bioversions 0.5.330__py3-none-any.whl → 0.5.331__py3-none-any.whl

bioversions/sources/__init__.py

@@ -16,6 +16,7 @@ from .cellosaurus import CellosaurusGetter
 from .chebi import ChEBIGetter
 from .chembl import ChEMBLGetter
 from .chemidplus import ChemIDplusGetter
+from .civic import CiVICGetter
 from .complexportal import ComplexPortalGetter
 from .daily import NCBIGeneGetter
 from .depmap import DepMapGetter
@@ -135,6 +136,7 @@ def get_getters() -> List[Type[Getter]]:
         ICFGetter,
         ICD10Getter,
         ICD11Getter,
+        CiVICGetter,
     ]
     getters.extend(iter_obo_getters())
     extend_ols_getters(getters)
@@ -151,9 +153,9 @@ def get_getter_dict() -> Mapping[str, Type[Getter]]:
             rv[norm(getter.bioregistry_id)] = getter
         rv[getter.name] = getter
         rv[norm(getter.name)] = getter
-    # TODO engineer this into the data model and backfill them
-    rv["omim.ps"] = OMIMGetter
-    rv["omimps"] = OMIMGetter
+        for pp in getter.collection or []:
+            rv[pp] = getter
+            rv[norm(pp)] = getter
     return rv
 
 

bioversions/sources/civic.py

@@ -0,0 +1,41 @@
+"""Get the version for CiVIC."""
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+URL = "https://civicdb.org/releases/main"
+API = "https://civicdb.org/api/graphql"
+GRAPHQL_QUERY = """\
+query dataReleases {
+  dataReleases {
+    geneTsv {
+      filename
+      path
+    }
+    name
+  }
+}
+"""
+# see https://griffithlab.github.io/civic-v2/#query-dataReleases
+# and https://griffithlab.github.io/civic-v2/#definition-DownloadableFile
+
+
+class CiVICGetter(Getter):
+    """A getter for CiVIC."""
+
+    name = "CiVIC"
+    date_fmt = "%d-%b-%Y"
+    version_type = VersionType.date
+    homepage = "https://civicdb.org"
+    collection = ["civic.gid", "civic.eid"]
+
+    def get(self):
+        """Get the latest ChEMBL version number."""
+        res = requests.post(API, json={"query": GRAPHQL_QUERY})
+        # 0 element is always nightly, 1 is latest
+        return res.json()["data"]["dataReleases"][1]["name"]
+
+
+if __name__ == "__main__":
+    CiVICGetter.print()

bioversions/sources/guidetopharmacology.py

@@ -23,6 +23,7 @@ class GuideToPharmacologyGetter(Getter):
     homepage_fmt = "https://www.guidetopharmacology.org/DATA/public_iuphardb_v{version}.zip"
     date_fmt = "%Y-%m-%d"
     version_type = VersionType.year_minor
+    collection = ["iuphar.family", "iuphar.ligand", "iuphar.receptor"]
 
     def get(self) -> Dict[str, str]:
         """Get the latest Guide to Pharmacology version number."""

bioversions/sources/kegg.py

@@ -16,10 +16,10 @@ URL = "https://www.kegg.jp/kegg/docs/relnote.html"
 class KEGGGetter(Getter):
     """A getter for KEGG."""
 
-    bioregistry_id = "kegg.pathway"
     name = "KEGG"
     date_fmt = "%B %d, %Y"
     version_type = VersionType.semver_minor
+    collection = ["kegg.pathway", "kegg.gene", "kegg.species"]  # TODO add more
 
     def get(self) -> Mapping[str, str]:
         """Get the latest KEGG version number."""

bioversions/sources/mirbase.py

@@ -18,6 +18,7 @@ class MirbaseGetter(Getter):
     name = "miRBase"
     homepage_fmt = "https://www.mirbase.org/download/PREVIOUS_RELEASES/{version}"
     version_type = VersionType.semver_minor
+    collection = ["mirbase", "mirbase.family", "mirbase.mature"]
 
     def get(self):
         """Get the latest miRBase version number."""

bioversions/sources/omim.py

@@ -13,10 +13,10 @@ __all__ = [
 class OMIMGetter(Getter):
     """A getter for OMIM."""
 
