12. Whats’ new, what has changed¶
12.1. Revision 1.8.0 roadmap¶
- make all services methods hidden or inside a single attributes to make the methods of a services more visible
- finalise pubchem, pfam and eva modules
- Wherever devtools is used to check input params, we should make sure the error message is informative. This may need to change easydev itself;
- All Classes/Services should hide the REST/WSDL methods to make the API easier. Instead of inheriting from REST, we should use an aggregation and store all methods in a single attribute
- Get rid of multifasta and fasta modules
12.2. Revision 1.7.12 (Jan 2021-July 2021)¶
- continous integration revisited with github actions
- NEWS: * COG services qdded * New module: mygeneinfom pdbe * added panther module (pantherdb.org)
- CHANGES * update dbbionet to fulfill future new API * Migrate to PDB new API (Jan 2021) * Update Quickgo service * Integration new Biomodels API following Combine/Harmony meetng * Update ChEMBL after an ChEMBL API change
- BUGS and FIXES * General fixes and update from @thobalose (https://github.com/cokelaer/bioservices/pull/149) to * PSICQUIC fix (https://github.com/cokelaer/bioservices/issues/189) to * Fix ENA new API * Fix NCBIBlast and Muscle services (new API)
- DEPRECATED: * deprecated PICR and TCGA modules (the latter was not really available anyway)
12.3. Revision 1.7.11 (Dec 2020)¶
- Fix https://github.com/cokelaer/bioservices/issues/183 (warning in uniprot
- Fix annoying warning https://github.com/cokelaer/bioservices/issues/184
- Implemented new PDB services (Update API changed in Nov/DEc 2020)
12.4. Revision 1.7.10 (Nov 2020)¶
- Fix KEGG https://github.com/cokelaer/bioservices/issues/182 adding NETWORK field
- Fix Pathway common with new API https://github.com/cokelaer/bioservices/issues/135
- Update the PathwayCommon service with new API
- Update the Rhea service with new API
12.5. Revision 1.7.9¶
- add missing field in KEgg Parser (REL_PATHWAY)
- fix panther.get_enrichment output (try/except)
12.6. Revision 1.7.8¶
- Fix ENA new API
- fix missing plugin in requirements-dev.txt
12.7. Revision 1.7.7¶
- small fix on pantherdb (autocorrect typo in pantherdb api)
12.8. Revision 1.7.6¶
- Fixing ncbiblast and muscle services
- Fixing quickgo services by adding new methods
- Fixing chembl and all failing tests and modules (omicdi, seqret,etc)
12.9. Revision 1.7.5¶
- NEW MODULE: mygeneinfo, pdbe
- Limits the request to 10 per seconds (3 for eutils). This fixes https://github.com/cokelaer/bioservices/issues/7
- update quickgo
- Update PDB module (will not be maintained in the future, to usePDB instead.)
- Fix issue in Eutils/ECitMatch reported here https://github.com/cokelaer/bioservices/issues/169 and here https://tinyurl.com/y6u2cyjq on stackoverflow
12.10. Revision 1.7.4 (March 2020 Combine/Harmany2020 hackathon)¶
- Integration of BioModels new API (REST instead of WSDL and different functionalities) in coordination with Mihai Glont and Tung Nguyen at EMBL-EBI during the Combine-Harmony hackathon.
- Integration of BiGG models service thanks to https://github.com/achillesrasquinha contribution.
- Fixing notebooks (biomodels and uniprot)
- Move the miriam services to the attic
12.11. Revision 1.7.3 (March 2020)¶
- fixing chembl after API changed. Fix the get_status_resources method by removing document_term and target_prediction. Changed acd_log into alogp: for some reasons this was changed. There was a warning on 4th March 2020 telling that changes may occur.
12.12. Revision 1.7.2 (March 2020)¶
- Fixing ReadTheDocs online documentation and Changelog
12.13. Revision 1.7.1 (Feb 2020)¶
- Just updating the README and setup metadata
12.14. Revision 1.7.0 (Feb 2020)¶
- Pull request
- from @thobalose (https://github.com/cokelaer/bioservices/pull/149) to update tests, travis recipes, pinned matplotlib to 3.0.3
- panther module (pantherdb.org)
- add a test for the pubchem, pfam and eva modules, which are still in draft version though
- PICR module is fully commented. The service is most probably deprecated. Not on EBI website anymore
- remove TCGA, which waws only a draft version with one method.
