diff options
Diffstat (limited to 'uploader/population')
| -rw-r--r-- | uploader/population/models.py | 22 | ||||
| -rw-r--r-- | uploader/population/views.py | 4 |
2 files changed, 19 insertions, 7 deletions
diff --git a/uploader/population/models.py b/uploader/population/models.py index d78a821..4d95065 100644 --- a/uploader/population/models.py +++ b/uploader/population/models.py @@ -26,13 +26,23 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: return tuple() +__GENERIC_POPULATION_FAMILIES__ = ( + "Reference Populations (replicate average, SE, N)", + "Crosses and Heterogeneous Stock (individuals)", + "Groups Without Genotypes") -def population_families(conn) -> tuple: +def population_families(conn, species_id: int) -> tuple[str]: """Fetch the families under which populations are grouped.""" with conn.cursor(cursorclass=DictCursor) as cursor: + paramstr = ", ".join(["%s"] * len(__GENERIC_POPULATION_FAMILIES__)) cursor.execute( - "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL") - return tuple(row["Family"] for row in cursor.fetchall()) + "SELECT DISTINCT(Family) FROM InbredSet " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL " + f"AND Family NOT IN ({paramstr})", + (species_id, *__GENERIC_POPULATION_FAMILIES__)) + return __GENERIC_POPULATION_FAMILIES__ + tuple( + row["Family"] for row in cursor.fetchall()) def population_genetic_types(conn) -> tuple: @@ -47,9 +57,11 @@ def population_genetic_types(conn) -> tuple: def save_population(cursor: mdb.cursors.Cursor, population_details: dict) -> dict: """Save the population details to the db.""" cursor.execute("SELECT DISTINCT(Family), FamilyOrder FROM InbredSet " - "WHERE Family IS NOT NULL AND Family != '' " + "WHERE SpeciesId=%s " + "AND Family IS NOT NULL AND Family != '' " "AND FamilyOrder IS NOT NULL " - "ORDER BY FamilyOrder ASC") + "ORDER BY FamilyOrder ASC", + (population_details["SpeciesId"],)) _families = { row["Family"]: int(row["FamilyOrder"]) for row in cursor.fetchall() diff --git a/uploader/population/views.py b/uploader/population/views.py index 270dd5f..87a33d9 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -100,7 +100,7 @@ def create_population(species_id: int): return render_template( "populations/create-population.html", species=species, - families = population_families(conn), + families = population_families(conn, species["SpeciesId"]), genetic_types = population_genetic_types(conn), mapping_methods=( {"id": "0", "value": "No mapping support"}, @@ -153,7 +153,7 @@ def create_population(species_id: int): "FullName": population_fullname, "InbredSetCode": request.form.get("population_code") or None, "Description": request.form.get("population_description") or None, - "Family": request.form.get("population_family") or None, + "Family": request.form.get("population_family").strip() or None, "MappingMethodId": request.form.get("population_mapping_method_id"), "GeneticType": request.form.get("population_genetic_type") or None }) |