diff options
Diffstat (limited to 'uploader/population')
| -rw-r--r-- | uploader/population/models.py | 26 | ||||
| -rw-r--r-- | uploader/population/views.py | 17 |
2 files changed, 39 insertions, 4 deletions
diff --git a/uploader/population/models.py b/uploader/population/models.py index 4485e52..782bc9f 100644 --- a/uploader/population/models.py +++ b/uploader/population/models.py @@ -26,21 +26,43 @@ def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: return tuple() + +def population_families(conn) -> tuple: + """Fetch the families under which populations are grouped.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT DISTINCT(Family) FROM InbredSet WHERE Family IS NOT NULL") + return tuple(row["Family"] for row in cursor.fetchall()) + + +def population_genetic_types(conn) -> tuple: + """Fetch the families under which populations are grouped.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT DISTINCT(GeneticType) FROM InbredSet WHERE GeneticType IS " + "NOT NULL") + return tuple(row["GeneticType"] for row in cursor.fetchall()) + + def save_population(conn: mdb.Connection, population_details: dict) -> dict: """Save the population details to the db.""" with conn.cursor(cursorclass=DictCursor) as cursor: + #TODO: Handle FamilyOrder here cursor.execute( "INSERT INTO InbredSet(" "InbredSetId, InbredSetName, Name, SpeciesId, FullName, " - "MenuOrderId, Description" + "public, MappingMethodId, GeneticType, Family, MenuOrderId, " + "InbredSetCode, Description" ") " "VALUES (" "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, " - "%(FullName)s, %(MenuOrderId)s, %(Description)s" + "%(FullName)s, %(public)s, %(MappingMethodId)s, %(GeneticType)s, " + "%(Family)s, %(MenuOrderId)s, %(InbredSetCode)s, %(Description)s" ")", { "MenuOrderId": 0, "InbredSetId": 0, + "public": 2, **population_details }) new_id = cursor.lastrowid diff --git a/uploader/population/views.py b/uploader/population/views.py index 84dffdb..5be19ae 100644 --- a/uploader/population/views.py +++ b/uploader/population/views.py @@ -18,7 +18,9 @@ from uploader.species.models import (all_species, order_species_by_family) from .models import (save_population, + population_families, populations_by_species, + population_genetic_types, population_by_species_and_id) __active_link__ = "populations" @@ -100,6 +102,14 @@ def create_population(species_id: int): return render_template( "populations/create-population.html", species=species, + families = population_families(conn), + genetic_types = population_genetic_types(conn), + mapping_methods=( + {"id": "0", "value": "No mapping support"}, + {"id": "1", "value": "GEMMA, QTLReaper, R/qtl"}, + {"id": "2", "value": "GEMMA"}, + {"id": "3", "value": "R/qtl"}, + {"id": "4", "value": "GEMMA, PLINK"}), activelink="create-population", **error_values) @@ -142,8 +152,11 @@ def create_population(species_id: int): "Name": population_name, "InbredSetName": population_fullname, "FullName": population_fullname, - "Family": request.form.get("inbredset_family") or None, - "Description": request.form.get("population_description") or None + "InbredSetCode": request.form.get("population_code") or None, + "Description": request.form.get("population_description") or None, + "Family": request.form.get("population_family") or None, + "MappingMethodId": request.form.get("population_mapping_method_id"), + "GeneticType": request.form.get("population_genetic_type") or None }) return redirect(url_for("species.populations.view_population", |