- BUGS and FIXES
- wikipathway: fixed getPathway, savePathway, getPathwayByLiterature and coloredPathway methods. Some are failing due to some wikipathway temporary failures.
- Fixed https://github.com/cokelaer/bioservices/issues/148 to have a more informative error message (array express)
- Fixed KeggParser for the GENE entries to have the correct ID name. https://github.com/cokelaer/bioservices/issues/151
12.15. Revision 1.6.0¶
- rewrote entirely the ChEMBL wrapper due to new ChEMBL API.
- removed the quickgo_old module and its tests
- Fix typo for a “valid colum,” in uniprot module
- Changed biomodels WSDL endpoint (thanks to https://github.com/thobalose. )
- uses colorlog to have more robust and consistent logging.
- Fix wikipathway XML issues by outputing dictionaries now. This fixes https://github.com/cokelaer/bioservices/issues/131
- Fix https://github.com/cokelaer/bioservices/issues/137 to handle KEGG GENE field properly in KEGGParse
- Fix https://github.com/cokelaer/bioservices/issues/125 thanks to https://github.com/thobalose.
12.16. Revision 1.5.2¶
- Fix retmode in EUtils.Efetch fonction. Was not taken into account but set to text by default but this seemed to have changed recently so this bug emerged while it was silent before.
- Issue in EUtils URL (trailing /) fixed in this PR https://github.com/cokelaer/bioservices/pull/116
- Major update of Reactome class. The old one is named ReactomeOld and the new one uses the new Reactome API
12.17. Revision 1.5.1¶
Support for Python 2.6 dropped.
- using proper logging
12.18. Revision 1.5¶
Support for Python 3.6 on Travis.
- kegg: fix #75 and #77 (missing keywords in KEGG)
- kegg: fix #79 (mis-interpreted cases reported by kirienko with examples.
- kegg: fix #85 (some entries are not interpreted)
- biodbnet: conversion from WSDL to REST. Note methods’ arguments changes: inputValues to input_values, dbPath to db_path. Uses pandas
- wikipathways: conversion from WSDL to REST. All wikipathways service uses Pandas and returns dataframes.
- Better implementation of secure host option and more xml customization #98
- move quickgo.py to quickgo_old.py
- move readseq to seqret (https://github.com/cokelaer/bioservices/issues/89)
- move wsdbfetch to dbfetch and move from WSDL to REST service
- quickgo uses the new API from EBI (see changes)
- seqret uses the new API (instead of readseq)
- dbfetch uses new API (instead of WSDL)
- Fixes the licensing (GPLv3 everywhere)
For developers: use pytest instead of nosetests.
12.19. Revision 1.4¶
- 1.4.17: rhea URL changed and add get_metabolites function. Fix pride test and
- add missing license file
- 1.4.16: simplify setup
- ensembl.org in biomart was not reachable anymore. This is fixed by using requests to check URL existence.
- in ensembl module tolist -> to_list
- Fix ensembl tests
- update http to https in EUtils
- missing TARGET field in KEGGParser reported in issue #66
- Add a download_fasta dedicated function to download a fasta file either from ENA or NCBI given its accession. See bioservices.apps.download_fasta. Used within Sequana project
- EUTils can now return a dictionary rather than a xml
- New method get_taxon in ENA class
- EnsemblFTP added to ensembl module
- 1.4.10: fixing a bug/typo in pypi
- NEW: add new module for the omnipath web service in
- NEW: add new module for the omnipath web service in
- NEWS: add method get_run in RNASEQ_EBI class.
- RNASEQ analysis REST API included (http://www.ebi.ac.uk/~rpetry/geteam/rnaseq/apispec.pdf)
- Fixes a python3 wrong import
- Uniprot: update valid columns
- https://github.com/cokelaer/bioservices/pull/35 with biocarta module updates
- NEWS: ENA module and class added
- BUG: fix typo in a draft tcga module
- CHANGES: update setup dependencies.
- BUG: Typo fixed in uniprot list of valid columns #47
- Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
- Updated all documentation to check examples
- Fixed tests and notebooks
- clean and tested doctests in the documentation
- Replace deprecated HGNC with the official web service from genenames.org
- Fully update EUtils since WSDL is now down; implementation uses REST now. This fixes https://github.com/cokelaer/bioservices/issues/41
- Remove the apps/taxonomy module now part of biokit.
