Add method to query cl slims #8
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pandasaurus_cxg/utils/exceptions.py
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| def __init__(self, invalid_slim_list: List[str], valid_slim_list: list[dict[str, str]]): | ||
| self.message = ( | ||
| f"The following slim names are invalid: " | ||
| f"{', '.join([slim for slim in invalid_slim_list])}. " |
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Can't we directly do ', '.join(invalid_slim_list)
| file_path: str, | ||
| cell_type_field: Optional[str] = "cell_type_ontology_term_id", | ||
| context_field: Optional[str] = "tissue_ontology_term_id", | ||
| ontology_list_for_slims: Optional[List[str]] = ["Cell Ontology"], |
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We should validate if all ontology titles are valid and raise an exception otherwise.
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Will having a Enum for ontology titles help users to find the correct ontology names?
from enum import Enum
class OntologyNames(Enum):
CL = "Cell Ontology"
ENVO = "The Environment Ontology"
DPO= "Drosophila Phenotype Ontology (DPO)"
....Then users can provide the list as [OntologyNames.CL.value, OntologyNames.ENVO.value]. If ubergraph is extended, users can still use the string values.
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In this particular case, I think we only care about CL but want to leave an option to over-ride.
Validation should be in pandasaurus itself. Pandasaurus also needs more support for letting users know what is possible. We could have a method that lists all ontologies (referencing that in docstring of method for listing slims.)
It looks like your method takes dc:title of ontology. Easy to retrieve a list of these (although be careful about consistency dc namespace).
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It looks like your method takes dc:title of ontology. Easy to retrieve a list of these (although be careful about consistency dc namespace).
This is the query I'm using to retrieve slim details; https://api.triplydb.com/s/lFTW8trIj.
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I have created INCATools/PandaSaurus#21 to keep track
pandasaurus_cxg/anndata_enricher.py
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| """ | ||
| self.__enricher = Query(self.__seed_list, property_list) | ||
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| def is_invalid_slim_list(self, slim_list): |
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The name is_invalid_slim_list makes me expect this function to return a boolean value. Should we rename it to validate_slim_list ?
I've added
slim_listattribute to keep track of slim lists. It is initialised with a list of ontology names, the default value is["Cell Ontology"]. I've also added added a custom exception class for invalid slim names.minimal_slim_enrichmentandfull_slim_enrichmentraises that exception in case they are called with invalid slim names.I've added missing anndata dependency.