Update with SILVA data

Author: cthoyt

docs/_data/versions.yml

@@ -1,7 +1,7 @@
 annotations:
   author: cthoyt
   date: '2025-01-28'
-  revision: 903
+  revision: 904
 database:
 - name: A nomenclatural ontology for biological names
   prefix: nomen
@@ -7102,6 +7102,14 @@ database:
   - retrieved: '2025-01-14'
     version: '2025-01-01'
   vtype: date
+- name: SILVA ribosomal RNA database
+  prefix: silva.taxon
+  releases:
+  - date: '2024-03-14'
+    homepage: https://www.arb-silva.de/
+    retrieved: '2025-01-28'
+    version: '138.2'
+  vtype: sequential
 - name: SNOMED CT (International Edition)
   prefix: snomedct
   releases:

docs/failures.md

@@ -10,10 +10,10 @@ Using class: `CiVICGetter`
 
 ```python-traceback
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 218, in _iter_versions
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 220, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 171, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
     return _resolve_helper_cached(name)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
@@ -22,22 +22,22 @@ Traceback (most recent call last):
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
     func_res = func(*args, **kwds)
                ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 178, in _resolve_helper_cached
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 180, in _resolve_helper_cached
     return _resolve_helper(name)
            ^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 184, in _resolve_helper
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 216, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 94, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/civic.py", line 41, in get
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/civic.py", line 41, in get
     value = res.json()["data"]["dataReleases"][1]["name"]
             ~~~~~~~~~~^^^^^^^^
 KeyError: 'data'
@@ -53,23 +53,23 @@ Traceback (most recent call last):
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/requests/models.py", line 974, in json
     return complexjson.loads(self.text, **kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/__init__.py", line 346, in loads
+  File "/opt/homebrew/Cellar/python@3.12/3.12.8/Frameworks/Python.framework/Versions/3.12/lib/python3.12/json/__init__.py", line 346, in loads
     return _default_decoder.decode(s)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 338, in decode
+  File "/opt/homebrew/Cellar/python@3.12/3.12.8/Frameworks/Python.framework/Versions/3.12/lib/python3.12/json/decoder.py", line 338, in decode
     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.12.8/x64/lib/python3.12/json/decoder.py", line 356, in raw_decode
+  File "/opt/homebrew/Cellar/python@3.12/3.12.8/Frameworks/Python.framework/Versions/3.12/lib/python3.12/json/decoder.py", line 356, in raw_decode
     raise JSONDecodeError("Expecting value", s, err.value) from None
 json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
 
 During handling of the above exception, another exception occurred:
 
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 218, in _iter_versions
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 220, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 171, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
     return _resolve_helper_cached(name)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
@@ -78,22 +78,22 @@ Traceback (most recent call last):
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
     func_res = func(*args, **kwds)
                ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 178, in _resolve_helper_cached
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 180, in _resolve_helper_cached
     return _resolve_helper(name)
            ^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 184, in _resolve_helper
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 216, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 94, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/disgenet.py", line 24, in get
     res_json = res.json()
                ^^^^^^^^^^
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/requests/models.py", line 978, in json
@@ -108,10 +108,10 @@ Using class: `DrugBankGetter`
 
 ```python-traceback
 Traceback (most recent call last):
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 218, in _iter_versions
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 220, in _iter_versions
     yv = resolve(cls.name)
          ^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 171, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 173, in resolve
     return _resolve_helper_cached(name)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 258, in func_wrapper
@@ -120,22 +120,22 @@ Traceback (most recent call last):
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/cachier/core.py", line 61, in _calc_entry
     func_res = func(*args, **kwds)
                ^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 178, in _resolve_helper_cached
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 180, in _resolve_helper_cached
     return _resolve_helper(name)
            ^^^^^^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/__init__.py", line 184, in _resolve_helper
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/__init__.py", line 186, in _resolve_helper
     return getter.resolve()
            ^^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 216, in resolve
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 216, in resolve
     version=cls.version,
             ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 94, in version
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 94, in version
     if isinstance(cls._cache_prop, str):
                   ^^^^^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/utils.py", line 88, in _cache_prop
     cls._cache = cls().get()
                  ^^^^^^^^^^^
-  File "/home/runner/work/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
+  File "/Users/cthoyt/dev/bioversions/src/bioversions/sources/drugbank.py", line 28, in get
     res.raise_for_status()
   File "/Users/cthoyt/.virtualenvs/biopragmatics/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
     raise HTTPError(http_error_msg, response=self)

src/bioversions/resources/versions.json

@@ -1,6 +1,6 @@
 {
   "annotations": {
-    "revision": 903,
+    "revision": 904,
     "date": "2025-01-28",
     "author": "cthoyt"
   },
@@ -12863,6 +12863,19 @@
       "name": "SIGNOR",
       "vtype": "date"
     },
+    {
+      "releases": [
+        {
+          "retrieved": "2025-01-28",
+          "version": "138.2",
+          "homepage": "https://www.arb-silva.de/",
+          "date": "2024-03-14"
+        }
+      ],
+      "name": "SILVA ribosomal RNA database",
+      "prefix": "silva.taxon",
+      "vtype": "sequential"
+    },
     {
       "releases": [
         {