From 61688c00e8734adee4d825571a9c43d926dca001 Mon Sep 17 00:00:00 2001 From: Frederick Muriuki Muriithi Date: Tue, 3 Sep 2024 14:55:48 -0500 Subject: Initialise the populations package and update references. --- uploader/__init__.py | 2 + uploader/db/__init__.py | 6 -- uploader/db/populations.py | 54 ---------- uploader/dbinsert.py | 2 +- uploader/expression_data/rqtl2.py | 8 +- uploader/expression_data/samples.py | 9 +- uploader/population/__init__.py | 3 + uploader/population/models.py | 54 ++++++++++ uploader/population/views.py | 120 +++++++++++++++++++++ uploader/static/css/styles.css | 2 +- uploader/templates/base.html | 1 + uploader/templates/populations/base.html | 12 +++ uploader/templates/populations/index.html | 16 +++ .../templates/populations/list-populations.html | 87 +++++++++++++++ uploader/templates/species/view-species.html | 3 +- 15 files changed, 305 insertions(+), 74 deletions(-) delete mode 100644 uploader/db/populations.py create mode 100644 uploader/population/__init__.py create mode 100644 uploader/population/models.py create mode 100644 uploader/population/views.py create mode 100644 uploader/templates/populations/base.html create mode 100644 uploader/templates/populations/index.html create mode 100644 uploader/templates/populations/list-populations.html (limited to 'uploader') diff --git a/uploader/__init__.py b/uploader/__init__.py index 347f170..5028f79 100644 --- a/uploader/__init__.py +++ b/uploader/__init__.py @@ -10,6 +10,7 @@ from flask_session import Session from uploader.oauth2.client import user_logged_in, authserver_authorise_uri from .base_routes import base +from .population import popbp from .species import speciesbp from .dbinsert import dbinsertbp from .oauth2.views import oauth2 @@ -83,6 +84,7 @@ def create_app(): app.register_blueprint(base, url_prefix="/") app.register_blueprint(oauth2, url_prefix="/oauth2") app.register_blueprint(speciesbp, url_prefix="/species") + app.register_blueprint(popbp, url_prefix="/populations") app.register_blueprint(dbinsertbp, url_prefix="/dbinsert") app.register_blueprint(exprdatabp, url_prefix="/expression-data") diff --git a/uploader/db/__init__.py b/uploader/db/__init__.py index 36e93e8..d2b1d9d 100644 --- a/uploader/db/__init__.py +++ b/uploader/db/__init__.py @@ -1,8 +1,2 @@ """Database functions""" -from .species import species, species_by_id -from .populations import ( - save_population, - population_by_id, - populations_by_species, - population_by_species_and_id) from .datasets import geno_datasets_by_species_and_population diff --git a/uploader/db/populations.py b/uploader/db/populations.py deleted file mode 100644 index 4485e52..0000000 --- a/uploader/db/populations.py +++ /dev/null @@ -1,54 +0,0 @@ -"""Functions for accessing the database relating to species populations.""" -import MySQLdb as mdb -from MySQLdb.cursors import DictCursor - -def population_by_id(conn: mdb.Connection, population_id) -> dict: - """Get the grouping/population by id.""" - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s", - (population_id,)) - return cursor.fetchone() - -def population_by_species_and_id( - conn: mdb.Connection, species_id, population_id) -> dict: - """Retrieve a population by its identifier and species.""" - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s", - (species_id, population_id)) - return cursor.fetchone() - -def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: - "Retrieve group (InbredSet) information from the database." - with conn.cursor(cursorclass=DictCursor) as cursor: - query = "SELECT * FROM InbredSet WHERE SpeciesId=%s" - cursor.execute(query, (speciesid,)) - return tuple(cursor.fetchall()) - - return tuple() - -def save_population(conn: mdb.Connection, population_details: dict) -> dict: - """Save the population details to the db.""" - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute( - "INSERT INTO InbredSet(" - "InbredSetId, InbredSetName, Name, SpeciesId, FullName, " - "MenuOrderId, Description" - ") " - "VALUES (" - "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, " - "%(FullName)s, %(MenuOrderId)s, %(Description)s" - ")", - { - "MenuOrderId": 0, - "InbredSetId": 0, - **population_details - }) - new_id = cursor.lastrowid - cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s", - (new_id, new_id)) - return { - **population_details, - "Id": new_id, - "InbredSetId": new_id, - "population_id": new_id - } diff --git a/uploader/dbinsert.py b/uploader/dbinsert.py index 328ccc8..2116031 100644 --- a/uploader/dbinsert.py +++ b/uploader/dbinsert.py @@ -12,8 +12,8 @@ from flask import ( current_app as app) from uploader.authorisation import require_login +from uploader.population.models import populations_by_species from uploader.db_utils import with_db_connection, database_connection -from uploader.db import species, species_by_id, populations_by_species from uploader.species.models import species_by_id, all_species as species from . import jobs diff --git a/uploader/expression_data/rqtl2.py b/uploader/expression_data/rqtl2.py index 975fc1f..a855699 100644 --- a/uploader/expression_data/rqtl2.py +++ b/uploader/expression_data/rqtl2.py @@ -36,11 +36,9 @@ from uploader.authorisation import require_login from uploader.db.platforms import platform_by_id, platforms_by_species from uploader.db.averaging import averaging_methods, averaging_method_by_id from uploader.db.tissues import