bioversions 0.5.319__py3-none-any.whl → 0.5.376__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
@@ -29,6 +30,9 @@ 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 +46,7 @@ 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 +132,11 @@ def get_getters() -> List[Type[Getter]]:
         RGDGetter,
         CellosaurusGetter,
         MGIGetter,
+        OMIMGetter,
+        ICFGetter,
+        ICD10Getter,
+        ICD11Getter,
+        CiVICGetter,
     ]
     getters.extend(iter_obo_getters())
     extend_ols_getters(getters)
@@ -143,6 +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
+        for pp in getter.collection or []:
+            rv[pp] = getter
+            rv[norm(pp)] = getter
     return rv
 
 

bioversions/sources/chembl.py

@@ -23,6 +23,7 @@ class ChEMBLGetter(Getter):
     homepage_fmt = "ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_{version}"
     date_fmt = "%d/%m/%Y"
     version_type = VersionType.sequential
+    collection = ["chembl", "chembl.target", "chembl.compound", "chembl.cell"]
 
     def get(self):
         """Get the latest ChEMBL version number."""

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/ensembl.py

@@ -12,17 +12,17 @@ URL = "https://useast.ensembl.org/index.html"
 
 
 class EnsemblGetter(Getter):
-    """A getter for DrugBank."""
+    """A getter for Ensembl."""
 
     bioregistry_id = "ensembl"
     name = "Ensembl"
     homepage_fmt = "https://www.ensembl.org"
-    date_fmt = "%b %Y"
+    date_fmt = "%B %Y"
     version_type = VersionType.sequential
 
     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/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/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/kegg.py

@@ -5,6 +5,7 @@
 from typing import Mapping
 
 from bioversions.utils import Getter, VersionType, get_soup
+import bioregistry
 
 __all__ = [
     "KEGGGetter",
@@ -16,10 +17,10 @@ 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", *bioregistry.get_has_parts("kegg")]
 
     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

@@ -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."""
+
+    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."""
+        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/pombase.py

@@ -2,9 +2,7 @@
 
 """A getter for PomBase."""
 
-import ftplib
-
-from bioversions.utils import Getter, VersionType
+from bioversions.utils import Getter, VersionType, get_soup
 
 __all__ = [
     "PombaseGetter",
@@ -22,13 +20,12 @@ class PombaseGetter(Getter):
 
     def get(self):
         """Get the latest pombase version number."""
-        with ftplib.FTP("www.pombase.org") as ftp:
-            ftp.login()
-            ftp.cwd("releases")
-            for name in sorted(ftp.nlst(), reverse=True):
-                if name.startswith("pombase-"):
-                    return name[len("pombase-") :]
-        raise ValueError
+        soup = get_soup("https://www.pombase.org/data/releases/")
+        tr = soup.find_all("tr")[-2]
+        text = tr.find_all("td")[1]
+        anchor = text.find("a")
+        text = anchor.text
+        return text[len("pombase-") :].rstrip("/")
 
 
 if __name__ == "__main__":

bioversions/sources/rhea.py

@@ -3,7 +3,6 @@
 """A getter for Rhea."""
 
 import requests
-import requests_ftp
 
 from bioversions.utils import Getter, VersionType
 
@@ -11,9 +10,7 @@ __all__ = [
     "RheaGetter",
 ]
 
-requests_ftp.monkeypatch_session()
-
-VERSION_FILE = "ftp://ftp.expasy.org/databases/rhea/rhea-release.properties"
+VERSION_FILE = "https://ftp.expasy.org/databases/rhea/rhea-release.properties"
 
 
 class RheaGetter(Getter):

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/sources/umls.py

@@ -23,8 +23,14 @@ class UMLSGetter(Getter):
     def get(self) -> datetime:
         """Get the latest UMLS version number."""
         soup = get_soup(URL)
-        raw_version = soup.find("div", {"id": "body"}).find("h2")
-        return raw_version.text.split()[0]
+        version_tag = (
+            soup.find("main")
+            .find("div", {"class": "grid-row grid-gap-1"})
+            .find("div", {"class": "tablet:grid-col-12"})
+            .find("h2")
+        )
+        version = version_tag.text.split()[0]
+        return version
 
 
 if __name__ == "__main__":

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
@@ -47,9 +47,23 @@ def norm(s: str) -> str:
     return s.lower().replace(" ", "").replace("-", "").replace(".", "")
 
 
-def get_soup(url: str, verify: bool = True) -> BeautifulSoup:
-    """Get a beautiful soup parsed version of the given web page."""
-    res = requests.get(url, verify=verify)
+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
+    :param verify: Should SSL be used? This is almost always true,
+        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
+    """
+    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
 
@@ -178,6 +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
@@ -262,7 +279,7 @@ class OBOFoundryGetter(Getter):
 
     def get(self) -> str:
         """Get the OBO version."""
-        url = f"http://purl.obolibrary.org/obo/{self.key}.obo"
+        url = f"https://purl.obolibrary.org/obo/{self.key}.obo"
         return self.process(get_obo_version(url))
 
     def process(self, version: str) -> str:

bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.319"
+VERSION = "0.5.376"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.319.dist-info → bioversions-0.5.376.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.319
+Version: 0.5.376
 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
@@ -37,6 +37,7 @@ Requires-Dist: more-click
 Requires-Dist: pyyaml
 Requires-Dist: tqdm
 Requires-Dist: bioregistry[align] >=0.10.0
+Requires-Dist: pandas
 Requires-Dist: lxml
 Requires-Dist: psycopg2-binary
 Provides-Extra: charts

{bioversions-0.5.319.dist-info → bioversions-0.5.376.dist-info}/RECORD

@@ -5,19 +5,20 @@ 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=I_wZZJjfEXnQjSYGLPo8IIvcorll00KCLwTdgqbxpBY,9712
-bioversions/version.py,sha256=MLMpX-W3NdvdejHXfA0r2YLO_6cJioo2yaZWHt8XVAw,645
+bioversions/utils.py,sha256=6ygaoe5rRArtrCXHrVygpl2cD7Otrbs4D1rADmpXDrA,10425
+bioversions/version.py,sha256=oh3AQZAHf44yxVc5pVNN8EWl5se-Kf4U_Sn19aCW3d0,645
 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=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
 bioversions/sources/cellosaurus.py,sha256=x3kAjDAoy2YQY3ZroiZxdsh7_-AQg1bWTWa-0y23uX0,986
 bioversions/sources/chebi.py,sha256=TRQ7DZ-Dz8b3mNaKRe52QVfQFahvTwVsBQjXapxBl_M,856
-bioversions/sources/chembl.py,sha256=HHasQ9F1Utm9LLsN1h-NrwfNifN-Y-Ss928_0Iz3CtY,1408
+bioversions/sources/chembl.py,sha256=LxOFFAgSYg4v3AkvAseHWAeAZZH8klRZv8HpD-rebBY,1487
 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
@@ -25,48 +26,52 @@ 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=LaAGNxaALDKeh4MmIdSGrdpUZsHNsCwMiyouSnRUvWE,775
+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
+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
-bioversions/sources/kegg.py,sha256=E5gQWlRs3HbcXy0MY0-tyo7TBKQfkZ4GkYk5I789S30,824
+bioversions/sources/kegg.py,sha256=Kk3S1uhGmzHgSYid1mUo_uDakk8WeUAZUsFap4eDVow,869
 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
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{bioversions-0.5.319.dist-info → bioversions-0.5.376.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any