diff options
| -rw-r--r-- | uploader/__init__.py | 3 | ||||
| -rw-r--r-- | uploader/phenotypes/models.py | 7 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 66 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/bulk-edit-upload.html | 3 |
4 files changed, 74 insertions, 5 deletions
diff --git a/uploader/__init__.py b/uploader/__init__.py index 4f3538c..734bdcd 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -8,6 +8,8 @@ from flask import Flask, request from flask_session import Session from cachelib import FileSystemCache +from gn_libs import jobs + from uploader.oauth2.client import user_logged_in, authserver_authorise_uri from . import session @@ -94,4 +96,5 @@ def create_app(): app.register_blueprint(speciesbp, url_prefix="/species") register_error_handlers(app) + jobs.init_app(app) return app 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 3d2ff76..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() @@ -957,4 +958,65 @@ def edit_upload_phenotype_data(# pylint: disable=[unused-argument] dataset=dataset, activelink="edit-phenotype") - return "NOT Implemented: Would do actual edit." + 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> + """ diff --git a/uploader/templates/phenotypes/bulk-edit-upload.html b/uploader/templates/phenotypes/bulk-edit-upload.html index 926bcf5..d0f38f5 100644 --- a/uploader/templates/phenotypes/bulk-edit-upload.html +++ b/uploader/templates/phenotypes/bulk-edit-upload.html @@ -42,9 +42,10 @@ Edited File</label> <div class="col-sm-10"> <input id="file-upload-bulk-edit-upload" - name="file_upload_bulk_edit_upload" + name="file-upload-bulk-edit-upload" class="form-control" type="file" + accept="text/tab-separated-values" required="required" /> </div> </div> |