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wikipathways / pywikipathways

Python Client Package for WikiPathways
https://pywikipathways.readthedocs.io/
MIT License
12 stars 3 forks source link

can't download pathway archive #8

Open wenyuhaokikika opened 1 month ago

wenyuhaokikika commented 1 month ago

can't download pathway archive,why? pwpw.__version__=0.0.2

└─(14:53:39)──> proxychains python -c 'import pywikipathways as pwpw;pwpw.download_pathway_archive(organism="Homo sapiens", format="gmt")'                                                                 130 ↵ ──(Mon,Jul15)─┘
[proxychains] config file found: /data/wenyuhao/software/proxychains/proxychains.conf
[proxychains] preloading /data/wenyuhao/software/proxychains/lib/libproxychains4.so
[proxychains] DLL init: proxychains-ng 4.14
[proxychains] Strict chain  ...  10.20.213.73:10808  ...  webservice.wikipathways.org:443  ...  OK
[proxychains] Strict chain  ...  10.20.213.73:10808  ...  wikipathways-data.wmcloud.org:443  ...  OK
[proxychains] Strict chain  ...  10.20.213.73:10808  ...  wikipathways-data.wmcloud.org:80  ...  OK
[proxychains] Strict chain  ...  10.20.213.73:10808  ...  wikipathways-data.wmcloud.org:443  ...  OK
Could not find a file matching your specifications. Try browsing http://data.wikipathways.org.
egonw commented 1 month ago

@kozo2, looks like the code needs to be updated. (cc @AlexanderPico)

kozo2 commented 1 month ago

@wenyuhaokikika @egonw Thanks for letting me know this. I will update the program. Give me some time.

AlexanderPico commented 4 weeks ago

@kozo2 You know about the new JSON-API for WikiPathways, right? I updated the rWikiPathways package, so you might look there for examples...

https://github.com/wikipathways/rWikiPathways

Let me know if you have any questions.

kozo2 commented 4 weeks ago

@AlexanderPico Thanks for the comment. Yes, I know about the new JSON-API https://www.wikipathways.org/json/. I will imitate https://github.com/wikipathways/rWikiPathways/blob/devel/R/listOrganisms.R and https://github.com/wikipathways/rWikiPathways/blob/devel/R/downloadPathwayArchive.R for new pywikipathways.