1 files changed, 72 insertions, 5 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py
index ac36ec8..7002ccd 100644
--- a/uploader/phenotypes/views.py
+++ b/uploader/phenotypes/views.py
@@ -60,6 +60,7 @@ from .models import (dataset_by_id,
                      datasets_by_population,
                      phenotype_publication_data)
 
+logger = logging.getLogger(__name__)
 phenotypesbp = Blueprint("phenotypes", __name__)
 render_template = make_template_renderer("phenotypes")
 
@@ -233,11 +234,6 @@ def view_phenotype(# pylint: disable=[unused-argument]
                                     population["Id"],
                                     dataset["Id"],
                                     xref_id)
-        def __non_empty__(value) -> bool:
-            if isinstance(value, str):
-                return value.strip() != ""
-            return bool(value)
-
         return render_template(
             "phenotypes/view-phenotype.html",
             species=species,
@@ -1008,3 +1004,74 @@ def load_data_success(
                                        fragment="")))
         except JobNotFound as _jnf:
             return render_template("jobs/job-not-found.html", job_id=job_id)
+
+
+@phenotypesbp.route(
+    "<int:species_id>/populations/<int:population_id>/phenotypes/datasets"
+    "/<int:dataset_id>/recompute-means",
+    methods=["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 recompute_means(# pylint: disable=[unused-argument]
+        species: dict,
+        population: dict,
+        dataset: dict,
+        **kwargs
+):
+    """Compute/Recompute the means for phenotypes in a particular population."""
+    _jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"]
+    _job_id = uuid.uuid4()
+    _xref_ids = tuple(int(item.split("_")[-1])
+                      for item in request.form.getlist("selected-phenotypes"))
+
+    _loglevel = logging.getLevelName(app.logger.getEffectiveLevel()).lower()
+    command = [
+        sys.executable,
+        "-u",
+        "-m",
+        "scripts.compute_phenotype_means",
+        app.config["SQL_URI"],
+        _jobs_db,
+        str(population["Id"]),
+        "--log-level",
+        _loglevel] + (
+            ["--cross-ref-ids", ",".join(str(_id) for _id in _xref_ids)]
+            if len(_xref_ids) > 0 else
+            [])
+    logger.debug("%s.recompute_means: command (%s)", __name__, command)
+
+    with sqlite3.connection(_jobs_db) as conn:
+        _job = gnlibs_jobs.launch_job(
+            gnlibs_jobs.initialise_job(
+                conn,
+                _job_id,
+                command,
+                "(re)compute-phenotype-means",
+                extra_meta={
+                    "species_id": species["SpeciesId"],
+                    "population_id": population["Id"],
+                    "dataset_id": dataset["Id"],
+                    "success_handler": (
+                        "uploader.phenotypes.views."
+                        "recompute_phenotype_means_success_handler")
+            }),
+            _jobs_db,
+            Path(f"{app.config['UPLOAD_FOLDER']}/job_errors"),
+            worker_manager="gn_libs.jobs.launcher",
+            loglevel=_loglevel)
+        return redirect(url_for("background-jobs.job_status",
+                                job_id=_job["job_id"]))
+
+
+def recompute_phenotype_means_success_handler(job):
+    """Handle loading new phenotypes into the database successfully."""
+    flash("Means computed successfully!", "alert alert-success")
+    return redirect(url_for(
+        "species.populations.phenotypes.view_dataset",
+        species_id=job["metadata"]["species_id"],
+        population_id=job["metadata"]["population_id"],
+        dataset_id=job["metadata"]["dataset_id"],
+        job_id=job["job_id"]))