bioversions 0.6.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

bioversions/resources/versions.json

@@ -1,7 +1,7 @@
 {
   "annotations": {
-    "revision": 864,
-    "date": "2024-12-08",
+    "revision": 866,
+    "date": "2024-12-10",
     "author": "runner"
   },
   "database": [
@@ -2184,6 +2184,12 @@
           "version": "2024-09-08",
           "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-09-08/",
           "date": "2024-09-08"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "2024-11-29",
+          "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/complex/2024-11-29/",
+          "date": "2024-11-29"
         }
       ],
       "vtype": "date"
@@ -5491,6 +5497,11 @@
           "retrieved": "2024-12-03",
           "version": "2024-11-01",
           "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-11-01.json"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2024-12-03",
+          "homepage": "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/hgnc_complete_set_2024-12-03.json"
         }
       ],
       "name": "HGNC",
@@ -6044,6 +6055,12 @@
           "version": "2024-09-08",
           "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-09-08/",
           "date": "2024-09-08"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "2024-11-29",
+          "homepage": "ftp://ftp.ebi.ac.uk/pub/databases/intact/2024-11-29/",
+          "date": "2024-11-29"
         }
       ],
       "vtype": "date"
@@ -7047,6 +7064,11 @@
           "retrieved": "2023-12-01",
           "version": "2024",
           "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2024"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2025",
+          "homepage": "ftp://nlmpubs.nlm.nih.gov/online/mesh/2025"
         }
       ],
       "name": "MeSH",
@@ -11645,6 +11667,10 @@
         {
           "retrieved": "2024-12-03",
           "version": "2024-11-29"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "2024-12-06"
         }
       ],
       "name": "Rat Genome Database",
@@ -11813,6 +11839,10 @@
         {
           "retrieved": "2024-10-03",
           "version": "90"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "91"
         }
       ],
       "vtype": "sequential"
@@ -14854,6 +14884,14 @@
         {
           "retrieved": "2024-12-08",
           "version": "2024-12-08"
+        },
+        {
+          "retrieved": "2024-12-09",
+          "version": "2024-12-09"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "2024-12-10"
         }
       ],
       "name": "SwissLipids",
@@ -19816,6 +19854,10 @@
         {
           "retrieved": "2024-12-08",
           "version": "2024-12-07"
+        },
+        {
+          "retrieved": "2024-12-10",
+          "version": "2024-12-08"
         }
       ],
       "name": "Zebrafish Information Network",

bioversions/sources/hgnc.py

@@ -1,6 +1,5 @@
 """A getter for HGNC."""
 
-import datetime
 import logging
 
 import requests
@@ -14,7 +13,8 @@ __all__ = [
 logger = logging.getLogger(__name__)
 
 PATH = "https://storage.googleapis.com/public-download-files/hgnc/archive/archive/monthly/json/"
-PREFIX = "hgnc_complete_set_"
+URL = "https://storage.googleapis.com/storage/v1/b/public-download-files/o?prefix=hgnc/archive/archive/monthly"
+PREFIX = "hgnc/archive/archive/monthly/json/hgnc_complete_set_"
 SUFFIX = ".json"
 
 
@@ -28,19 +28,14 @@ class HGNCGetter(Getter):
     version_type = VersionType.date
 
     def get(self) -> str:
-        """Get the latest HGNC version number."""
-        today = datetime.date.today()
-        this_year = int(today.strftime("%Y"))
-        this_month = int(today.strftime("%m"))
-        maybe = today.strftime("%Y-%m-01")
-        res = requests.head(self.homepage_fmt.format(version=maybe), timeout=15)
-        if res.status_code == 200:
-            return maybe
-        if this_month == 1:
-            maybe_last_month = f"{this_year - 1}-12-01"
-        else:
-            maybe_last_month = f"{this_year}-{this_month - 1}-01"
-        return maybe_last_month
+        """Get the latest monthly HGNC version number."""
+        res = requests.get(URL, timeout=5)
+        items = res.json()["items"]
+        return max(
+            item["name"].removeprefix(PREFIX).removesuffix(SUFFIX)
+            for item in items
+            if (name := item["name"]).startswith(PREFIX) and name.endswith(SUFFIX)
+        )
 
 
 if __name__ == "__main__":

bioversions/sources/mesh.py

@@ -8,6 +8,10 @@ __all__ = [
     "MeshGetter",
 ]
 
