Merge pull request #37 from multimeric/regenerate-2024-08

Regenerate 2024-08

Author: multimeric

CHANGELOG.md

@@ -1,6 +1,14 @@
 
 ## Changelog
 
+### 1.4.0
+
+#### Changed
+
+* Auto-generated type definitions for the datasets have been regenerated [[#37](https://github.com/multimeric/Unipressed/pull/37)]. This pulls upstream changes from Uniprot. For a full list of changes [view this commit diff](https://github.com/multimeric/Unipressed/pull/31/commits/7e620c46175b6ec03e073fc78444a43e96821c31).
+    * Uniref's `created` `query` parameter has been replaced by `last_modified`
+    * UniprotKB has lost various `fields`: `xref_genevisible`, `xref_dosac-cobs-2dpage"`, `xref_swiss-2dpage`, `xref_ucd-2dpage`, `xref_world-2dpage`, `xref_epd`, `xref_maxqb`, `xref_ko` and `xref_genevisible`
+
 ### 1.3.0
 
 #### Changed

test/test_dataset/test_request.py

@@ -88,6 +88,7 @@ def test_main_example():
     ).each_record():
         assert isinstance(record, dict)
         assert set(record.keys()) == {
+            "extraAttributes",
             "primaryAccession",
             "genes",
             "sequence",

test/test_id_mapping/test_id_mapping.py

@@ -126,7 +126,7 @@ def test_gene_names():
     )
     # At this point it might be already finished
     assert request.get_status() in {"RUNNING", "FINISHED"}
-    sleep(1)
+    sleep(5)
     # At this point it should definitely be finished
     assert request.get_status() == "FINISHED"
     for result in request.each_result():

unipressed/dataset/generated_types/uniparc.py

@@ -128,6 +128,8 @@ class UniparcQueryDict(TypedDict):
     "Feature ID\ne.g. IPR004251"
     proteomecomponent: NotRequired[str]
     "Proteome Component\ne.g. chromosome"
+    organism_id: NotRequired[int]
+    "Organism ID\ne.g. 10254"
 
 
 UniparcQuery: TypeAlias = Union[UniparcQueryDict, str]

unipressed/dataset/generated_types/uniprotkb.py

@@ -728,7 +728,6 @@ class UniprotkbQueryDict(TypedDict):
 UniprotkbProteinFamilygroup: TypeAlias = Literal[
     "xref_allergome",
     "xref_cazy",
-    "xref_clae",
     "xref_esther",
     "xref_imgt_gene-db",
     "xref_merops",
@@ -755,19 +754,11 @@ class UniprotkbQueryDict(TypedDict):
     "xref_alzforum", "xref_biomuta", "xref_dmdm", "xref_dbsnp"
 ]
 UniprotkbTwodGel: TypeAlias = Literal[
-    "xref_compluyeast-2dpage",
-    "xref_dosac-cobs-2dpage",
-    "xref_ogp",
-    "xref_reproduction-2dpage",
-    "xref_swiss-2dpage",
-    "xref_ucd-2dpage",
-    "xref_world-2dpage",
+    "xref_compluyeast-2dpage", "xref_ogp", "xref_reproduction-2dpage"
 ]
 UniprotkbProteomic: TypeAlias = Literal[
     "xref_cptac",
-    "xref_epd",
     "xref_massive",
-    "xref_maxqb",
     "xref_pride",
     "xref_paxdb",
     "xref_peptideatlas",
@@ -841,7 +832,6 @@ class UniprotkbQueryDict(TypedDict):
     "xref_genetree",
     "xref_hogenom",
     "xref_inparanoid",
-    "xref_ko",
     "xref_oma",
     "xref_orthodb",
     "xref_phylomedb",
@@ -875,11 +865,7 @@ class UniprotkbQueryDict(TypedDict):
     "xref_emind",
 ]
 UniprotkbGeneExpression: TypeAlias = Literal[
-    "xref_bgee",
-    "xref_cleanex",
-    "xref_collectf",
-    "xref_expressionatlas",
-    "xref_genevisible",
+    "xref_bgee", "xref_cleanex", "xref_collectf", "xref_expressionatlas"
 ]
 UniprotkbFamilyAndDomain: TypeAlias = Literal[
     "xref_cdd",

unipressed/dataset/generated_types/uniref.py

@@ -47,7 +47,7 @@ class UnirefQueryDict(TypedDict):
         ]
     ]
     "Sequence length\ne.g. [100 TO 300]"
-    created: NotRequired[
+    date_modified: NotRequired[
         tuple[
             Union[
                 date,
@@ -59,7 +59,7 @@ class UnirefQueryDict(TypedDict):
             ],
         ]
     ]
-    "Date published\ne.g. [2011-10-10 TO 2019-10-10]"
+    "Date of last modification\ne.g. [2011-10-10 TO 2019-10-10]"
     uniprot_id: NotRequired[str]
     "UniProtKB ID/AC\ne.g. sample uniprot id"
     upi: NotRequired[str]
@@ -78,7 +78,7 @@ class UnirefQueryDict(TypedDict):
 ]
 UnirefSequences: TypeAlias = Literal["identity", "length", "sequence"]
 UnirefMiscellaneous: TypeAlias = Literal["types", "members", "count"]
-UnirefDateOf: TypeAlias = Literal["created",]
+UnirefDateOf: TypeAlias = Literal["date_modified",]
 UnirefFields: TypeAlias = Literal[
     UnirefNamesTaxonomy, UnirefSequences, UnirefMiscellaneous, UnirefDateOf
 ]