diff options
Diffstat (limited to 'uploader/genotypes')
| -rw-r--r-- | uploader/genotypes/models.py | 21 | ||||
| -rw-r--r-- | uploader/genotypes/views.py | 29 |
2 files changed, 41 insertions, 9 deletions
diff --git a/uploader/genotypes/models.py b/uploader/genotypes/models.py index 29acd0b..1fe5929 100644 --- a/uploader/genotypes/models.py +++ b/uploader/genotypes/models.py @@ -44,19 +44,26 @@ def genotype_markers( def genotype_dataset( conn: mdb.Connection, species_id: int, - population_id: int + population_id: int, + dataset_id: Optional[int] = None ) -> Optional[dict]: """Retrieve genotype datasets from the database. Apparently, you should only ever have one genotype dataset for a population. """ + _query = ( + "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset " + "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf " + "ON iset.Id=gf.InbredSetId " + "WHERE s.Id=%s AND iset.Id=%s") + _params = (species_id, population_id) + if bool(dataset_id): + _query = _query + " AND gf.Id=%s" + _params = _params + (dataset_id,) + with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute( - "SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset " - "ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf " - "ON iset.Id=gf.InbredSetId " - "WHERE s.Id=%s AND iset.Id=%s", - (species_id, population_id)) + cursor.execute(_query, _params) + debug_query(cursor) result = cursor.fetchone() if bool(result): return dict(result) diff --git a/uploader/genotypes/views.py b/uploader/genotypes/views.py index 8752b02..4158491 100644 --- a/uploader/genotypes/views.py +++ b/uploader/genotypes/views.py @@ -136,5 +136,30 @@ def list_markers(species_id: int): @require_login def view_dataset(species_id: int, population_id: int, dataset_id: int): """View details regarding a specific dataset.""" - return (f"Genotype dataset '{dataset_id}, from population '{population_id}' " - f"of species '{species_id}'.") + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("Invalid species provided!", "alert-danger") + return redirect(url_for("species.populations.genotypes.index")) + + population = population_by_species_and_id( + conn, species_id, population_id) + if not bool(population): + flash("Invalid population selected!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.select_population", + species_id=species_id)) + + dataset = genotype_dataset(conn, species_id, population_id, dataset_id) + if not bool(dataset): + flash("Could not find such a dataset!", "alert-danger") + return redirect(url_for( + "species.populations.genotypes.list_genotypes", + species_id=species_id, + population_id=population_id)) + + return render_template("genotypes/view-dataset.html", + species=species, + population=population, + dataset=dataset, + activelink="view-dataset") |