bioversions 0.5.513__py3-none-any.whl → 0.5.514__py3-none-any.whl

bioversions/resources/update.py

@@ -7,6 +7,7 @@ import sys
 from datetime import datetime
 
 import click
+from tqdm import tqdm
 from tqdm.contrib.logging import logging_redirect_tqdm
 
 from bioversions.resources import (
@@ -83,7 +84,7 @@ def _update(force: bool):
             v["releases"].append(append_dict)
 
     if not changes and not force:
-        click.secho(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True)
+        tqdm.write(click.style(f"No changes to {EXPORT_PATH}", fg="yellow", bold=True))
     else:
         rv_database = sorted(versions.values(), key=lambda version: version["name"].lower())
         rv = {
@@ -94,7 +95,7 @@ def _update(force: bool):
             },
             "database": rv_database,
         }
-        click.secho(f"Writing new {EXPORT_PATH}", fg="green", bold=True)
+        tqdm.write(click.style(f"Writing new {EXPORT_PATH}", fg="green", bold=True))
         write_export(rv)
         write_versions(rv)
 
@@ -106,7 +107,7 @@ def _log_update(bv) -> None:
     if bv.homepage:
         text += f". See {bv.homepage}"
 
-    click.secho(text, fg="green", bold=True)
+    tqdm.write(click.style(text, fg="green", bold=True))
 
     try:
         from .. import slack_client

bioversions/sources/dgi.py

@@ -21,7 +21,7 @@ class DGIGetter(Getter):
     def get(self):
         """Get the latest DGI version number."""
         res = requests.get(GITHUB_PAGE)
-        soup = bs4.BeautifulSoup(res.content)
+        soup = bs4.BeautifulSoup(res.content, features="html.parser")
         time_tag = soup.find("relative-time")
         if time_tag is None:
             raise ValueError

bioversions/sources/hgnc.py

@@ -2,9 +2,12 @@
 
 """A getter for HGNC."""
 
+import datetime
 import logging
 
-from bioversions.utils import Getter, VersionType, get_soup
+import requests
+
+from bioversions.utils import Getter, VersionType
 
 __all__ = [
     "HGNCGetter",
@@ -12,7 +15,7 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 
-PATH = "https://ftp.ebi.ac.uk/pub/databases/genenames/new/archive/monthly/json/"
+PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
 PREFIX = "hgnc_complete_set_"
 SUFFIX = ".json"
 
@@ -22,21 +25,18 @@ class HGNCGetter(Getter):
 
     bioregistry_id = "hgnc"
     name = "HGNC"
-    homepage_fmt = (
-        "http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/"
-        "archive/monthly/json/hgnc_complete_set_{version}.json"
-    )
+    homepage_fmt = PATH + "hgnc_complete_set_{version}.json"
 
     version_type = VersionType.date
 
     def get(self) -> str:
         """Get the latest HGNC version number."""
-        soup = get_soup(PATH)
-        return max(
-            anchor.attrs["href"][len(PREFIX) : -len(SUFFIX)]
-            for anchor in soup.find_all("a")
-            if anchor.attrs["href"].startswith(PREFIX)
-        )
+        today = datetime.date.today()
+        maybe = today.strftime("%Y-%m-01")
+        res = requests.head(self.homepage_fmt.format(version=maybe))
+        if res.status_code == 200:
+            return maybe
+        raise ValueError(f"HGNC hasn't posted new data for this month under version {maybe}")
 
 
 if __name__ == "__main__":

bioversions/version.py

@@ -9,7 +9,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.5.513"
+VERSION = "0.5.514"
 
 
 def get_git_hash() -> str:

{bioversions-0.5.513.dist-info → bioversions-0.5.514.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bioversions
-Version: 0.5.513
+Version: 0.5.514
 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-0.5.513.dist-info → bioversions-0.5.514.dist-info}/RECORD

