diff options
Diffstat (limited to 'uploader/phenotypes')
| -rw-r--r-- | uploader/phenotypes/models.py | 7 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 90 |
2 files changed, 94 insertions, 3 deletions
diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index ce7720c..4a229e6 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -262,8 +262,11 @@ def phenotypes_data_by_ids( ) -> tuple[dict, ...]: """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Phenotype AS pheno " + _query = ("SELECT " + "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " + "FROM Publication AS pub " + "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " + "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " "INNER JOIN Strain AS str ON pd.StrainId=str.Id " diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 2f6e926..00da78b 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -920,7 +920,8 @@ def edit_download_phenotype_data(# pylint: disable=[unused-argument] "Pre_publication_abbreviation", "Pre_publication_description", "Original_description", - "Post_publication_abbreviation" + "Post_publication_abbreviation", + "PubMed_ID" ] + samples_list, dialect="excel-tab") writer.writeheader() @@ -932,3 +933,90 @@ def edit_download_phenotype_data(# pylint: disable=[unused-argument] mimetype="text/csv", as_attachment=True, download_name=secure_filename(f"{dataset['Name']}_data")) + + +@phenotypesbp.route( + "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" + "/<int:dataset_id>/edit-upload", + methods=["GET", "POST"]) +@require_login +@with_dataset( + species_redirect_uri="species.populations.phenotypes.index", + population_redirect_uri="species.populations.phenotypes.select_population", + redirect_uri="species.populations.phenotypes.list_datasets") +def edit_upload_phenotype_data(# pylint: disable=[unused-argument] + species: dict, + population: dict, + dataset: dict, + **kwargs +): + if request.method == "GET": + return render_template( + "phenotypes/bulk-edit-upload.html", + species=species, + population=population, + dataset=dataset, + activelink="edit-phenotype") + + edit_file = save_file(request.files["file-upload-bulk-edit-upload"], + Path(app.config["UPLOAD_FOLDER"])) + + from gn_libs import jobs as gnlibs_jobs + from gn_libs import sqlite3 + jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] + with sqlite3.connection(jobs_db) as conn: + job_id = uuid.uuid4() + _job = gnlibs_jobs.launch_job( + gnlibs_jobs.initialise_job(conn, + job_id, + [ + sys.executable, + "-m", + "scripts.phenotypes_bulk_edit", + jobs_db, + str(job_id) + ], + "phenotype-bulk-edit", + extra_meta = { + "edit-file": str(edit_file) + }), + jobs_db, + f"{app.config['UPLOAD_FOLDER']}/job_errors", + worker_manager="gn_libs.scripts.worker") + + + return """ + <p>The following steps need to be performed: + <ol> + <li>Check that all IDs exist</li> + <li>Check for mandatory values</li> + <li>Update descriptions in the database (where changed)</li> + <li>Update publications in the database (where changed): + <ol> + <li>If <strong>PubMed_ID</strong> exists in our database, simply update the + 'PublicationId' value in the 'PublishXRef' table.</li> + <li>If <strong>PubMed_ID</strong> does not exists in our database: + <ol> + <li>fetch the publication's details from PubMed using the new + <strong>PubMed_ID</strong> value.</li> + <li>create a new publication in our database using the fetched data</li> + <li>Update 'PublicationId' value in 'PublishXRef' with ID of newly created + publication</li> + </ol> + </ol> + </li> + <li>Update values in the database (where changed)</li> + </ol> + </p> + + <p><strong>Note:</strong> + <ul> + <li>If a strain that did not have a value is given a value, then we need to + add a new cross-reference for the new DataId created.</li> + <li>If a strain that had a value has its value deleted and left blank, we + need to remove the cross-reference for the existing DataId — or, should we + enter the NULL value instead? Removing the cross-reference might be more + trouble than it is worth.</li> + </ul> + </p> + """ |