Begin processing the uploadeded bulk-edit file.

1 files changed, 62 insertions, 1 deletions

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index a50a8e7..00da78b 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -958,4 +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>
+    """