", line 114, in main
File "", line 45, in popen
File "/usr/lib/python2.7/subprocess.py", line 390, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1024, in _execute_child
raise child_exception
TypeError: coercing to Unicode: need string or buffer, int found

Error in installing R dependencies

When I am executing the command to install the R dependencies , it has some problem installing the Bioconductor. I am using ubuntu 16.04.

screenshot from 2018-02-16 17-55-34

Windows installation error.

###pip installation error
pip doesn't recognize the Visual c++ version in the system even though i have visual c++ 2015 and have set the environment variables.
Error below:

C:\Users\Arpit\AppData\Local\Programs\Python\Python36>pip install candis
Collecting candis
Using cached candis-0.0.5-py2.py3-none-any.whl
Requirement already satisfied: rpy2 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Collecting PyYAML (from candis)
Using cached PyYAML-3.12.tar.gz
Requirement already satisfied: seaborn in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: matplotlib in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: pandas in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: Cython in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: requests in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Collecting python-weka-wrapper3 (from candis)
Using cached python-weka-wrapper3-0.1.4.tar.gz
Requirement already satisfied: django-htmlmin in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: Flask-SocketIO in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Collecting pygraphviz (from candis)
Using cached pygraphviz-1.3.1.zip
Requirement already satisfied: scipy in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: gunicorn in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: numpy in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: addict in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Collecting javabridge (from candis)
Using cached javabridge-1.0.15.tar.gz
Requirement already satisfied: Flask in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: Pillow in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: liac-arff in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from candis)
Requirement already satisfied: jinja2 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from rpy2->candis)
Requirement already satisfied: six in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from rpy2->candis)
Requirement already satisfied: python-dateutil>=2.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from matplotlib->candis)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from matplotlib->candis)
Requirement already satisfied: cycler>=0.10 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from matplotlib->candis)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from matplotlib->candis)
Requirement already satisfied: pytz in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from matplotlib->candis)
Requirement already satisfied: idna<2.7,>=2.5 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from requests->candis)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from requests->candis)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from requests->candis)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from requests->candis)
Requirement already satisfied: beautifulsoup4 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from django-htmlmin->candis)
Requirement already satisfied: html5lib in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from django-htmlmin->candis)
Requirement already satisfied: python-socketio>=1.6.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from Flask-SocketIO->candis)
Requirement already satisfied: click>=2.0 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from Flask->candis)
Requirement already satisfied: Werkzeug>=0.7 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from Flask->candis)
Requirement already satisfied: itsdangerous>=0.21 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from Flask->candis)
Requirement already satisfied: MarkupSafe>=0.23 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from jinja2->rpy2->candis)
Requirement already satisfied: setuptools in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from kiwisolver>=1.0.1->matplotlib->candis)
Requirement already satisfied: webencodings in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from html5lib->django-htmlmin->candis)
Requirement already satisfied: python-engineio>=1.2.1 in c:\users\arpit\appdata\local\programs\python\python36\lib\site-packages (from python-socketio>=1.6.1->Flask-SocketIO->candis)
Installing collected packages: PyYAML, javabridge, python-weka-wrapper3, pygraphviz, candis
Running setup.py install for PyYAML ... done
Running setup.py install for javabridge ... error
Complete output from command c:\users\arpit\appdata\local\programs\python\python36\python.exe -u -c "import setuptools, tokenize;file='C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record C:\Users\Arpit\AppData\Local\Temp\pip-5_iszptg-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\javabridge
copying javabridge\jutil.py -> build\lib.win-amd64-3.6\javabridge
copying javabridge\locate.py -> build\lib.win-amd64-3.6\javabridge
copying javabridge\noseplugin.py -> build\lib.win-amd64-3.6\javabridge
copying javabridge\wrappers.py -> build\lib.win-amd64-3.6\javabridge
copying javabridge_version.py -> build\lib.win-amd64-3.6\javabridge
copying javabridge_init_.py -> build\lib.win-amd64-3.6\javabridge
creating build\lib.win-amd64-3.6\javabridge\tests
copying javabridge\tests\test_cpython.py -> build\lib.win-amd64-3.6\javabridge\tests
copying javabridge\tests\test_javabridge.py -> build\lib.win-amd64-3.6\javabridge\tests
copying javabridge\tests\test_jutil.py -> build\lib.win-amd64-3.6\javabridge\tests
copying javabridge\tests\test_wrappers.py -> build\lib.win-amd64-3.6\javabridge\tests
copying javabridge\tests_init_.py -> build\lib.win-amd64-3.6\javabridge\tests
creating build\lib.win-amd64-3.6\javabridge\jars
copying javabridge\jars\cpython.jar -> build\lib.win-amd64-3.6\javabridge\jars
copying javabridge\jars\rhino-1.7R4.jar -> build\lib.win-amd64-3.6\javabridge\jars
copying javabridge\jars\runnablequeue.jar -> build\lib.win-amd64-3.6\javabridge\jars
copying javabridge\jars\test.jar -> build\lib.win-amd64-3.6\javabridge\jars
running build_ext
C:\Program Files\Java\JDK181.0_1\bin\javac.exe -source 6 -target 6 C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\java\org\cellprofiler\runnablequeue\RunnableQueue.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
1 warning
C:\Program Files\Java\JDK18
1.0_1\bin\javac.exe -source 6 -target 6 C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\java\org\cellprofiler\javabridge\test\RealRect.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
1 warning
C:\Program Files\Java\JDK181.0_1\bin\javac.exe -source 6 -target 6 C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\java\org\cellprofiler\javabridge\CPython.java C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
Note: C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\java\org\cellprofiler\javabridge\CPythonInvocationHandler.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
1 warning
building 'javabridge._javabridge' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.13.26128\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ic:\users\arpit\appdata\local\programs\python\python36\lib\site-packages\numpy\core\include "-IC:\Program Files\Java\JDK18
1.0_1\include" "-IC:\Program Files\Java\JDK18~1.0_1\include\win32" -Ic:\users\arpit\appdata\local\programs\python\python36\include -Ic:\users\arpit\appdata\local\programs\python\python36\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.13.26128\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.13.26128\include" /Tc_javabridge.c /Fobuild\temp.win-amd64-3.6\Release_javabridge.obj
_javabridge.c
c:\users\arpit\appdata\local\programs\python\python36\include\pyconfig.h(59): fatal error C1083: Cannot open include file: 'io.h': No such file or directory
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.13.26128\bin\HostX86\x64\cl.exe' failed with exit status 2

