kazu.ontology_preprocessing.downloads¶
Some functions to update public resources in the kazu model pack.
Classes
Downloads the ChEMBL database and exports a subset of it as a parquet file. |
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Used when version info is contained within the ontology. |
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- class kazu.ontology_preprocessing.downloads.ChemblParquetOntologyDownloader[source]¶
Bases:
OntologyDownloaderDownloads the ChEMBL database and exports a subset of it as a parquet file.
- version(local_path=None)[source]¶
Get the version of the ontology.
Note that this method should be idempotent, i.e. it should not change the state of the ontology. Also, it may be able to determine the version of the ontology without querying it directly (e.g. by looking at the file name, or if it is known a priori). If this is not the case, you can implement a method here to do something more sophisticated, such as querying the ontology directly via sparql.
Alternatively, it may only be known prior to calling the download method. In this case, implementations should store the version as a field, so it can be returned from there.
- CHEMBL_FILENAME_TEMPLATE = 'chembl_%s_subset.parquet'¶
- CHEMBL_QUERY = "SELECT DISTINCT * FROM (\n SELECT chembl_id AS idx, pref_name AS default_label, synonyms AS syn, syn_type AS mapping_type\n FROM molecule_dictionary AS md\n JOIN molecule_synonyms ms ON md.molregno = ms.molregno\n UNION ALL\n SELECT chembl_id AS idx, pref_name AS default_label, pref_name AS syn, 'pref_name' AS mapping_type\n FROM molecule_dictionary) as t1\n WHERE t1.DEFAULT_LABEL is not null;\n "¶
- CHEMBL_TEMPLATE = 'https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_%s/chembl_%s_sqlite.tar.gz'¶
- class kazu.ontology_preprocessing.downloads.OBOOntologyDownloader[source]¶
Bases:
SimpleOntologyDownloader- version(local_path=None)[source]¶
Get the version of the ontology.
Note that this method should be idempotent, i.e. it should not change the state of the ontology. Also, it may be able to determine the version of the ontology without querying it directly (e.g. by looking at the file name, or if it is known a priori). If this is not the case, you can implement a method here to do something more sophisticated, such as querying the ontology directly via sparql.
Alternatively, it may only be known prior to calling the download method. In this case, implementations should store the version as a field, so it can be returned from there.
- class kazu.ontology_preprocessing.downloads.OntologyDownloader[source]¶
Bases:
ABC- delete_previous(local_path)[source]¶
Delete the previous version of the ontology.
- Parameters:
local_path (Path) – the path to the ontology to delete
- Return type:
None
- abstract download(local_path, skip_download=False)[source]¶
Download the ontology to the local path.
- abstract version(local_path=None)[source]¶
Get the version of the ontology.
Note that this method should be idempotent, i.e. it should not change the state of the ontology. Also, it may be able to determine the version of the ontology without querying it directly (e.g. by looking at the file name, or if it is known a priori). If this is not the case, you can implement a method here to do something more sophisticated, such as querying the ontology directly via sparql.
Alternatively, it may only be known prior to calling the download method. In this case, implementations should store the version as a field, so it can be returned from there.
- class kazu.ontology_preprocessing.downloads.OpenTargetsOntologyDownloader[source]¶
Bases:
OntologyDownloader- delete_previous(local_path)[source]¶
We could use rmtree here but it’s safer to just remove the files we know we downloaded.
- Parameters:
local_path (Path)
- Returns:
- Return type:
None
- version(local_path=None)[source]¶
Get the version of the ontology.
Note that this method should be idempotent, i.e. it should not change the state of the ontology. Also, it may be able to determine the version of the ontology without querying it directly (e.g. by looking at the file name, or if it is known a priori). If this is not the case, you can implement a method here to do something more sophisticated, such as querying the ontology directly via sparql.
Alternatively, it may only be known prior to calling the download method. In this case, implementations should store the version as a field, so it can be returned from there.
- OT_PREFIX = 'ftp://ftp.ebi.ac.uk/pub/databases/opentargets/platform/'¶
- class kazu.ontology_preprocessing.downloads.OwlOntologyDownloader[source]¶
Bases:
SimpleOntologyDownloaderUsed when version info is contained within the ontology.
- class kazu.ontology_preprocessing.downloads.SimpleOntologyDownloader[source]¶
Bases:
OntologyDownloader- version(local_path=None)[source]¶
Get the version of the ontology.
Note that this method should be idempotent, i.e. it should not change the state of the ontology. Also, it may be able to determine the version of the ontology without querying it directly (e.g. by looking at the file name, or if it is known a priori). If this is not the case, you can implement a method here to do something more sophisticated, such as querying the ontology directly via sparql.
Alternatively, it may only be known prior to calling the download method. In this case, implementations should store the version as a field, so it can be returned from there.