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Merge pull request #37 from multimeric/regenerate-2024-08
Regenerate 2024-08
2 parents 736dd25 + 5e6d806 commit 2ba4238

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CHANGELOG.md

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## Changelog
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### 1.4.0
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#### Changed
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* 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).
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* Uniref's `created` `query` parameter has been replaced by `last_modified`
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* 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`
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### 1.3.0
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#### Changed

test/test_dataset/test_request.py

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).each_record():
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assert isinstance(record, dict)
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assert set(record.keys()) == {
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"extraAttributes",
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"primaryAccession",
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"genes",
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"sequence",

test/test_id_mapping/test_id_mapping.py

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

unipressed/dataset/generated_types/uniparc.py

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"Feature ID\ne.g. IPR004251"
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proteomecomponent: NotRequired[str]
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"Proteome Component\ne.g. chromosome"
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organism_id: NotRequired[int]
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"Organism ID\ne.g. 10254"
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UniparcQuery: TypeAlias = Union[UniparcQueryDict, str]

unipressed/dataset/generated_types/uniprotkb.py

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

unipressed/dataset/generated_types/uniref.py

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

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