+#: In 2024 and before, these were .gz, but after
+#: became .xml files
+SUFFIXES = [".xml", ".xml.gz", ".gz"]
+
 
 class MeshGetter(Getter):
     """A getter for MeSH."""
@@ -22,9 +26,12 @@ class MeshGetter(Getter):
         with ftplib.FTP("nlmpubs.nlm.nih.gov") as ftp:
             ftp.login()
             ftp.cwd("/online/mesh/MESH_FILES/xmlmesh/")
-            for name, _ in ftp.mlsd():
-                if name.startswith("desc") and name.endswith(".gz"):
-                    return name[len("desc") : -len(".gz")]
+            names = [name for name, _ in ftp.mlsd()]
+
+        for name in names:
+            for suffix in SUFFIXES:
+                if name.startswith("desc") and name.endswith(suffix):
+                    return name[len("desc") : -len(suffix)]
         raise ValueError
 
 

bioversions/version.py

@@ -7,7 +7,7 @@ __all__ = [
     "VERSION",
 ]
 
-VERSION = "0.6.0"
+VERSION = "0.6.2"
 
 
 def get_git_hash() -> str:

{bioversions-0.6.0.dist-info → bioversions-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioversions
-Version: 0.6.0
+Version: 0.6.2
 Summary: Get the current version for biological databases
 Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
 Project-URL: Homepage, https://github.com/biopragmatics/bioversions

