Implement UI logic to trigger phenotype deletion job.

2 files changed, 105 insertions, 15 deletions

diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index 2cf0ca0..9b635e2 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -612,6 +612,11 @@ def load_phenotypes_success_handler(job):
         job_id=job["job_id"]))
 
 
+def proceed_to_job_status(job):
+    app.logger.debug("The new job: %s", job)
+    return redirect(url_for("background-jobs.job_status", job_id=job["job_id"]))
+
+
 @phenotypesbp.route(
     "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
     "/<int:dataset_id>/load-data-to-database",
@@ -654,11 +659,6 @@ def load_data_to_database(
         def __handle_error__(resp):
             return render_template("http-error.html", *resp.json())
 
-        def __handle_success__(load_job):
-            app.logger.debug("The phenotypes loading job: %s", load_job)
-            return redirect(url_for(
-                "background-jobs.job_status", job_id=load_job["job_id"]))
-
 
         return request_token(
             token_uri=urljoin(oauth2client.authserver_uri(), "auth/token"),
@@ -689,7 +689,7 @@ def load_data_to_database(
                 Path(f"{uploads_dir(app)}/job_errors"),
                 worker_manager="gn_libs.jobs.launcher",
                 loglevel=_loglevel)
-        ).either(__handle_error__, __handle_success__)
+        ).either(__handle_error__, proceed_to_job_status)
 
 
 def update_phenotype_metadata(conn, metadata: dict):
@@ -1158,6 +1158,12 @@ def rerun_qtlreaper_success_handler(job):
     return return_to_dataset_view_handler(job, "QTLReaper ran successfully!")
 
 
+def delete_phenotypes_success_handler(job):
+    """Handle success running the 'delete-phenotypes' script."""
+    return return_to_dataset_view_handler(
+        job, "Phenotypes deleted successfully.")
+
+
 @phenotypesbp.route(
     "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
     "/<int:dataset_id>/delete",
@@ -1174,7 +1180,21 @@ def delete_phenotypes(# pylint: disable=[unused-argument]
         **kwargs
 ):
     """Delete the specified phenotype data."""
-    with database_connection(app.config["SQL_URI"]) as conn:
+    _dataset_page = redirect(url_for(
+        "species.populations.phenotypes.view_dataset",
+        species_id=species["SpeciesId"],
+        population_id=population["Id"],
+        dataset_id=dataset["Id"]))
+
+    def __handle_error__(resp):
+        flash(
+            "Error retrieving authorisation token. Phenotype deletion "
+            "failed. Please try again later.")
+        return _dataset_page
+
+    _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]
+    with (database_connection(app.config["SQL_URI"]) as conn,
+          sqlite3.connection(_jobs_db) as jobsconn):
         form = request.form
         xref_ids = tuple(int(item) for item in set(form.getlist("xref_ids")))
 
@@ -1186,16 +1206,64 @@ def delete_phenotypes(# pylint: disable=[unused-argument]
                     population_id=population["Id"],
                     dataset_id=dataset["Id"]))
             case "delete":
-                # delete everything
-                # python3 -m scripts.phenotypes.delete_phenotypes <mariadburi> <authdburi> <speciesid> <populationid>
-                #
-                # delete selected phenotypes
-                # python3 -m scripts.phenotypes.delete_phenotypes <mariadburi> <authdburi> <speciesid> <populationid> --xref-ids-file=/path/to/file.txt
-                return "Would actually delete the data!"
+                _loglevel = logging.getLevelName(
+                    app.logger.getEffectiveLevel()).lower()
+                if form.get("confirm_delete_all_phenotypes", "") == "on":
+                    _cmd = ["--delete-all"]
+                else:
+                    # setup phenotypes xref_ids file
+                    _xref_ids_file = Path(
+                        app.config["SCRATCH_DIRECTORY"],
+                        f"delete-phenotypes-{uuid.uuid4()}.txt")
+                    with _xref_ids_file.open(mode="w", encoding="utf8") as ptr:
+                        ptr.write("\n".join(str(_id) for _id in xref_ids))
+
+                    _cmd = ["--xref_ids_file", str(_xref_ids_file)]
+
+                _job_id = uuid.uuid4()
+                return request_token(
+                    token_uri=urljoin(
+                        oauth2client.authserver_uri(), "auth/token"),
+                    user_id=session.user_details()["user_id"]
+                ).then(
+                    lambda token: gnlibs_jobs.initialise_job(
+                        jobsconn,
+                        _job_id,
+                        [
+                            sys.executable,
+                            "-u",
+                            "-m",
+                            "scripts.phenotypes.delete_phenotypes",
+                            "--log-level", _loglevel,
+                            app.config["SQL_URI"],
+                            str(species["SpeciesId"]),
+                            str(population["Id"]),
+                            str(dataset["Id"]),
+                            app.config["AUTH_SERVER_URL"],
+                            token["access_token"]] + _cmd,
+                        "delete-phenotypes",
+                        extra_meta={
+                            "species_id": species["SpeciesId"],
+                            "population_id": population["Id"],
+                            "dataset_id": dataset["Id"],
+                            "success_handler": (
+                                "uploader.phenotypes.views."
+                                "delete_phenotypes_success_handler")
+                        },
+                        external_id=session.logged_in_user_id())
+                ).then(
+                    lambda _job: gnlibs_jobs.launch_job(
+                        _job,
+                        _jobs_db,
+                        Path(f"{uploads_dir(app)}/job_errors"),
+                        worker_manager="gn_libs.jobs.launcher",
+                        loglevel=_loglevel)
+                ).either(__handle_error__, proceed_to_job_status)
             case _:
                 return render_template(
                     "phenotypes/confirm-delete-phenotypes.html",
                     species=species,
                     population=population,
                     dataset=dataset,
-                    phenotypes=xref_ids)
+                    phenotypes=[{"xref_id": xref_id}
+                                for xref_id in xref_ids])
diff --git a/uploader/templates/phenotypes/confirm-delete-phenotypes.html b/uploader/templates/phenotypes/confirm-delete-phenotypes.html
index b59fd7b..3b16698 100644
--- a/uploader/templates/phenotypes/confirm-delete-phenotypes.html
+++ b/uploader/templates/phenotypes/confirm-delete-phenotypes.html
@@ -56,9 +56,10 @@
       {%for phenotype in phenotypes%}
       <tr>
         <td>
-          <input id="chk-xref-id-{{phenotype}}"
+          <input id="chk-xref-id-{{phenotype.xref_id}}"
                  name="xref_ids"
                  type="checkbox"
+                 value="{{phenotype.xref_id}}"
                  class="chk-row-select" />
         </td>
         <td>{{phenotype}}</td>
@@ -166,6 +167,27 @@
       $("#btn-deselect-all-phenotypes").on("click", function(event) {
           dt.deselectAll();
       });
+
+      $("#btn-delete-phenotypes-selected").on("click", function(event) {
+          event.preventDefault();
+          form = $("#frm-delete-phenotypes-selected");
+          form.find(".dynamically-added-element").remove();
+          dt.rows({selected: true}).nodes().each(function(node, index) {
+              var xref_id = $(node)
+                  .find('input[type="checkbox"]:checked')
+                  .val();
+              var chk = $('<input type="checkbox">');
+              chk.attr("class", "dynamically-added-element");
+              chk.attr("value", xref_id);
+              chk.attr("name", "xref_ids");
+              chk.attr("style", "display: none");
+              chk.prop("checked", true);
+              form.append(chk);
+          });
+          form.append(
+              $('<input type="hidden" name="action" value="delete" />'));
+          form.submit();
+      })
   });
 </script>
 {%endblock%}