- add small XML tools to parse XML dynamically in xmltools module
- add http_delete in services.py
12.20. Revision 1.3¶
- cache files are now stored in the ./config/bioservices directory, this fixes https://github.com/cokelaer/bioservices/issues/40
- ArrayExpress: add new 2 methods to ease the usage
- BUG FIXES
- BUG FIXES
- KEGG: Fixed during the major changes described here below
- IntactL rename Intact class into IntactComplex
- KEGG: revisited the parsing following requests from user https://github.com/cokelaer/bioservices/issues/30
- KEGG: remove useless function (check_dbentries)
- KEGG: The KEGGParser does not inherit from KEGG anymore and there is
- now a parse() method inside KEGG so user do not need to play with the 2 classes. Only KEGG is required. KEGGParser can still be used but will not have the KEGG methods anymore
- BUG FIXES
- BUG FIXES:
- add Intact complex web services
- BUG FIXES
- CHANGES * clinvitae: tests and doc added * services modules: DevTools class moved to easydev
- add PRIDE service + test + doc
- uniprot fixing a python 3 typo
- pdb: add a method
- hgnc: add new class related to HGNC
- services.py: add a method to ease conversion of dict to json. add attribute to limit number of requests per seconds but not yet used.
- taxonomy module: add new method in Taxon to look for a taxon identifier given a name
- NEW module ensembl completed
- NEW module clinvitae added (contribution from Patrick Short)
- services: http_get and http_post now accepts all optional arguments from requests.
- services: get_headers default content is now same as urrlib2
- pdb module: more functions added
- ensembl module added with some functionalities
- uniprot: multi_mapping is deprecated. mapping can now handle long queries by itself.
- removed get_bioservices_env function, which is not used anymore
- move urlencode in Service class into WSDLService, which will be deprecated
- add TIMEOUT in WSDLService and REST as alias to settings.TIMEOUT so timeout can now be used in both REST and WSDL.
- readseq module added.
- BUG fixes:
- CACHING attribute had a typo
- added REST class that uses the requests module. This class replaces of instance of RESTservice that uses urllib2, which will be deprecated later on. This speeds up the code significantly not only because requests is faster but also because we now do not need trial/time hack that was implemented inside RESTService. We also use the requests_cache module that could be used to speed go but requires to store cache files locally. Asynchronous requests is available but used only in a few places for now.
- EUtils has been fully implemented excepting EPost. API may still change to make its usage easier but functionalities are there.
- update code to be python-3 compatible. There are still issues with suds/requests/gevent but the code itself is python3 executable.
- WSDLservice now uses suds instead of SOAP package by default
- all paramters called format have been renamed frmt (format is a python keyword)
- chembldb module and class renamed to chembl and
- All classes that depends on RESTService have been updated to use the new REST class.
- get_assay_by_chemblId renamed in get_assays_by_chemblId
- renamed get_target_by_refSeqId into get_target_by_refseq
- kegg module: all Kegg strings replaced by KEGG so the kegg.Kegg class is now kegg.KEGG
- ChEBI: getUpdatedPolymer: remove useless parameters (was failing with python3)
- Wikipathway class renamed as WikiPathways to agree with official name
- biomart now uses python3 and we had to remove the threaded_request module, which does not seem to ba available. So, we used the new implementation using requests but gevent is not available for python3 either so, we use requests but without the asynchronous call. This is working for now. Transparent for the user.
- geneprof: parameter called type and format are renamed output and frmt to not clash with python keywords. Use REST class instead of RESTService but should be transparent for the users.
- services do not have the checkParam method. use devtools.check_param_in_list instead.
- BUG FIXES:
- Fixing bug #24/25 posted on assembla related to parse_kgml_pathway second argument can now be used.
- wikipathway: findInteractions had a typo in i
12.21. Revision 1.2¶
- fixing bug report 22 related to KEGG.pathway2sif function that was failing.
- add option in biomart to use different host. This is to fix an issue where biomart hangs forever. This was reported by Daniel D bug report 23 on assembla.
- add try/except for pandas library.
- fixing typo in the init that fails bioservices ito be used if pkg_resources is not available.