-    bioregistry_id = "omim"
     name = "Online Mendelian Inheritance in Man"
     date_version_fmt = "%B %d, %Y"
     version_type = VersionType.date
+    collection = ["omim.ps", "omim"]
 
     def get(self) -> str:
         """Get the latest OMIM version number."""

bioversions/utils.py

@@ -6,7 +6,7 @@ import datetime
 import enum
 import ftplib
 import os
-from typing import Any, ClassVar, Mapping, Optional, Union
+from typing import Any, ClassVar, List, Mapping, Optional, Union
 
 import bioregistry
 import pydantic
@@ -47,7 +47,9 @@ def norm(s: str) -> str:
     return s.lower().replace(" ", "").replace("-", "").replace(".", "")
 
 
-def get_soup(url: str, verify: bool = True, timeout: Optional[int] = None) -> BeautifulSoup:
+def get_soup(
+    url: str, verify: bool = True, timeout: Optional[int] = None, user_agent: Optional[str] = None
+) -> BeautifulSoup:
     """Get a beautiful soup parsed version of the given web page.
 
     :param url: The URL to download and parse with BeautifulSoup
@@ -55,9 +57,13 @@ def get_soup(url: str, verify: bool = True, timeout: Optional[int] = None) -> Be
         except for Ensembl, which makes a big pain
     :param timeout: How many integer seconds to wait for a response?
         Defaults to 15 if none given.
+    :param user_agent: A custom user-agent to set, e.g., to avoid anti-crawling mechanisms
     :returns: A BeautifulSoup object
     """
-    res = requests.get(url, verify=verify, timeout=timeout or 15)
+    headers = {}
+    if user_agent:
+        headers["User-Agent"] = user_agent
+    res = requests.get(url, verify=verify, timeout=timeout or 15, headers=headers)
     soup = BeautifulSoup(res.text, features="html.parser")
     return soup
 
@@ -186,6 +192,9 @@ class Getter(metaclass=MetaGetter):
     date: ClassVar[str]
     homepage: ClassVar[str]
 
+    #: Prefixes this getter works for
+    collection: ClassVar[Optional[List[str]]] = None
+
     def get(self) -> Union[str, Mapping[str, str], datetime.datetime]:
         """Get the latest of this database."""
         raise NotImplementedError

bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.330"
+VERSION = "0.5.331"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.330.dist-info → bioversions-0.5.331.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.330
+Version: 0.5.331
 Summary: What's the current version for each biological database?
 Home-page: https://github.com/biopragmatics/bioversions
 Download-URL: https://github.com/biopragmatics/bioversions/releases

