diff options
Diffstat (limited to 'uploader/samples')
| -rw-r--r-- | uploader/samples/models.py | 13 | ||||
| -rw-r--r-- | uploader/samples/views.py | 25 |
2 files changed, 24 insertions, 14 deletions
diff --git a/uploader/samples/models.py b/uploader/samples/models.py index d7d5384..1e9293f 100644 --- a/uploader/samples/models.py +++ b/uploader/samples/models.py @@ -15,11 +15,11 @@ def samples_by_species_and_population( """Fetch the samples by their species and population.""" with conn.cursor(cursorclass=DictCursor) as cursor: cursor.execute( - "SELECT iset.InbredSetId, s.* FROM InbredSet AS iset " - "INNER JOIN StrainXRef AS sxr ON iset.InbredSetId=sxr.InbredSetId " - "INNER JOIN Strain AS s ON sxr.StrainId=s.Id " - "WHERE s.SpeciesId=%(species_id)s " - "AND iset.InbredSetId=%(population_id)s", + "SELECT InbredSet.InbredSetId, Strain.* FROM InbredSet " + "INNER JOIN StrainXRef ON InbredSet.InbredSetId=StrainXRef.InbredSetId " + "INNER JOIN Strain ON StrainXRef.StrainId=Strain.Id " + "WHERE Strain.SpeciesId=%(species_id)s " + "AND InbredSet.InbredSetId=%(population_id)s", {"species_id": species_id, "population_id": population_id}) return tuple(cursor.fetchall()) @@ -34,8 +34,7 @@ def read_samples_file(filepath, separator: str, firstlineheading: bool, **kwargs else ("Name", "Name2", "Symbol", "Alias")), delimiter=separator, quotechar=kwargs.get("quotechar", '"')) - for row in reader: - yield row + yield from reader def save_samples_data(conn: mdb.Connection, diff --git a/uploader/samples/views.py b/uploader/samples/views.py index 27e5d3c..4705a96 100644 --- a/uploader/samples/views.py +++ b/uploader/samples/views.py @@ -96,7 +96,7 @@ def list_samples(species: dict, population: dict, **kwargs):# pylint: disable=[u activelink="list-samples") -def build_sample_upload_job(# pylint: disable=[too-many-arguments] +def build_sample_upload_job(# pylint: disable=[too-many-arguments, too-many-positional-arguments] speciesid: int, populationid: int, samplesfile: Path, @@ -159,7 +159,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma "alert-error") return samples_uploads_page - firstlineheading = (request.form.get("first_line_heading") == "on") + firstlineheading = request.form.get("first_line_heading") == "on" separator = request.form.get("separator", ",") if separator == "other": @@ -172,7 +172,7 @@ def upload_samples(species_id: int, population_id: int):#pylint: disable=[too-ma redisuri = app.config["REDIS_URL"] with Redis.from_url(redisuri, decode_responses=True) as rconn: - #TODO: Add a QC step here — what do we check? + #T0DO: Add a QC step here — what do we check? # 1. Does any sample in the uploaded file exist within the database? # If yes, what is/are its/their species and population? # 2. If yes 1. above, provide error with notes on which species and @@ -221,7 +221,10 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): if status == "error": return redirect(url_for( - "species.populations.samples.upload_failure", job_id=job_id)) + "species.populations.samples.upload_failure", + species_id=species["SpeciesId"], + population_id=population["Id"], + job_id=job_id)) error_filename = Path(jobs.error_filename( job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")) @@ -241,9 +244,14 @@ def upload_status(species: dict, population: dict, job_id: uuid.UUID, **kwargs): species=species, population=population), 400 -@samplesbp.route("/upload/failure/<uuid:job_id>", methods=["GET"]) + +@samplesbp.route("<int:species_id>/populations/<int:population_id>/" + "upload-samples/failure/<uuid:job_id>", + methods=["GET"]) @require_login -def upload_failure(job_id: uuid.UUID): +@with_population(species_redirect_uri="species.populations.samples.index", + redirect_uri="species.populations.samples.select_population") +def upload_failure(species: dict, population: dict, job_id: uuid.UUID, **kwargs):# pylint: disable=[unused-argument] """Display the errors of the samples upload failure.""" job = with_redis_connection(lambda rconn: jobs.job( rconn, jobs.jobsnamespace(), job_id)) @@ -257,4 +265,7 @@ def upload_failure(job_id: uuid.UUID): if stat.st_size > 0: return render_template("worker_failure.html", job_id=job_id) - return render_template("samples/upload-failure.html", job=job) + return render_template("samples/upload-failure.html", + species=species, + population=population, + job=job) |