----------------------------------------

Command "c:\users\arpit\appdata\local\programs\python\python36\python.exe -u -c "import setuptools, tokenize;file='C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record C:\Users\Arpit\AppData\Local\Temp\pip-5_iszptg-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\Arpit\AppData\Local\Temp\pip-build-tw1be2wd\javabridge\

Affy package not found while using importr function of rpy2.

When running candis quickstart inpython notbook, I get following error.

RRuntimeError                             Traceback (most recent call last)
<ipython-input-4-ebad1c6879e6> in <module>()
----> 1 cdata.toARFF('data/sample.arff')

~/opensource/candisVENV/lib/python3.6/site-packages/candis/ios/cdata/cdata.py in toARFF(self, path, express_config, verbose)
    115             raise ValueError('No valid DNA microarray found.')
    116         else:
--> 117             importr('affy')
    118 
    119             robj = robjects.r('read.affybatch')

~/opensource/candisVENV/lib/python3.6/site-packages/rpy2/robjects/packages.py in importr(name, lib_loc, robject_translations, signature_translation, suppress_messages, on_conflict, symbol_r2python, symbol_check_after, data)
    451     if _package_has_namespace(rname, 
    452                               _system_file(package = rname)):
--> 453         env = _get_namespace(rname)
    454         version = _get_namespace_version(rname)[0]
    455         exported_names = set(_get_namespace_exports(rname))

RRuntimeError: Error in loadNamespace(name) : there is no package called โ€˜affyโ€™

problem is there is no Affy package, I found following packages availble (which doesn't include affy), link : FAQs .
rpackages

I could download the above pacakge with same method but not affy. Also CRAN don't have 'affy' package too.
rpy2.robjects.pacakges.importr(<package_name>)

There is a package name affy in Bioconductor website , website used to search- https://master.bioconductor.org/packages/release/BiocViews.html#___Software. But I am not able to import using rpy2's importr function any of the pacakges from above list.

affy: Methods for Affymetrix Oligonucleotide Arrays
https://master.bioconductor.org/packages/release/bioc/html/affy.html

@achillesrasquinha

After adding new pipeline, adding stages in the new pipe creates error when their values are set.

