bioversions 0.5.321__py3-none-any.whl → 0.5.323__py3-none-any.whl

bioversions/sources/__init__.py

@@ -29,6 +29,9 @@ from .flybase import FlybaseGetter
 from .guidetopharmacology import GuideToPharmacologyGetter
 from .hgnc import HGNCGetter
 from .homologene import HomoloGeneGetter
+from .icd10 import ICD10Getter
+from .icd11 import ICD11Getter
+from .icf import ICFGetter
 from .intact import IntActGetter
 from .interpro import InterProGetter
 from .itis import ITISGetter
@@ -42,6 +45,7 @@ from .ncit import NCItGetter
 from .npass import NPASSGetter
 from .obo import iter_obo_getters
 from .ols import extend_ols_getters
+from .omim import OMIMGetter
 from .oncotree import OncoTreeGetter
 from .pathbank import PathBankGetter
 from .pathwaycommons import PathwayCommonsGetter
@@ -127,6 +131,10 @@ def get_getters() -> List[Type[Getter]]:
         RGDGetter,
         CellosaurusGetter,
         MGIGetter,
+        OMIMGetter,
+        ICFGetter,
+        ICD10Getter,
+        ICD11Getter,
     ]
     getters.extend(iter_obo_getters())
     extend_ols_getters(getters)
@@ -143,6 +151,8 @@ 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
     return rv
 
 

bioversions/sources/ensembl.py

@@ -22,7 +22,7 @@ class EnsemblGetter(Getter):
 
     def get(self):
         """Get the latest Ensembl version number."""
-        soup = get_soup(URL, verify=False)
+        soup = get_soup(URL)
         manifest = soup.find(**{"class": "box-header"}).text
         version, date = manifest.rstrip(")").split("(", 1)
         return dict(version=version.split()[-1], date=date)

bioversions/sources/icd10.py

@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for ICD10."""
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "ICD10Getter",
+]
+
+URL = "https://icd.who.int/browse10/"
+
+
+class ICD10Getter(Getter):
+    """A getter for ICD10."""
+
+    bioregistry_id = "icd10"
+    name = "International Classification of Diseases, 10th Revision"
+    version_type = VersionType.date
+    date_version_fmt = "%Y"
+
+    def get(self) -> str:
+        """Get the latest ICD10 version number."""
+        response = requests.get(URL, allow_redirects=True)
+        final_url = response.url
+        return final_url[len("https://icd.who.int/browse10/") :].split("/")[0]
+
+
+if __name__ == "__main__":
+    ICD10Getter.print()

bioversions/sources/icd11.py

@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for ICD11."""
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "ICD11Getter",
+]
+
+URL = "https://icd.who.int/browse/latest-release/mms/en"
+
+
+class ICD11Getter(Getter):
+    """A getter for ICD11."""
+
+    bioregistry_id = "icd11"
+    name = "International Classification of Diseases, 11th Revision"
+    version_type = VersionType.date
+    date_version_fmt = "%Y-%m"
+
+    def get(self) -> str:
+        """Get the latest ICD11 version number."""
+        response = requests.get(URL, allow_redirects=True)
+        final_url = response.url
+        return final_url[len("https://icd.who.int/browse/") :].split("/")[0]
+
+
+if __name__ == "__main__":
+    ICD11Getter.print()

bioversions/sources/icf.py

@@ -0,0 +1,32 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for ICF."""
+
+import requests
+
+from bioversions.utils import Getter, VersionType
+
+__all__ = [
+    "ICFGetter",
+]
+
+URL = "https://icd.who.int/browse/latest-release/icf/en"
+
+
+class ICFGetter(Getter):
+    """A getter for ICF."""
+
+    bioregistry_id = "icf"
+    name = "International Classification of Functioning, Disability and Health"
+    version_type = VersionType.date
+    date_version_fmt = "%Y-%m"
+
+    def get(self) -> str:
+        """Get the latest ICF version number."""
+        response = requests.get(URL, allow_redirects=True)
+        final_url = response.url
+        return final_url[len("https://icd.who.int/browse/") :].split("/")[0]
+
+
+if __name__ == "__main__":
+    ICFGetter.print()

bioversions/sources/omim.py

@@ -0,0 +1,34 @@
+# -*- coding: utf-8 -*-
+
+"""A getter for the OMIM."""
+
+
+from bioversions.utils import Getter, VersionType, get_soup
+
+__all__ = [
+    "OMIMGetter",
+]
+
+
+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
+
+    def get(self) -> str:
+        """Get the latest OMIM version number."""
+        soup = get_soup("https://omim.org/")
+        for tag in soup.find_all("h5"):
+            text = tag.text.strip()
+            if text.startswith("Updated"):
+                rv = text[len("Updated") :].strip()
+                rv = rv.replace("nd", "").replace("st", "").replace("rd", "").replace("th", "")
+                return rv
+        raise ValueError
+
+
+if __name__ == "__main__":
+    OMIMGetter.print()

bioversions/sources/rxnorm.py

@@ -24,7 +24,7 @@ class RxNormGetter(Getter):
     def get(self) -> datetime:
         """Get the latest RxNorm version number."""
         soup = get_soup(URL)
-        raw_version = soup.find("th", {"class": "current"}).contents[2]
+        raw_version = soup.find("th", {"class": "current"}).contents[2].strip()
         raw_fmt = "%B %d, %Y"
         return datetime.strptime(raw_version, raw_fmt)
 

bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.321"
+VERSION = "0.5.323"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.321.dist-info → bioversions-0.5.323.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.321
+Version: 0.5.323
 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-0.5.321.dist-info → bioversions-0.5.323.dist-info}/RECORD