{bioversions-0.5.330.dist-info → bioversions-0.5.331.dist-info}/RECORD

@@ -5,12 +5,12 @@ bioversions/cli.py,sha256=vFwSyuWWFly07g_9hcd_70pwKV7U-OZPqRWhn4FxIjU,1589
 bioversions/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioversions/slack_client.py,sha256=42kl4TbjtXimVRULcBfe8i3pdJLScEPvJr1vw72tv-4,1271
 bioversions/twitter_client.py,sha256=TQhsdp6avlzoZLoZlndJlwsYhIYI-uabehZJ1W1mNuY,1353
-bioversions/utils.py,sha256=QKnfFNU8aYmKBpXspODCRk7VgSRUI8fTeGK3SuydEZc,10100
-bioversions/version.py,sha256=63vKCY-6BETFZK4G0XMrPjyNT0pKtbnEuqq27yyr7VE,645
+bioversions/utils.py,sha256=6ygaoe5rRArtrCXHrVygpl2cD7Otrbs4D1rADmpXDrA,10425
+bioversions/version.py,sha256=cz88ucmI9DBByfmOw7rfMs3LNxfOcxrHZnjhKCYqK_Y,645
 bioversions/wsgi.py,sha256=Z1HYFmnrWKNGwHq4R4DRfBuLzAEAAZ5UfHjvJUpnDfs,826
 bioversions/resources/__init__.py,sha256=0E1yGGT5SztSGEa30Tai4wCUki4nqfynqCSNAvjzEOk,1173
 bioversions/resources/update.py,sha256=21LprPktMKXdFI7llKjn7gsAQq01TGSKFbWQEhhwDJ0,3215
-bioversions/sources/__init__.py,sha256=4jY2a9HuF1u27PqjDtXbXBz2cfcL9-yWknIlZqWZSpI,5929
+bioversions/sources/__init__.py,sha256=gxSQDIbe0bURXXEvQmD-7QWOEa8gCubr62CSUH-nbNQ,5962
 bioversions/sources/antibodyregistry.py,sha256=VIgnYZ_Jtcx0u19X60Ee7qTqDgbub5C2EBtK_Bz7Twc,705
 bioversions/sources/bigg.py,sha256=qPBpX8qap8MlnlcntWO30jIgWD4c9RV57cKp_EZhnE0,672
 bioversions/sources/biogrid.py,sha256=k32iXtno-Q2M2SVDX_S-22_B1rwSTzQNZwJCL9nwoW4,759
@@ -18,6 +18,7 @@ bioversions/sources/cellosaurus.py,sha256=x3kAjDAoy2YQY3ZroiZxdsh7_-AQg1bWTWa-0y
 bioversions/sources/chebi.py,sha256=TRQ7DZ-Dz8b3mNaKRe52QVfQFahvTwVsBQjXapxBl_M,856
 bioversions/sources/chembl.py,sha256=HHasQ9F1Utm9LLsN1h-NrwfNifN-Y-Ss928_0Iz3CtY,1408
 bioversions/sources/chemidplus.py,sha256=USdDBPGcNULiw19ZFzz5QFIVzG_h80IaFbxsJH4Fb1w,1207
+bioversions/sources/civic.py,sha256=1uGaTy2ipZ2Nm5Nn_Ojv6biJfLr3sB3djc6AmOT3sO0,970
 bioversions/sources/complexportal.py,sha256=SPJ3ryJNtXwvArtHaeeWCSau6uVBJTDxPX6XPvKmDlY,696
 bioversions/sources/daily.py,sha256=mq8NLnhRRDjTzwGQl9LxCBiO6BSWyGOJcfyg7qqNsno,281
 bioversions/sources/depmap.py,sha256=EjpScMRwqItvitso57ah3f53bkWbTK0bjLWOBr4ym1E,654
@@ -28,7 +29,7 @@ bioversions/sources/drugcentral.py,sha256=EWYatYEqZbwjH-0lUXYEfe5P5VNHsNJAtNDlSP
 bioversions/sources/ensembl.py,sha256=BHssnbJMI-jONB8W1mKERYsccRmIETI0NeWLnTTiDdk,760
 bioversions/sources/expasy.py,sha256=EQXDz1LJSc0J-BE5Gy5tI-T4e6j4D5jid6c6ajzQjG8,830
 bioversions/sources/flybase.py,sha256=5S0gI8tULx3sfNVy2O4grvyqIUwI4teS9S6khDh-JzQ,779
-bioversions/sources/guidetopharmacology.py,sha256=Lw0H0QDCwVMdvXdfIzySNLtP1WO7BANpab6gwPeURwc,1306
+bioversions/sources/guidetopharmacology.py,sha256=B3W5I01v1a0OuvPJB-LHoSYvuJBN_cpXulnGrBs009o,1377
 bioversions/sources/hgnc.py,sha256=OH8E9dF2oPbh_BshPgKrWSFkYWDq9rj9J7DN06pVFxQ,970
 bioversions/sources/homologene.py,sha256=_f6SQRXe67t1jqQ6HjQIEOGApPUHLlfHMZojChumWzc,647
 bioversions/sources/icd10.py,sha256=cfiJcueTr6Z1dIzdP68QeCPlnJhr3Yd3U97TZplR1JI,716