Expected Behaviour

Adding a new pipeline alongside the previously active should have stages working similar to the previously active pipeline's stages.

Actual Behaviour

After adding new pipeline, adding stages in the new pipe creates error when their values are set.
Currently for setting value of any stage following error comes up:
Uncaught TypeError: Cannot read property 'code' of null

Steps to Reproduce:

Create a pipeline, then add a new one and in the this new one start setting up value of any stage added, it will give the above error.

NOTE: Add a GIF/Screenshot if required.
screenshot from 2018-06-26 21-57-24

Can't call setState (or forceUpdate) on an unmounted component.

Expected Behaviour

Solve the above warning on login and sign up.

Actual Behaviour

Currently after logging in and sign up, above warning pops up.
Warning is :
Warning: Can't call setState (or forceUpdate) on an unmounted component. This is a no-op, but it indicates a memory leak in your application. To fix, cancel all subscriptions and asynchronous tasks in the componentWillUnmount method.
This is related to formik form - refer jaredpalmer/formik#597

Steps to Reproduce:

Login or signup and then see the console.
NOTE: Add a GIF/Screenshot if required.

Add Test cases for frontend using Jest and Enzyme.

This issue is to achieve 100% code coverage on frontend.

Cheklist:

  • Add JEST - refer #45
  • Add coverage tool - refer #49
  • Add enzyme. - Update: 11th June: Well using enzyme is not going to work because of no official support to Preact. Might be removed in upcoming PRs.
  • Complete actions test
  • Complete Reducers test
  • Complete Components test

