Comments (5)
A similar error related to building the database is:
2021-02-14 18:17:31,592 - importer - ERROR - Writing Stats object full_stats_1_0 in file:/CKG/src/graphdb_builder/../../data/imports/stats/stats.hdf > Trying to store a string with len [9] in [date] column but
this column has a limit of [8]!
Consider using min_itemsize to preset the sizes on these columns.
2021-02-14 18:17:31,296 - ontologies_controller - ERROR - Error: Tag-value pair parsing failed for:
A000 Cholera due to Vibrio cholerae 01, biovar cholerae
. Ontology ICD-10: (<class 'ValueError'>, ValueError('Tag-value pair parsing failed for:\nA000 Cholera due to Vibrio cholerae 01, biovar cholerae\n'), <traceback object at 0x18fc147d0>), file: ontologies_controller.py,line: 134
2021-02-14 18:40:09,476 - database_controller - ERROR - Database UniProt: (<class 'Exception'>, Exception('Something went wrong. Exception raised when an error code signifying a permanent error. 550 Failed to open file..\nURL:ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606.fasta.gz.\nURL:ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606.fasta.gz'), <traceback object at 0x10a961780>), file: databases_controller.py,line: 66
-1 / unknownDone Parsing database GWASCatalog
2021-02-15 04:28:00,160 - database_controller - ERROR - Database DGIdb: (<class 'Exception'>, Exception("mapping - No mapping file ../../../data/databases/DrugBank/complete_mapping.tsv for entity Drug. Error: [Errno 2] No such file or directory: '../../../data/databases/DrugBank/complete_mapping.tsv'"), <traceback object at 0x1927e3640>), file: databases_controller.py,line: 143
from ckg.
The first error: 2021-02-14 18:18:26,308 - database_controller - ERROR - Database DrugBank: (<class 'lxml.etree.XMLSyntaxError'>, XMLSyntaxError('Document is empty, line 1, column 1'), <traceback object at 0x19d61a3c0>), file: databases_controller.py,line: 205
Came from the download from the DrugBank decompressing the file. Using the OS X compress created a directory in the archive __MACOSX, which was causing the issue during parsing.
Fixed by : Can be fixed after the fact by zip -d filename.zip __MACOSX/*
as detailed here:
https://stackoverflow.com/questions/10924236/mac-zip-compress-without-macosx-folder
from ckg.
uniprot error:
2021-02-14 18:40:09,476 - database_controller - ERROR - Database UniProt: (<class 'Exception'>, Exception('Something went wrong. Exception raised when an error code signifying a permanent error. 550 Failed to open file..\nURL:ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606.fasta.gz.\nURL:ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640_9606.fasta.gz'), <traceback object at 0x10a961780>), file: databases_controller.py,line: 66
updated to this line to fix the file path:
9 uniprot_fasta_file: 'ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz'
./src/graphdb_builder/databases/config/uniprotConfig.yml
from ckg.
The error for ICD10 code import fails because the input file seems incompatible with the parser. I am not sure what the correct file should be, the parser (ontologies/parsers/icdParser.py) seems to suggest that it should be a tab separated file with at least 6 columns, the downloaded file is just two columns and does not have any tabs:
ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Publications/ICD10CM/2020/icd10cm_codes_2020.txt
from ckg.
Hi, apologies for the late response.
ICD10 codes are not included in this version of CKG. The parser we committed last year was in development and was not finalized. Closing until there is a parser supporting this node type.
from ckg.
Related Issues (20)
- Pre-built image on Docker Hub
- missing some files in cancerGenomeInterpreter
- got no results from ckg app HOT 1
- SNF: TypeError: spectral_clustering() takes 1 positional argument but 2 were given
- apt-key is deprecated (Docker building)
- CKG Data Upload does not work
- missing data
- R package install error HOT 1
- can not import name"get_current_traceback" from 'werkzeug_debug_tbttools'.
- when click the "import" 500 error occurred
- Internal server error when logging in http://localhost:8050/ HOT 6
- Failed to generate report after uploading data HOT 3
- Node and edge lists in TSV format HOT 6
- Permission denied: '/CKG/data/reports/
- TypeError: argument of type 'NoneType' is not iterable HOT 2
- Dataset of paper HOT 1
- "Out of memory" crash and a little question
- The ckg_config.yml file doesn't exist. HOT 1
- Failed to receive a keyserver [16/78]
- Neo4j database is not online or page cannot be opened
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ckg.