@@ -37,17 +38,17 @@ bioversions/sources/icf.py,sha256=iTWjjScSlKDJZRRi1cKTZyTpP4p5Illv6LoZEvo-PSw,73
 bioversions/sources/intact.py,sha256=bRBnGm3-PHGdKlyYGkCabzQue9RG2MmF1A3CVF_U9e4,621
 bioversions/sources/interpro.py,sha256=UELzp1FBKBcul09DiK3eqkHZ31kkBPT4vuDD9A_9hz0,1261
 bioversions/sources/itis.py,sha256=u9h72y5JijXTprOe1SlaTW0adllj6NNoRP95AwuhzjE,831
-bioversions/sources/kegg.py,sha256=E5gQWlRs3HbcXy0MY0-tyo7TBKQfkZ4GkYk5I789S30,824
+bioversions/sources/kegg.py,sha256=3JpmkmQJNw-Txp7LQFXgW975zGOz4ekfgEOZKhPtYis,868
 bioversions/sources/mesh.py,sha256=U3brzrzPjhzgSWxG2MILP-bqIgZpr62ns_izFnZzqe0,807
 bioversions/sources/mgi.py,sha256=68xCDcnWUckM_GDGW24MjtWwFf0vZHkS0H3NWKwUdr0,866
-bioversions/sources/mirbase.py,sha256=4qvzOQAvZmS8dIJ_dJfP-td9daDFxUzCnyHpv8weD_U,840
+bioversions/sources/mirbase.py,sha256=5_D4EeB-K64eQ897xOSzoZQYFOiXNqtAugcexzR9oBg,905
 bioversions/sources/moalmanac.py,sha256=HxrJmOzqVJiHn9FQKCbOlBPCvxBHst1DI420TYERCvU,774
 bioversions/sources/msigdb.py,sha256=KGYZjjhqm0uUT0Wg_pb5kF9OVW33dgIh2r-yKMBqbWg,803
 bioversions/sources/ncit.py,sha256=ylubS3ntMyimaZDHFNFrjc2pkDfpyrBkhrl8Dq4duyQ,1064
 bioversions/sources/npass.py,sha256=-EL6Ej-23cdGKehn8nusP8LJ3z4oRX4ZPPDnjx_ItXQ,739
 bioversions/sources/obo.py,sha256=n2_Auh0ccu3WKOwq8JqFldzS8-KY0GVC1fReazPLr78,1735
 bioversions/sources/ols.py,sha256=PqL_CfpS0NxAfo1iSh2shakcnywRl_zfHXBcNrcLdiA,2754
-bioversions/sources/omim.py,sha256=l1dApi8xBidUIwWZTYwc7bHtPQBuernxDfdOVOnf34s,847
+bioversions/sources/omim.py,sha256=y586CrSXrwldoiiGOJwL64yAPbJBkwwHCgFNDjsPMYk,856
 bioversions/sources/oncotree.py,sha256=Z-zZWFeVEfCyZcEMcrdVTcEoHIDfYB-v7oK_iYVSGEI,1026
 bioversions/sources/pathbank.py,sha256=_oMfaJs02FBJ6kIWHPW-M2euxAn5ylsGKqseRSJ3m2M,718
 bioversions/sources/pathwaycommons.py,sha256=lLVmJkf3qDuMk316Aia0CzJyp_-ahAASLupaAuQS9iw,686
@@ -68,9 +69,9 @@ bioversions/sources/uniprot.py,sha256=_rootal_mrESkiXJh3udfr1UGrlzP7CQQIMsa35tyc
 bioversions/sources/unversioned.py,sha256=noHxGmy9cpVv5xegMHouBF6oCbW6CP1jpOeCVdE7Eak,78
 bioversions/sources/wikipathways.py,sha256=HTva8vsXRQWU6bia83Et4vveo-QhzJS6dDWeu9Syc6c,823
 bioversions/sources/zfin.py,sha256=D7csziZ3UsW8dncm6XKA0t3x6XB4cFbG9PTYcT-g2bg,708
-bioversions-0.5.330.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
-bioversions-0.5.330.dist-info/METADATA,sha256=YMyFW9Uj8qqGxzSOeDBKAf91d8S6dwyWECXCH6pySp4,9443
-bioversions-0.5.330.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-bioversions-0.5.330.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.5.330.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
-bioversions-0.5.330.dist-info/RECORD,,
+bioversions-0.5.331.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
+bioversions-0.5.331.dist-info/METADATA,sha256=t-VZ8z1ZiX5hUJOTL0zIj16H83D2rRQNj0o36hMX7B4,9443
+bioversions-0.5.331.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+bioversions-0.5.331.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
+bioversions-0.5.331.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
+bioversions-0.5.331.dist-info/RECORD,,