{bioversions-0.6.0.dist-info → bioversions-0.6.2.dist-info}/RECORD

@@ -6,11 +6,11 @@ bioversions/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bioversions/slack_client.py,sha256=p9HmnyRCVuQvje0RbdDK9QuRlSw__WwFCJ8Be9cIkzM,1209
 bioversions/twitter_client.py,sha256=9d5Am0FSs7_EgGdjkxqpo98vPir9rjIXIxhZMmLgK5Q,1285
 bioversions/utils.py,sha256=x5d4p12VMlD5F8-y_J6JE5sct7BCV1d-zO-y5bSamSM,10342
-bioversions/version.py,sha256=sDNDSFIE7ThrJGabQa02d6NA_lTyKrKJ7mKsLm62e_g,585
+bioversions/version.py,sha256=FzgFvx_u7smueA0g2SHMrCOMcrg6T7pi3I5A1MX27jM,585
 bioversions/wsgi.py,sha256=-F7pUZipcQgj1T_f-9QCZBVdQ9sZBH93x3hxh9h7klU,794
 bioversions/resources/__init__.py,sha256=Nxw6w6_gRC4B_JwvbAAKpNR2rIpkNRZ5UkBIMdNqldY,1659
 bioversions/resources/update.py,sha256=btT_tdp0NKBRdshf4VuOe-vHWq0QQtcWWFcXS8QUfLU,3626
-bioversions/resources/versions.json,sha256=et5337SBwDq0fe5H6iEZM_iZKjLjkFWo0E1fM0xnJfY,483299
+bioversions/resources/versions.json,sha256=L_-UF04Fw5a493zTPRoJXt-FPmQIWqxxttkpeq3hGs0,484555
 bioversions/sources/__init__.py,sha256=pXONlDoxWIVRTSdCN3RDr3aMY38QGPOt0EwPAMCaIF8,6248
 bioversions/sources/antibodyregistry.py,sha256=6GF_9v8A_8Y4o6_nsZ9cAOP5vK3ZbPQ5qeL99UefR80,680
 bioversions/sources/bigg.py,sha256=iVrxyvKiEIUXs6FM2AiLDYa-yYDNGMONmiIv_R6KBg4,661
@@ -32,7 +32,7 @@ bioversions/sources/expasy.py,sha256=5C9m9Okygaq2D7zuuTnkOD4V24QU4C89ldztfLtiqnI
 bioversions/sources/flybase.py,sha256=L1qs0OF0OhjdknwV6DfvnnlxP37Z09hjuk-pz1Un2GM,754
 bioversions/sources/gtdb.py,sha256=lbtmSh4uhy6-Ve_slwO-Y7_wHRVySuof1I_rR-FQ05k,1001
 bioversions/sources/guidetopharmacology.py,sha256=WAasA6ZlyqJiqP70VrrCEpi2-JW7UMrUunAuE6pTk_g,1377
-bioversions/sources/hgnc.py,sha256=FPrpdsNRw0sj8GJ-tq6vzh0Zpmp8cKXgZDS8C5HxobU,1183
+bioversions/sources/hgnc.py,sha256=Wy0M8aT-SKsMKUWxEdPpWs32SjL7UZyiANLtCQC4Wp0,1099
 bioversions/sources/homologene.py,sha256=TaW0A33PLS4804zrRWZKDmo_zwEzK9bxX_zAiaUmd5w,622
 bioversions/sources/icd10.py,sha256=86zl9yxeUyy3WKgQS55I-1bK-kegH59sZFiwYGKFaAU,703
 bioversions/sources/icd11.py,sha256=a8kpwP6P3-Qowj6fGFFlsbL1ibhaWN48wez_qANiCE0,723
@@ -41,7 +41,7 @@ bioversions/sources/intact.py,sha256=BuZ-2n6O7e3HT2PrHHPbBkhmXa54Mj19kmJcdv9PfAU
 bioversions/sources/interpro.py,sha256=H6dZI71gUXo7L2YefCTiJD4quQRAvyYh5nDDbh2iuvE,1238
 bioversions/sources/itis.py,sha256=hh5zg61OAJIC76-5pwR5gd9YyWWUy_FY53X9vEAwLIQ,815
 bioversions/sources/kegg.py,sha256=dI7uQpaZh65rZOdutqcXNOkxn3HGwDNzaXyUhxiTdRU,905
-bioversions/sources/mesh.py,sha256=OWt3dOe8OjVxnQ6DBIq2dFRMKTPjwsvygYc6LrBUnPk,782
+bioversions/sources/mesh.py,sha256=XqjPU5UJgOHVc28c_6N7RiJd1F9RoUGPXGmmIaNopvM,971
 bioversions/sources/mgi.py,sha256=TX-V0xcWFmktssjRldjYb591HCtoheY99w0FTH2cIZk,841
 bioversions/sources/mirbase.py,sha256=q3C6-Cy-vELyJCQCnpg4pveoRrlYfqgb4313mHG5Cp4,996
 bioversions/sources/moalmanac.py,sha256=DMotSYD4sGOTZaJgn_iPeUfEdhjlgmzoKKLYS-L6Tro,749
@@ -73,8 +73,8 @@ bioversions/sources/wikipathways.py,sha256=STw8Bivc3IZLYIx-KwpxHLUmRTqNfHm0wQywD
 bioversions/sources/zfin.py,sha256=3Ooz3lDx8J42OAoyU8eJI-fRnMRiYyUMcj4fDE5DVLQ,683
 bioversions/templates/base.html,sha256=AKB6aT39U9VtOM2zvW_Um5IgYO9Ky-CLpByxy5XXO5M,713
 bioversions/templates/home.html,sha256=z98FSslCRP2K39xbHpSPgk19j7Z21PSbRGAtaXI0Md0,2756
-bioversions-0.6.0.dist-info/METADATA,sha256=tiPzbnLwFUCnp5amhoolYKR5Tt2_bayD9YxwC3bbuCc,19674
-bioversions-0.6.0.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-bioversions-0.6.0.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
-bioversions-0.6.0.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-bioversions-0.6.0.dist-info/RECORD,,
+bioversions-0.6.2.dist-info/METADATA,sha256=48A1kYWak3ieiU4qlfIlQsecxF7GKmnp36n0CaQ3DzA,19674
+bioversions-0.6.2.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+bioversions-0.6.2.dist-info/entry_points.txt,sha256=A3qrS-nvKNZPZWQbYlmsmiDTge524C4yR-arRJwdHls,53
+bioversions-0.6.2.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+bioversions-0.6.2.dist-info/RECORD,,