diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/metadata_edits.py | 118 |
1 files changed, 44 insertions, 74 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py index fee80a5f..c242e9b1 100644 --- a/wqflask/wqflask/metadata_edits.py +++ b/wqflask/wqflask/metadata_edits.py @@ -2,8 +2,6 @@ import re import datetime import json import os - -import logging from pathlib import Path from functools import reduce @@ -61,12 +59,9 @@ from gn3.db.phenotypes import ( fetch_publication_by_pubmed_id, update_phenotype as _update_phenotype) from gn3.db.sample_data import ( - delete_mrna_sample_data, - delete_pheno_sample_data, - insert_mrna_sample_data, - insert_pheno_sample_data, - update_mrna_sample_data, - update_pheno_sample_data, + delete_sample_data, + insert_sample_data, + update_sample_data, get_pheno_sample_data, get_pheno_csv_sample_data, get_mrna_sample_data, @@ -149,7 +144,7 @@ def display_probeset_metadata(name: str): _d = {"probeset": fetch_probeset_metadata_by_name(conn, name)} dataset_name=request.args["dataset_name"] - group_name = retrieve_mrna_group_name(conn, _d["probeset"]["id_"]) + group_name = retrieve_mrna_group_name(conn, _d["probeset"]["id_"], dataset_name) sample_list = retrieve_sample_list(group_name) sample_data = get_mrna_sample_data(conn, _d["probeset"]["id_"], dataset_name) @@ -416,7 +411,7 @@ def update_probeset(name: str): ) diff_data = {} with database_connection(get_setting("SQL_URI")) as conn: - group_name = retrieve_mrna_group_name(conn, str(data_.get("id"))) + group_name = retrieve_mrna_group_name(conn, probeset_id, dataset_name) sample_list = retrieve_sample_list(group_name) headers = ["Strain Name", "Value", "SE", "Count"] @@ -424,8 +419,7 @@ def update_probeset(name: str): conn=conn, probeset_id=probeset_id, dataset_name=dataset_name, - sample_list=retrieve_sample_list( - retrieve_mrna_group_name(conn, probeset_id)) + sample_list=retrieve_sample_list(group_name) ) if not (file_) and data_.get('edited') == "true": delta_csv = create_delta_csv(base_csv, data_, sample_list) @@ -615,7 +609,7 @@ def get_mrna_sample_data_as_csv(probeset_id: int, dataset_name: str): probeset_id=str(probeset_id), dataset_name=str(dataset_name), sample_list=retrieve_sample_list( - retrieve_mrna_group_name(conn, probeset_id)) + retrieve_mrna_group_name(conn, probeset_id, dataset_name)) ) return Response( get_mrna_csv_sample_data( @@ -623,7 +617,7 @@ def get_mrna_sample_data_as_csv(probeset_id: int, dataset_name: str): probeset_id=str(probeset_id), dataset_name=str(dataset_name), sample_list=retrieve_sample_list( - retrieve_mrna_group_name(conn, probeset_id)) + retrieve_mrna_group_name(conn, probeset_id, dataset_name)) ), mimetype="text/csv", headers={ @@ -842,54 +836,41 @@ def approve_data(resource_id: str, file_name: str): flash("You are not authorised to edit that trait.", "alert-danger") return redirect(url_for("metadata_edit.list_diffs")) + # Define the trait_info that is passed into the update functions, by data type + if sample_data.get("probeset_id"): # if trait is ProbeSet + trait_info = { + 'probeset_id': int(sample_data.get("probeset_id")), + 'dataset_name': sample_data.get("dataset_name") + } + else: # if trait is Publish + trait_info = { + 'trait_name': sample_data.get("trait_name"), + 'phenotype_id': int(sample_data.get("phenotype_id")) + } + for modification in ( modifications := [d for d in sample_data.get("Modifications")]): if modification.get("Current"): - 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( + update_sample_data( conn=conn, - data=data, + 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: - __deletions = delete_mrna_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")), + trait_info=trait_info ) + + # Deletions + for data in [d for d in sample_data.get("Deletions")]: + __deletions = delete_sample_data( + conn=conn, + data=data, + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + trait_info=trait_info + ) if __deletions: n_deletions += 1 # Remove any data that already exists from sample_data deletes @@ -898,26 +879,15 @@ def approve_data(resource_id: str, file_name: str): ## Insertions for data in [d for d in sample_data.get("Additions")]: - 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")), - ) + + __insertions = insert_sample_data( + conn=conn, + data=data, + csv_header=sample_data.get( + "Columns", "Strain Name,Value,SE,Count" + ), + trait_info=trait_info + ) if __insertions: n_insertions += 1 else: |