uniprot_data: boş indirme sonucu için koruma (None-guard)#320
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bushushow wants to merge 48 commits into
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uniprot_data: boş indirme sonucu için koruma (None-guard)#320bushushow wants to merge 48 commits into
bushushow wants to merge 48 commits into
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…re full of NaN values
…stic Ontology Term and Factor Value Ontology Term does not have any equal rows
BioGRID's Cloudflare CDN returns HTTP 403/429 to pypath's default User-Agent. Add browser-like headers to the curl.Curl calls in biogrid_interactions() and biogrid_all_interactions() to avoid blocking.
Refactor column dropping logic to protect specific columns from being dropped when all values are NaN. Added stripping of whitespace from column names.
Refactor async download method to improve error handling and streamline content type checks.
Fix OffSIDES URL and CSV parsing bug
`uniprot_data`, indirmenin başarılı olup olmadığını kontrol etmeden `next(c.result)` çağırıyordu. `curl.Curl` `None` döndüğünde (örn. büyük `organism='*'` sorgularında geçici ağ/sunucu hatası), bu satır anlaşılmaz bir `TypeError: 'NoneType' object is not an iterator` fırlatıyor ve CROssBAR UniProt adaptörünün `download_uniprot_data()` adımı gibi çağıranları çökertiyordu. Sonuç boş geldiğinde, istenen alan ve organizmayı belirten anlaşılır bir `RuntimeError` fırlatılır; böylece hata anlaşılır ve yeniden denenebilir olur.
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Hello Busra @bushushow & everyone else, Bunyamin, Erva, Havvanur, Sila, and others! :) Many thanks for the PRs, I'm happy to review and merge them. Did you close it because you wanna include more commits? Maybe it would also make sense to have a chat about what are you up to, how the entire OmniPath stack evolves, and how we could collaborate more efficiently. At this point we refactored and reimplemented almost all key components of OmniPath, and in many instances it would be better for you to use the new stack. We can continue in email, feel free to write me |
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Özet
pypath.inputs.uniprot.uniprot_data, indirme sonucunu kontrol etmedennext(c.result)çağırıyordu.curl.CurlNonedöndüğünde anlaşılmaz birTypeError: 'NoneType' object is not an iteratorfırlıyor ve çağıranlar (ör. CROssBAR UniProt adaptörünündownload_uniprot_data()adımı) çöküyordu.Değişiklik
curl.Curlçağrısından sonrac.result is Nonekontrolü eklendi; boşsa istenen alan ve organizmayı belirten anlaşılır birRuntimeErrorfırlatılıyor.Bağlam
test_uniprot.ipynb) sırasında bulundu.organism='*'ile büyük cross-reference alanları (xref_geneid,xref_kegg, ...) indirilirken geçici ağ/throttling nedeniylec.resultNone/bozuk gelebiliyor ve cryptic hatayla adaptörü çökertiyordu.curl.Curlreq_headerseklemesine benzer, pypath-seviyesi küçük bir sağlamlık iyileştirmesi.Etki
Başarılı indirmelerde davranış aynı; yalnızca başarısız/boş indirmede anlaşılır hata veriliyor.