@@ -6,10 +6,10 @@ 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=6ygaoe5rRArtrCXHrVygpl2cD7Otrbs4D1rADmpXDrA,10425
-bioversions/version.py,sha256=0qeErUBI7JvONX3OWJTI0lNI-7R0CwPoWd2U-CnN9lE,645
+bioversions/version.py,sha256=RT-f7Ub4h10avu1N6H8Yt832qnUnOfM8WpntTbyv5mY,645
 bioversions/wsgi.py,sha256=Z1HYFmnrWKNGwHq4R4DRfBuLzAEAAZ5UfHjvJUpnDfs,826
 bioversions/resources/__init__.py,sha256=0E1yGGT5SztSGEa30Tai4wCUki4nqfynqCSNAvjzEOk,1173
-bioversions/resources/update.py,sha256=21LprPktMKXdFI7llKjn7gsAQq01TGSKFbWQEhhwDJ0,3215
+bioversions/resources/update.py,sha256=CfvtoUJ3Ai_--Y5DHBx2zZ4vfIGgDsQaE4asb2kp3bg,3273
 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
@@ -22,7 +22,7 @@ bioversions/sources/civic.py,sha256=1uGaTy2ipZ2Nm5Nn_Ojv6biJfLr3sB3djc6AmOT3sO0,
 bioversions/sources/complexportal.py,sha256=SPJ3ryJNtXwvArtHaeeWCSau6uVBJTDxPX6XPvKmDlY,696
 bioversions/sources/daily.py,sha256=mq8NLnhRRDjTzwGQl9LxCBiO6BSWyGOJcfyg7qqNsno,281
 bioversions/sources/depmap.py,sha256=EjpScMRwqItvitso57ah3f53bkWbTK0bjLWOBr4ym1E,654
-bioversions/sources/dgi.py,sha256=GK2cyReEOsxYeiRQGSDlXIuUDsWtsyHBVwveKje0-K8,929
+bioversions/sources/dgi.py,sha256=WbiOPH2nJwxSQrQHNnkAskJBSB6KzVNrHVKV2ZFDDo4,953
 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
@@ -30,7 +30,7 @@ bioversions/sources/ensembl.py,sha256=BHssnbJMI-jONB8W1mKERYsccRmIETI0NeWLnTTiDd
 bioversions/sources/expasy.py,sha256=EQXDz1LJSc0J-BE5Gy5tI-T4e6j4D5jid6c6ajzQjG8,830
 bioversions/sources/flybase.py,sha256=5S0gI8tULx3sfNVy2O4grvyqIUwI4teS9S6khDh-JzQ,779
 bioversions/sources/guidetopharmacology.py,sha256=B3W5I01v1a0OuvPJB-LHoSYvuJBN_cpXulnGrBs009o,1377
-bioversions/sources/hgnc.py,sha256=OH8E9dF2oPbh_BshPgKrWSFkYWDq9rj9J7DN06pVFxQ,970
+bioversions/sources/hgnc.py,sha256=yFQz_Yb0BvevNaaP6Jmh4Lh0YWw-VoTGBKVVnGDe_RE,1001
 bioversions/sources/homologene.py,sha256=_f6SQRXe67t1jqQ6HjQIEOGApPUHLlfHMZojChumWzc,647
 bioversions/sources/icd10.py,sha256=cfiJcueTr6Z1dIzdP68QeCPlnJhr3Yd3U97TZplR1JI,716
 bioversions/sources/icd11.py,sha256=EsdUrPxio_VIv9tkPoauxozKY-fdjwesbb5Kh_bijU0,736
@@ -69,9 +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-0.5.513.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
-bioversions-0.5.513.dist-info/METADATA,sha256=Dal1xzmeDAqNHR68_yxGfGLyI-lyRU99GlvMi6hC1UY,9434
-bioversions-0.5.513.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-bioversions-0.5.513.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.5.513.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
-bioversions-0.5.513.dist-info/RECORD,,
+bioversions-0.5.514.dist-info/LICENSE,sha256=GzLA83qaovFgoZWRYwaAmY-lkHZyDySJHU-YKE9NdVs,1076
+bioversions-0.5.514.dist-info/METADATA,sha256=aNmGTe8HgElwJHm1HmtWnagv4PW8UEQ8Wq3pLahx-8Q,9434
+bioversions-0.5.514.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+bioversions-0.5.514.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
+bioversions-0.5.514.dist-info/top_level.txt,sha256=0QO2OEUMchj5GSlWEFi0cvUpsm4b_uwuuvr6uSEmfY0,12
+bioversions-0.5.514.dist-info/RECORD,,