diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 115 |
1 files changed, 80 insertions, 35 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index 60b2ffd6..fee80a5f 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -60,11 +60,13 @@ from gn3.db.phenotypes import ( fetch_publication_by_id, fetch_publication_by_pubmed_id, update_phenotype as _update_phenotype) -from gn3.db.sample_data import delete_sample_data from gn3.db.sample_data import ( - delete_sample_data, - insert_sample_data, - update_sample_data, + delete_mrna_sample_data, + delete_pheno_sample_data, + insert_mrna_sample_data, + insert_pheno_sample_data, + update_mrna_sample_data, + update_pheno_sample_data, get_pheno_sample_data, get_pheno_csv_sample_data, get_mrna_sample_data, @@ -497,7 +499,6 @@ def update_probeset(name: str): url = url_for("metadata_edit.list_diffs") flash(f"Sample-data has been successfully uploaded. \ View the diffs <a href='{url}' target='_blank'>here</a>", "success") - with database_connection(get_setting("SQL_URI")) as conn: data_ = request.form.to_dict() probeset_ = { @@ -844,28 +845,51 @@ def approve_data(resource_id: str, file_name: str): for modification in ( modifications := [d for d in sample_data.get("Modifications")]): if modification.get("Current"): - update_sample_data( + if sample_data.get("probeset_id"): # if trait is ProbeSet + update_mrna_sample_data( + conn=conn, + original_data=modification.get("Original"), + updated_data=modification.get("Current"), + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + probeset_id=int(sample_data.get("probeset_id")), + dataset_name=sample_data.get("dataset_name") + ) + else: + update_pheno_sample_data( + conn=conn, + trait_name=sample_data.get("trait_name"), + original_data=modification.get("Original"), + updated_data=modification.get("Current"), + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + phenotype_id=int(sample_data.get("phenotype_id")), + ) + + # Deletions + for data in [d for d in sample_data.get("Deletions")]: + if sample_data.get("probeset_id"): # if trait is ProbeSet + __deletions = delete_mrna_sample_data( + conn=conn, + data=data, + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + probeset_id=int(sample_data.get("probeset_id")), + dataset_name=sample_data.get("dataset_name") + ) + else: + __deletions = delete_mrna_sample_data( conn=conn, trait_name=sample_data.get("trait_name"), - original_data=modification.get("Original"), - updated_data=modification.get("Current"), + data=data, csv_header=sample_data.get( "Columns", "Strain Name,Value,SE,Count" ), phenotype_id=int(sample_data.get("phenotype_id")), ) - - # Deletions - for data in [d for d in sample_data.get("Deletions")]: - __deletions = delete_sample_data( - conn=conn, - trait_name=sample_data.get("trait_name"), - data=data, - csv_header=sample_data.get( - "Columns", "Strain Name,Value,SE,Count" - ), - phenotype_id=int(sample_data.get("phenotype_id")), - ) if __deletions: n_deletions += 1 # Remove any data that already exists from sample_data deletes @@ -874,16 +898,30 @@ def approve_data(resource_id: str, file_name: str): ## Insertions for data in [d for d in sample_data.get("Additions")]: - if insert_sample_data( - conn=conn, - trait_name=sample_data.get("trait_name"), - data=data, - csv_header=sample_data.get( - "Columns", "Strain Name,Value,SE,Count" - ), - phenotype_id=int(sample_data.get("phenotype_id")), - ): + if sample_data.get("probeset_id"): # if trait is ProbeSet + __insertions = insert_mrna_sample_data( + conn=conn, + data=data, + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + probeset_id=int(sample_data.get("probeset_id")), + dataset_name=sample_data.get("dataset_name") + ) + else: + __insertions = insert_pheno_sample_data( + conn=conn, + trait_name=sample_data.get("trait_name"), + data=data, + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + phenotype_id=int(sample_data.get("phenotype_id")), + ) + if __insertions: n_insertions += 1 + else: + sample_data.get("Additions").remove(data) if any( [ sample_data.get("Additions"), @@ -892,11 +930,18 @@ def approve_data(resource_id: str, file_name: str): ] ): with database_connection(get_setting("SQL_URI")) as conn: - create_metadata_audit(conn, { - "dataset_id": sample_data.get("dataset_id"), - "editor": sample_data.get("author"), - "json_data": json.dumps(sample_data, cls=CustomJSONEncoder) - }) + if sample_data.get("dataset_id"): # if phenotype + create_metadata_audit(conn, { + "dataset_id": sample_data.get("dataset_id"), + "editor": sample_data.get("author"), + "json_data": json.dumps(sample_data, cls=CustomJSONEncoder) + }) + else: + create_metadata_audit(conn, { + "dataset_id": sample_data.get("probeset_id"), + "editor": sample_data.get("author"), + "json_data": json.dumps(sample_data, cls=CustomJSONEncoder) + }) # Once data is approved, rename it! os.rename( os.path.join(f"{TMPDIR}/sample-data/diffs", file_name), @@ -907,7 +952,7 @@ def approve_data(resource_id: str, file_name: str): if n_deletions: flash(f"# Deletions: {n_deletions}", "success") if n_insertions: - flash(f"# Additions: {len(modifications)}", "success") + flash(f"# Additions: {len(n_insertions)}", "success") if len(modifications): flash(f"# Modifications: {len(modifications)}", "success") else: # Edge case where you need to automatically reject the file |