diff options
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 75 |
1 files changed, 33 insertions, 42 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index bed3a44a..fdcb6597 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -42,26 +42,27 @@ from gn3.csvcmp import csv_diff from gn3.csvcmp import extract_invalid_csv_headers from gn3.csvcmp import remove_insignificant_edits from gn3.db import diff_from_dict -from gn3.db import update from gn3.db.datasets import retrieve_sample_list, retrieve_phenotype_group_name from gn3.db.metadata_audit import ( create_metadata_audit, fetch_probeset_metadata_audit_by_trait_name, fetch_phenotype_metadata_audit_by_dataset_id) -from gn3.db.phenotypes import Phenotype -from gn3.db.probesets import Probeset, probeset_mapping, fetch_probeset_metadata_by_name -from gn3.db.phenotypes import Publication -from gn3.db.phenotypes import PublishXRef +from gn3.db.probesets import ( + update_probeset, + fetch_probeset_metadata_by_name) from gn3.db.phenotypes import ( fetch_trait, fetch_metadata, update_publication, fetch_publication_by_id, - fetch_publication_by_pubmed_id) -from gn3.db.sample_data import delete_sample_data -from gn3.db.sample_data import get_trait_sample_data, get_trait_csv_sample_data -from gn3.db.sample_data import insert_sample_data -from gn3.db.sample_data import update_sample_data + fetch_publication_by_pubmed_id, + update_phenotype as _update_phenotype) +from gn3.db.sample_data import ( + delete_sample_data, + insert_sample_data, + update_sample_data, + get_trait_sample_data, + get_trait_csv_sample_data) metadata_edit = Blueprint("metadata_edit", __name__) @@ -273,13 +274,10 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success") } updated_phenotypes = "" with database_connection(get_setting("SQL_URI")) as conn: - updated_phenotypes = update( - conn, - "Phenotype", - data=Phenotype(**phenotype_), - where=Phenotype(id_=data_.get("phenotype-id")), - ) - conn.commit() + updated_phenotypes = _update_phenotype( + conn, {"id_": data_["phenotype-id"], **{ + key: value for key,value in phenotype_.items() + if value is not None}}) diff_data = {} if updated_phenotypes: diff_data.update( @@ -294,19 +292,19 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success") ) } ) - publication_ = { - key: val for key, val in { - "pubmed_id": data_.get("pubmed-id"), - "abstract": data_.get("abstract"), - "authors": data_.get("authors"), - "title": data_.get("title"), - "journal": data_.get("journal"), - "volume": data_.get("volume"), - "pages": data_.get("pages"), - "month": data_.get("month"), - "year": data_.get("year"), - }.items() if val is not None - } + publication_ = { + key: val for key, val in { + "pubmed_id": data_.get("pubmed-id"), + "abstract": data_.get("abstract"), + "authors": data_.get("authors"), + "title": data_.get("title"), + "journal": data_.get("journal"), + "volume": data_.get("volume"), + "pages": data_.get("pages"), + "month": data_.get("month"), + "year": data_.get("year"), + }.items() if val is not None + } updated_publications = "" with database_connection(get_setting("SQL_URI")) as conn: existing_publication = (# fetch publication @@ -314,12 +312,10 @@ View the diffs <a href='{url}' target='_blank'>here</a>", "success") fetch_publication_by_pubmed_id(conn, data_["pubmed-id"])) if existing_publication: - update( - conn, - "PublishXRef", - data=PublishXRef(publication_id=existing_publication.id_), - where=PublishXRef(id_=name, inbred_set_id=dataset_id) - ) + update_cross_reference(conn, + dataset_id, + name, + {"publication_id": existing_publication.id_}) else: updated_publications = update_publication( conn, {"id_": data_["old_id_"], **publication_}) @@ -403,12 +399,7 @@ def update_probeset(name: str): or g.user_session.record.get("user_id") or "" ) - if update( - conn, - "ProbeSet", - data=Probeset(**probeset_), - where=Probeset(id_=data_.get("id")), - ): + if update_probeset(conn, data["id"], probeset_): diff_data.update( { "Probeset": diff_from_dict( |