bioversions 0.5.319__py3-none-any.whl → 0.5.321__py3-none-any.whl

bioversions/sources/ensembl.py

@@ -12,12 +12,12 @@ 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):

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/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

@@ -47,9 +47,17 @@ 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) -> 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.
+    :returns: A BeautifulSoup object
+    """
+    res = requests.get(url, verify=verify, timeout=timeout or 15)
     soup = BeautifulSoup(res.text, features="html.parser")
     return soup
 

bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.319"
+VERSION = "0.5.321"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.319.dist-info → bioversions-0.5.321.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.319
+Version: 0.5.321
 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-0.5.321.dist-info}/RECORD

@@ -5,8 +5,8 @@ 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=AZ0h5Pjc8WfuWIaDL9yJiD75JYYxcnr5dKkIIH7JuoM,10099
+bioversions/version.py,sha256=yQzBR3nvaVyuGwWqSmFt9L47S-Qw93zXVGKa-IKgpGk,645
 bioversions/wsgi.py,sha256=Z1HYFmnrWKNGwHq4R4DRfBuLzAEAAZ5UfHjvJUpnDfs,826
 bioversions/resources/__init__.py,sha256=0E1yGGT5SztSGEa30Tai4wCUki4nqfynqCSNAvjzEOk,1173
 bioversions/resources/update.py,sha256=21LprPktMKXdFI7llKjn7gsAQq01TGSKFbWQEhhwDJ0,3215
@@ -25,7 +25,7 @@ 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=VySAE7kEeD1Fk6SCSU0t3j4_89u2f5wGF40F-mxInbk,774
 bioversions/sources/expasy.py,sha256=EQXDz1LJSc0J-BE5Gy5tI-T4e6j4D5jid6c6ajzQjG8,830
 bioversions/sources/flybase.py,sha256=5S0gI8tULx3sfNVy2O4grvyqIUwI4teS9S6khDh-JzQ,779
 bioversions/sources/guidetopharmacology.py,sha256=Lw0H0QDCwVMdvXdfIzySNLtP1WO7BANpab6gwPeURwc,1306
@@ -48,25 +48,25 @@ bioversions/sources/oncotree.py,sha256=Z-zZWFeVEfCyZcEMcrdVTcEoHIDfYB-v7oK_iYVSG
 bioversions/sources/pathbank.py,sha256=_oMfaJs02FBJ6kIWHPW-M2euxAn5ylsGKqseRSJ3m2M,718
 bioversions/sources/pathwaycommons.py,sha256=lLVmJkf3qDuMk316Aia0CzJyp_-ahAASLupaAuQS9iw,686
 bioversions/sources/pfam.py,sha256=BAy1NJefxjMNDeUAzjV5sdQyZR_YpEEhgWphAWeZKVw,1000
-bioversions/sources/pombase.py,sha256=RtUSeFpmeETFCZjRoCh2ydPIzF7-R7IevU0mD-U7wEE,836
+bioversions/sources/pombase.py,sha256=JGrpBJUZO8ohsXYyUPSCJ5z2XFn3VyA5mDAwgbLRmEc,791
 bioversions/sources/pr.py,sha256=OoAbpw1PODTatpd7c2cQCY_GbDsZ6ikF2vxJFpdDx2I,899
 bioversions/sources/pubchem.py,sha256=wF2cx-VzLCobpTeE0KzzTk6_n7-UFjoOsOkf9u9xBFI,551
 bioversions/sources/reactome.py,sha256=Oy3huY1ihuWmLZqxM92Y44eZQ7DXmVAwGMzTFhqByPg,621
 bioversions/sources/rfam.py,sha256=sz_9lCGS-h6cTp3d2MCQVRkvlFkjF5mijwj1MfZpRbc,565
 bioversions/sources/rgd.py,sha256=x7Mks8qp_dE4xWkA7OQu4eM8__oPsr13M-bFd5otcoA,791
-bioversions/sources/rhea.py,sha256=ovqsunji0Y_OgocyMuQJYVjdFMFaVt1o1nSL8_boloo,885
+bioversions/sources/rhea.py,sha256=LERbsgy5ZI8Jy5v9r1IXGRBe70_bd8YwBa8a3_uumWg,831
 bioversions/sources/rxnorm.py,sha256=ocFtWX_xce9U4IeDxgGvZp5x02GETljLyW9oza3tkNw,1027
 bioversions/sources/sgd.py,sha256=xLZdpA0WBJVIkgwuLmosVpXo9WBeiqCAA8_4taSrLsA,1109
 bioversions/sources/slm.py,sha256=nttj-mrzwgosK-Vv3UVlyAI0EX1WkJRFBkGmkTnhdU0,709
 bioversions/sources/stringdb.py,sha256=6D3rcGGzdkgVOw4refJgjsorkyZuPswTYe4rNT4bQRQ,810
-bioversions/sources/umls.py,sha256=zLis6zZJi52jACqL7Kbkaru7MxKr5AhblZO2AR1tttM,677
+bioversions/sources/umls.py,sha256=4c9vVTD_eIshX3lzBVRPUGZXuUfvmecj_aVs9OfYV2k,842
 bioversions/sources/uniprot.py,sha256=_rootal_mrESkiXJh3udfr1UGrlzP7CQQIMsa35tycA,962
 bioversions/sources/unversioned.py,sha256=noHxGmy9cpVv5xegMHouBF6oCbW6CP1jpOeCVdE7Eak,78
 bioversions/sources/wikipathways.py,sha256=HTva8vsXRQWU6bia83Et4vveo-QhzJS6dDWeu9Syc6c,823
 bioversions/sources/zfin.py,sha256=D7csziZ3UsW8dncm6XKA0t3x6XB4cFbG9PTYcT-g2bg,708
-bioversions-0.5.319.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
-bioversions-0.5.319.dist-info/METADATA,sha256=XxeS7O4chD7k8hsi1xrv24LiB-WCFTy1z7x46VEPRzY,9421
-bioversions-0.5.319.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-bioversions-0.5.319.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.5.319.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
-bioversions-0.5.319.dist-info/RECORD,,
+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,,