diff options
| -rw-r--r-- | uploader/phenotypes/views.py | 61 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 32 |
2 files changed, 87 insertions, 6 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index ac36ec8..350c4ae 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") @@ -1008,3 +1009,63 @@ 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( + species: dict, + population: dict, + dataset: dict, + **kwargs +): + """Compute/Recompute the means for phenotypes in a particular population.""" + form = request.form + _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_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"])) diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 306dcce..6a261fc 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -46,12 +46,32 @@ </div> <div class="row"> - <p><a href="{{url_for('species.populations.phenotypes.add_phenotypes', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id)}}" - title="Add a bunch of phenotypes" - class="btn btn-primary">Add phenotypes</a></p> + <div class="col"> + <a href="{{url_for('species.populations.phenotypes.add_phenotypes', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id)}}" + title="Add a bunch of phenotypes" + class="btn btn-primary">Add phenotypes</a> + </div> + + <div class="col"> + <form id="frm-recompute-phenotype-means" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.recompute_means', + species_id=species['SpeciesId'], + population_id=population['Id'], + dataset_id=dataset['Id'])}}" + class="d-flex flex-row align-items-center flex-wrap" + style="display: inline;"> + <input type="submit" + title="Compute/Recompute the means for all phenotypes." + class="btn btn-info" + value="(rec/c)ompute means" + id="submit-frm-recompute-phenotype-means" /> + </form> + </div> </div> <div class="row"> |