diff options
Diffstat (limited to 'uploader/phenotypes/views.py')
| -rw-r--r-- | uploader/phenotypes/views.py | 150 |
1 files changed, 0 insertions, 150 deletions
diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index bc15f2d..97bcafe 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -987,156 +987,6 @@ def edit_phenotype_data(# pylint: disable=[unused-argument] xref_id=xref_id)) -def process_phenotype_data_for_download(pheno: dict) -> dict: - """Sanitise data for download.""" - return { - "UniqueIdentifier": f"phId:{pheno['Id']}::xrId:{pheno['xref_id']}", - **{ - key: val for key, val in pheno.items() - if key not in ("Id", "xref_id", "data", "Units") - }, - **{ - data_item["StrainName"]: data_item["value"] - for data_item in pheno.get("data", {}).values() - } - } - - -BULK_EDIT_COMMON_FIELDNAMES = [ - "UniqueIdentifier", - "Post_publication_description", - "Pre_publication_abbreviation", - "Pre_publication_description", - "Original_description", - "Post_publication_abbreviation", - "PubMed_ID" -] - - -@phenotypesbp.route( - "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" - "/<int:dataset_id>/edit-download", - 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 edit_download_phenotype_data(# pylint: disable=[unused-argument] - species: dict, - population: dict, - dataset: dict, - **kwargs -): - formdata = request.json - with database_connection(app.config["SQL_URI"]) as conn: - samples_list = [ - sample["Name"] for sample in samples_by_species_and_population( - conn, species["SpeciesId"], population["Id"])] - data = ( - process_phenotype_data_for_download(pheno) - for pheno in phenotypes_data_by_ids(conn, tuple({ - "population_id": population["Id"], - "phenoid": row["phenotype_id"], - "xref_id": row["xref_id"] - } for row in formdata))) - - with (tempfile.TemporaryDirectory( - prefix=app.config["TEMPORARY_DIRECTORY"]) as tmpdir): - filename = Path(tmpdir).joinpath("tempfile.tsv") - with open(filename, mode="w") as outfile: - outfile.write( - "# **DO NOT** delete the 'UniqueIdentifier' row. It is used " - "by the system to identify and edit the correct rows and " - "columns in the database.\n") - outfile.write( - "# The '…_description' fields are useful for you to figure out " - "what row you are working on. Changing any of this fields will " - "also update the database, so do be careful.\n") - outfile.write( - "# Leave a field empty to delete the value in the database.\n") - outfile.write( - "# Any line beginning with a '#' character is considered a " - "comment line. This line, and all the lines above it, are " - "all comment lines. Comment lines will be ignored.\n") - writer = csv.DictWriter(outfile, - fieldnames= ( - BULK_EDIT_COMMON_FIELDNAMES + - samples_list), - dialect="excel-tab") - writer.writeheader() - writer.writerows(data) - outfile.flush() - - return send_file( - filename, - mimetype="text/csv", - as_attachment=True, - download_name=secure_filename(f"{dataset['Name']}_data")) - - -@phenotypesbp.route( - "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" - "/<int:dataset_id>/edit-upload", - methods=["GET", "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 edit_upload_phenotype_data(# pylint: disable=[unused-argument] - species: dict, - population: dict, - dataset: dict, - **kwargs -): - if request.method == "GET": - return render_template( - "phenotypes/bulk-edit-upload.html", - species=species, - population=population, - dataset=dataset, - activelink="edit-phenotype") - - edit_file = save_file(request.files["file-upload-bulk-edit-upload"], - Path(app.config["UPLOAD_FOLDER"])) - - jobs_db = app.config["ASYNCHRONOUS_JOBS_SQLITE_DB"] - with sqlite3.connection(jobs_db) as conn: - job_id = uuid.uuid4() - job_cmd = [ - sys.executable, "-u", - "-m", "scripts.phenotypes_bulk_edit", - app.config["SQL_URI"], - jobs_db, - str(job_id), - "--log-level", - logging.getLevelName( - app.logger.getEffectiveLevel() - ).lower() - ] - app.logger.debug("Phenotype-edit, bulk-upload command: %s", job_cmd) - _job = gnlibs_jobs.launch_job( - gnlibs_jobs.initialise_job(conn, - job_id, - job_cmd, - "phenotype-bulk-edit", - extra_meta = { - "edit-file": str(edit_file), - "species-id": species["SpeciesId"], - "population-id": population["Id"], - "dataset-id": dataset["Id"] - }), - jobs_db, - f"{app.config['UPLOAD_FOLDER']}/job_errors", - worker_manager="gn_libs.jobs.launcher") - - - return redirect(url_for("background-jobs.job_status", - job_id=job_id, - job_type="phenotype-bulk-edit")) - - @phenotypesbp.route( "<int:species_id>/populations/<int:population_id>/phenotypes/datasets" "/<int:dataset_id>/load-data-success/<uuid:job_id>", |