diff --git a/.github/workflows/add_dunder_methods.yaml b/.github/workflows/add_dunder_methods.yaml index c56c931..81b8b56 100644 --- a/.github/workflows/add_dunder_methods.yaml +++ b/.github/workflows/add_dunder_methods.yaml @@ -32,6 +32,10 @@ jobs: run: | git config --global user.name 'github-actions' git config --global user.email 'github-actions@github.com' - git add bkbit/models/genome_annotation.py - git commit -m 'Update genome_annotation.py with dunder methods' - git push \ No newline at end of file + if ! git diff --quiet; then + git add bkbit/models/genome_annotation.py + git commit -m 'Update genome_annotation.py with dunder methods' + git push + else + echo "No changes to commit" + fi \ No newline at end of file diff --git a/bkbit/model_converters/sheets_converter.py b/bkbit/model_converters/sheets_converter.py index 4fa1f33..a0770e4 100644 --- a/bkbit/model_converters/sheets_converter.py +++ b/bkbit/model_converters/sheets_converter.py @@ -123,7 +123,8 @@ def bican_fix(schema: SchemaDefinition) -> SchemaDefinition: """ # fixing values for categories for nm, cl in schema.classes.items(): - cl.slot_usage["category"] = SlotDefinition(name="category", pattern=r"^bican:[A-Z][A-Za-z]+$") + if "category" in cl.slots: + cl.slot_usage["category"] = SlotDefinition(name="category", pattern=r"^bican:[A-Z][A-Za-z]+$") # not needed anymore # if "name_pr" in cl.slots: # cl.slots["name"] = cl.slots.pop("name_pr") diff --git a/bkbit/models/library_generation.py b/bkbit/models/library_generation.py index 9771a85..e94913e 100644 --- a/bkbit/models/library_generation.py +++ b/bkbit/models/library_generation.py @@ -9581,7 +9581,7 @@ class Library(ProvEntity, MaterialSample): 'local_names': {'NIMP': {'local_name_source': 'NIMP', 'local_name_value': 'library_quantification_ng'}}, 'slot_uri': 'bican:318b2d3a-dae7-4c63-bfbb-93862b92f63e'} }) - R1/R2_index_name: Optional[LibraryR1R2Index] = Field(None, description="""Name of the pair of library indexes used for sequencing. Indexes allow libraries to be pooled together for sequencing. Sequencing output (fastq) are demultiplexed by using the indexes for each library. The name will be associated with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing. The required direction of the sequence (sense or antisense) of the index can differ depending on sequencing instruments.""", json_schema_extra = { "linkml_meta": {'alias': 'R1/R2 index name', + R1_R2_index_name: Optional[LibraryR1R2Index] = Field(None, description="""Name of the pair of library indexes used for sequencing. Indexes allow libraries to be pooled together for sequencing. Sequencing output (fastq) are demultiplexed by using the indexes for each library. The name will be associated with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing. The required direction of the sequence (sense or antisense) of the index can differ depending on sequencing instruments.""", json_schema_extra = { "linkml_meta": {'alias': 'R1/R2 index name', 'domain_of': ['Library'], 'exact_mappings': ['NIMP:PD-VLLMWZ60'], 'in_subset': ['analysis', 'tracking'],