Installation error

$ sudo pip3 install candis
Collecting candis
  Downloading candis-0.0.5-py2.py3-none-any.whl (1.4MB)
    100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 1.4MB 271kB/s 
Requirement already satisfied: django-htmlmin in /usr/local/lib/python3.5/dist-packages (from candis)
Collecting PyYAML (from candis)
  Downloading PyYAML-3.12.tar.gz (253kB)
    100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 256kB 257kB/s 
Requirement already satisfied: Flask in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: Pillow in /usr/lib/python3/dist-packages (from candis)
Collecting javabridge (from candis)
  Downloading javabridge-1.0.15.tar.gz (1.3MB)
    100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 1.3MB 159kB/s 
Requirement already satisfied: addict in /usr/local/lib/python3.5/dist-packages (from candis)
Collecting rpy2 (from candis)
  Downloading rpy2-2.9.2.tar.gz (194kB)
    100% |โ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆโ–ˆ| 194kB 277kB/s 
Collecting python-weka-wrapper3 (from candis)
  Downloading python-weka-wrapper3-0.1.3.tar.gz (85kB)
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Requirement already satisfied: numpy in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: scipy in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: pandas in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: Cython in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: matplotlib in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: Flask-SocketIO in /usr/local/lib/python3.5/dist-packages (from candis)
Collecting pygraphviz (from candis)
  Downloading pygraphviz-1.3.1.zip (123kB)
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Requirement already satisfied: gunicorn in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: seaborn in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: requests in /usr/lib/python3/dist-packages (from candis)
Requirement already satisfied: liac-arff in /usr/local/lib/python3.5/dist-packages (from candis)
Requirement already satisfied: html5lib in /usr/local/lib/python3.5/dist-packages (from django-htmlmin->candis)
Requirement already satisfied: beautifulsoup4 in /usr/local/lib/python3.5/dist-packages (from django-htmlmin->candis)
Requirement already satisfied: Jinja2>=2.4 in /home/gopu/.local/lib/python3.5/site-packages (from Flask->candis)
Requirement already satisfied: Werkzeug>=0.7 in /usr/local/lib/python3.5/dist-packages (from Flask->candis)
Requirement already satisfied: itsdangerous>=0.21 in /usr/local/lib/python3.5/dist-packages (from Flask->candis)
Requirement already satisfied: click>=2.0 in /usr/local/lib/python3.5/dist-packages (from Flask->candis)
Requirement already satisfied: six in /home/gopu/.local/lib/python3.5/site-packages (from rpy2->candis)
Requirement already satisfied: pytz>=2011k in /home/gopu/.local/lib/python3.5/site-packages (from pandas->candis)
Requirement already satisfied: python-dateutil>=2 in /usr/local/lib/python3.5/dist-packages (from pandas->candis)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.5/dist-packages (from matplotlib->candis)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.5/dist-packages (from matplotlib->candis)
Requirement already satisfied: python-socketio>=1.6.1 in /usr/local/lib/python3.5/dist-packages (from Flask-SocketIO->candis)
Requirement already satisfied: webencodings in /usr/local/lib/python3.5/dist-packages (from html5lib->django-htmlmin->candis)
Requirement already satisfied: MarkupSafe>=0.23 in /home/gopu/.local/lib/python3.5/site-packages (from Jinja2>=2.4->Flask->candis)
Requirement already satisfied: python-engineio>=1.2.1 in /usr/local/lib/python3.5/dist-packages (from python-socketio>=1.6.1->Flask-SocketIO->candis)
Installing collected packages: PyYAML, javabridge, rpy2, python-weka-wrapper3, pygraphviz, candis
  Running setup.py install for PyYAML ... error
    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-y_e82tw7/PyYAML/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-2aj7doh6-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.5
    creating build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/dumper.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/parser.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/representer.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/constructor.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/__init__.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/resolver.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/scanner.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/events.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/loader.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/reader.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/error.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/tokens.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/serializer.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/cyaml.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/emitter.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/composer.py -> build/lib.linux-x86_64-3.5/yaml
    copying lib3/yaml/nodes.py -> build/lib.linux-x86_64-3.5/yaml
    running build_ext
    creating build/temp.linux-x86_64-3.5
    checking if libyaml is compilable
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c build/temp.linux-x86_64-3.5/check_libyaml.c -o build/temp.linux-x86_64-3.5/check_libyaml.o
    checking if libyaml is linkable
    x86_64-linux-gnu-gcc -pthread build/temp.linux-x86_64-3.5/check_libyaml.o -lyaml -o build/temp.linux-x86_64-3.5/check_libyaml
    skipping 'ext/_yaml.c' Cython extension (up-to-date)
    building '_yaml' extension
    creating build/temp.linux-x86_64-3.5/ext
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c ext/_yaml.c -o build/temp.linux-x86_64-3.5/ext/_yaml.o
    ext/_yaml.c:4:20: fatal error: Python.h: No such file or directory
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-y_e82tw7/PyYAML/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-2aj7doh6-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-y_e82tw7/PyYAML/

Operating System: Linux Mint 18.2 Sonya

Integrate frontend entrez form with backend

Expected Behaviour

  • Add entrez form to hit api/data/search endpoint and fetch results.
  • Put results from above into data-grid, and then download the CEL file as per user selection.

Good luck for GSoC!

I'll try to follow what you will develop during you GSoC project, I wish you all the best to make it progress!

Remove backend 404 error showing up on console when creating a new pipeline.

Expected Behaviour

If new pipe's name doesn't match with any existing, backend read api error should not be reflected back in the console.

Actual Behaviour

Currently, while creating a new pipeline, we check if pipeline with the same name if already present, if not we create it. But if there is no match, a error is caught for the read request to backend, which gets shown up as 404 error in the console.

Steps to Reproduce:

Create a new pipeline with a new name, and see your console.

node-sass command is incorrect.

Expected Behaviour

node-sass was added in #13.
node-sass is great because of its fast compilation over sass (refer Libsass vs sass )
with reference to https://github.com/sass/node-sass#command-line-interface, --style should be replaced with --output-style, and there should be no : in between input and output file path.

Actual Behaviour

currently running yarn run sass creates error. which can be solved with above suggestion.

Steps to Reproduce:

I will correct this in PR #30
Corrected locally:
2018-05-05 1

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