@@ -6,11 +6,11 @@ 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=AZ0h5Pjc8WfuWIaDL9yJiD75JYYxcnr5dKkIIH7JuoM,10099
-bioversions/version.py,sha256=yQzBR3nvaVyuGwWqSmFt9L47S-Qw93zXVGKa-IKgpGk,645
+bioversions/version.py,sha256=PkTgUBVYnJrIjAZoci_F5bZPlP1peNfTCtLbMACux7I,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=MmBb67Cq_eETTmHipOkVoGuxkK6My0igCq5VI--ffXw,5606
+bioversions/sources/__init__.py,sha256=XFN0iJriSFQRpAVQm2b8p8P31I8he7rcbZAAEq81OMo,5899
 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
@@ -25,12 +25,15 @@ bioversions/sources/dgi.py,sha256=2TSzl4XeTUt_I8Keuu51NuuShhhtiITHKMCbp1wf6uo,97
 bioversions/sources/disgenet.py,sha256=iRd1K2o_m8xSlJrWoSD8-plnTS1nO0Ur_OCCRD2V9u8,752
 bioversions/sources/drugbank.py,sha256=ZZ2yw34bRcLFT6n_Ygn1daGWk_oVx4A7ovUKSM_EQek,1005
 bioversions/sources/drugcentral.py,sha256=EWYatYEqZbwjH-0lUXYEfe5P5VNHsNJAtNDlSP_OuZM,1117
-bioversions/sources/ensembl.py,sha256=VySAE7kEeD1Fk6SCSU0t3j4_89u2f5wGF40F-mxInbk,774
+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/hgnc.py,sha256=OH8E9dF2oPbh_BshPgKrWSFkYWDq9rj9J7DN06pVFxQ,970
 bioversions/sources/homologene.py,sha256=_f6SQRXe67t1jqQ6HjQIEOGApPUHLlfHMZojChumWzc,647
+bioversions/sources/icd10.py,sha256=cfiJcueTr6Z1dIzdP68QeCPlnJhr3Yd3U97TZplR1JI,716
+bioversions/sources/icd11.py,sha256=EsdUrPxio_VIv9tkPoauxozKY-fdjwesbb5Kh_bijU0,736
+bioversions/sources/icf.py,sha256=iTWjjScSlKDJZRRi1cKTZyTpP4p5Illv6LoZEvo-PSw,733
 bioversions/sources/intact.py,sha256=bRBnGm3-PHGdKlyYGkCabzQue9RG2MmF1A3CVF_U9e4,621
 bioversions/sources/interpro.py,sha256=UELzp1FBKBcul09DiK3eqkHZ31kkBPT4vuDD9A_9hz0,1261
 bioversions/sources/itis.py,sha256=u9h72y5JijXTprOe1SlaTW0adllj6NNoRP95AwuhzjE,831
@@ -44,6 +47,7 @@ bioversions/sources/ncit.py,sha256=ylubS3ntMyimaZDHFNFrjc2pkDfpyrBkhrl8Dq4duyQ,1
 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/oncotree.py,sha256=Z-zZWFeVEfCyZcEMcrdVTcEoHIDfYB-v7oK_iYVSGEI,1026
 bioversions/sources/pathbank.py,sha256=_oMfaJs02FBJ6kIWHPW-M2euxAn5ylsGKqseRSJ3m2M,718
 bioversions/sources/pathwaycommons.py,sha256=lLVmJkf3qDuMk316Aia0CzJyp_-ahAASLupaAuQS9iw,686
@@ -55,7 +59,7 @@ bioversions/sources/reactome.py,sha256=Oy3huY1ihuWmLZqxM92Y44eZQ7DXmVAwGMzTFhqBy
 bioversions/sources/rfam.py,sha256=sz_9lCGS-h6cTp3d2MCQVRkvlFkjF5mijwj1MfZpRbc,565
 bioversions/sources/rgd.py,sha256=x7Mks8qp_dE4xWkA7OQu4eM8__oPsr13M-bFd5otcoA,791
 bioversions/sources/rhea.py,sha256=LERbsgy5ZI8Jy5v9r1IXGRBe70_bd8YwBa8a3_uumWg,831
-bioversions/sources/rxnorm.py,sha256=ocFtWX_xce9U4IeDxgGvZp5x02GETljLyW9oza3tkNw,1027
+bioversions/sources/rxnorm.py,sha256=qZLCiw-HjsyYsFTa4ZtCtLqXcU8LDoxRSEx9YuFp7Ys,1035
 bioversions/sources/sgd.py,sha256=xLZdpA0WBJVIkgwuLmosVpXo9WBeiqCAA8_4taSrLsA,1109
 bioversions/sources/slm.py,sha256=nttj-mrzwgosK-Vv3UVlyAI0EX1WkJRFBkGmkTnhdU0,709
 bioversions/sources/stringdb.py,sha256=6D3rcGGzdkgVOw4refJgjsorkyZuPswTYe4rNT4bQRQ,810
@@ -64,9 +68,9 @@ 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-0.5.321.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
-bioversions-0.5.321.dist-info/METADATA,sha256=u8P_JEnbU9TBJD0eo7u0A_lEJA9O9yhTkTH1KhI4cCI,9443
-bioversions-0.5.321.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-bioversions-0.5.321.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.5.321.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
-bioversions-0.5.321.dist-info/RECORD,,
+bioversions-0.5.323.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
+bioversions-0.5.323.dist-info/METADATA,sha256=1BeWHhJ2xPlmNzJaQRF-aunp8DoXjD7yGSm9PPLTny8,9443
+bioversions-0.5.323.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+bioversions-0.5.323.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
+bioversions-0.5.323.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
+bioversions-0.5.323.dist-info/RECORD,,