- updating some apps (fasta,peptides, taxon) in bioservices.apps directory
- Improves UniProt module by adding a dataframe export where performing a search
- added the BioDBnet service.
- added Pathway Common
- fixed UniChem: add new database identifiers and fix interpretation of the output
- NEW Service:
- uniprot: add multi_mapping method to use mapping method on large queries and added timeout/trials inside uniprot functions
- NEW Service:
- same as 1.2.0 but fixed missing mapping and apps directory in the distribution available on pypi
- Kegg class has now an alias called KEGG
- NEW Services:
- fix bug in get_fasta from uniprot class
- add aliases to quickGO to retrieve annotation
- NEW Service:
- NEW Service:
- uniprot add function to get uniprot fasta sequence
- add apps.peptides module
12.22. Revision 1.1¶
- fix bug in chembldb.get_all_targets() that was failing to return the
- json/dictionary as expected.
- add biocarta, pfam modules (and htmltools. maybe not required.)
- fix bug in uniprot.mapping to return list of values instead of a string (assembla ticket 19).
- services.py: move print statements into loggin.warning
- add documentation and examples related to Galaxy/BioPython.
- uniprot mapping function now returns a dictionary instead of a list
- NEW Service : class:bioservices.hgnc.HGNC + doc + test
12.23. Revision 1.1¶
- in psicquic when performing the conversion, we now use a try/except since some fields (in rare case) may be missing
- add faqs in the doc + update of the README and metadata.
- fix typo in the list of uniprot mapping
- Use BeautifulSoup4 instead of 3
- add the ChEBI Web Service.
- add the UniChem Web Service.
- logging ERROR in Service when data cannot be converted to XML is now a simple warning
- kegg.conv method now returns a dictionary instead of list of tuples.
12.24. Revision 1.0¶
- add a draft version of PDB just to be able to fetch PDB data and use it with external tool such as PyMOL as shown in the new pymol.rst documentation.
- add a missing docstring in uniprot + check to/fr parameters in UniProt.mapping method.
- Fix a typo in PSICQUIC module.
- uniprot.UniPort.search method: default value of the parameter format is now “tab”
- fix 1 quickgo test
- a few documentation updates in biomart/uniprot/chembldb and tutorial.
- add SOAPpy in the setup requirements
- finished ArrayExpress +doc + tests
- fixed a bug in KEGGParser.parseGene
- add methods in psicquic to parse all databases and convert to uniprot if
- possible. These methods are used to build an application provided in the
- add biomart + doc + test
- add onWeb method in Service class
- add chemspider draft
- complete eutils
- Add miriam module
- Add arrayexpress
- First release of bioservices
12.25. Revision 0.9¶
- add new feature in KEgg module to instrospect kgml data sets
- add biogrid test and documentation.
- chembldb improvments
- uniprot bug fixes (search if working as expected now)
- Finalising the Kegg module
- add parser for all KEGG entries (enzyme, genome, pathway, …)
- add a show_pathway to highlight element in a pathway
- cleaning up the modules
- documentation cleanup
- fix tests
- fix a few small bugs in biomodels
- adding getattr method for all databases in kegg model
- Service class has new method call pubmed to load pubmed in browser
- uniprot search method improved
- 0.9.1: fix typo in biomodel. add uniprot search method. add keggParser class
- 0.9.0: Stable version of bioservices including the following services:
- BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt, WSDbfetch, NCBIblast, PSICQUIC, Wikipath
12.26. Up to Revision 0.5¶
- 0.4.9: finalise wikipathway
- 0.4.8: finalise doc of half of the services.
- 0.4.7: add psicquic service and carry on reactome
- 0.4.6: finalise kegg module and test
- 0.4.5: finalise biomodels. keff WSDL is not maintained anymore: started REST version.
- 0.4.4: finalise quickgo,rhea, picr, uniprot. Update servie to use logging module.
- 0.4.3: add quickgo
- 0.4.2: add wsdbfetch/uniprot
- 0.4.1: add wikipathways module +test .
- 0.4.0: add rhea service + test. Updating the documentation.
- 0.3.0: add reactome + uniprot.
- 0.2.0: finalise biomodels and add picr service + test for biomdodel service..
- 0.1.0: add database and kegg modules + its documentation and tests