all_tissues, tissue_by_id, create_new_tissue -from uploader.db import ( - species_by_id, - save_population, - populations_by_species, - population_by_species_and_id,) +from uploader.population.models import (save_population, + populations_by_species, + population_by_species_and_id) from uploader.species.models import species_by_id from uploader.db.datasets import ( geno_dataset_by_id, diff --git a/uploader/expression_data/samples.py b/uploader/expression_data/samples.py index 0715d14..d430aa9 100644 --- a/uploader/expression_data/samples.py +++ b/uploader/expression_data/samples.py @@ -28,13 +28,10 @@ from uploader.db_utils import ( with_db_connection, database_connection, with_redis_connection) -from uploader.db import ( - species_by_id, - save_population, - population_by_id, - populations_by_species, - species as fetch_species) from uploader.species.models import species_by_id, all_species as fetch_species +from uploader.population.models import(save_population, + population_by_id, + populations_by_species) samples = Blueprint("samples", __name__) diff --git a/uploader/population/__init__.py b/uploader/population/__init__.py new file mode 100644 index 0000000..bf6bf3c --- /dev/null +++ b/uploader/population/__init__.py @@ -0,0 +1,3 @@ +"""Package to handle creation and management of Populations/InbredSets""" + +from .views import popbp diff --git a/uploader/population/models.py b/uploader/population/models.py new file mode 100644 index 0000000..4485e52 --- /dev/null +++ b/uploader/population/models.py @@ -0,0 +1,54 @@ +"""Functions for accessing the database relating to species populations.""" +import MySQLdb as mdb +from MySQLdb.cursors import DictCursor + +def population_by_id(conn: mdb.Connection, population_id) -> dict: + """Get the grouping/population by id.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM InbredSet WHERE InbredSetId=%s", + (population_id,)) + return cursor.fetchone() + +def population_by_species_and_id( + conn: mdb.Connection, species_id, population_id) -> dict: + """Retrieve a population by its identifier and species.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM InbredSet WHERE SpeciesId=%s AND Id=%s", + (species_id, population_id)) + return cursor.fetchone() + +def populations_by_species(conn: mdb.Connection, speciesid) -> tuple: + "Retrieve group (InbredSet) information from the database." + with conn.cursor(cursorclass=DictCursor) as cursor: + query = "SELECT * FROM InbredSet WHERE SpeciesId=%s" + cursor.execute(query, (speciesid,)) + return tuple(cursor.fetchall()) + + return tuple() + +def save_population(conn: mdb.Connection, population_details: dict) -> dict: + """Save the population details to the db.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "INSERT INTO InbredSet(" + "InbredSetId, InbredSetName, Name, SpeciesId, FullName, " + "MenuOrderId, Description" + ") " + "VALUES (" + "%(InbredSetId)s, %(InbredSetName)s, %(Name)s, %(SpeciesId)s, " + "%(FullName)s, %(MenuOrderId)s, %(Description)s" + ")", + { + "MenuOrderId": 0, + "InbredSetId": 0, + **population_details + }) + new_id = cursor.lastrowid + cursor.execute("UPDATE InbredSet SET InbredSetId=%s WHERE Id=%s", + (new_id, new_id)) + return { + **population_details, + "Id": new_id, + "InbredSetId": new_id, + "population_id": new_id + } diff --git a/uploader/population/views.py b/uploader/population/views.py new file mode 100644 index 0000000..cd5e20b --- /dev/null +++ b/uploader/population/views.py @@ -0,0 +1,120 @@ +"""Views dealing with populations/inbredsets""" +from flask import (flash, + request, + url_for, + redirect, + Blueprint, + current_app as app) + +from uploader.ui import make_template_renderer +from uploader.authorisation import require_login +from uploader.db_utils import database_connection +from uploader.species.models import (all_species, + species_by_id, + order_species_by_family) + +from .models import (save_population, + populations_by_species) + +__active_link__ = "populations" +popbp = Blueprint("populations", __name__) +render_template = make_template_renderer("populations") + + +@popbp.route("/", methods=["GET", "POST"]) +@require_login +def index(): + """Entry point for populations.""" + with database_connection(app.config["SQL_URI"]) as conn: + if not bool(request.args.get("species_id")): + return render_template( + "populations/index.html", + species=order_species_by_family(all_species(conn))) + species = species_by_id(conn, request.args.get("species_id")) + if not bool(species): + flash("Invalid species identifier provided!", "alert-danger") + return redirect(url_for("populations.index")) + return redirect(url_for("populations.list_species_populations", + species_id=species["SpeciesId"])) + +@popbp.route("/", methods=["GET"]) +@require_login +def list_species_populations(species_id: int): + """List a particular species' populations.""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + if not bool(species): + flash("No species was found for given ID.", "alert-danger") + return redirect(url_for("populations.index")) + return render_template( + "populations/list-populations.html", + species=species, + populations=populations_by_species(conn, species_id), + activelink="list-populations") + + +def valid_population_name(population_name) -> bool: + """Check whether the given name is a valid population name.""" + raise NotImplementedError("Please implement this…") + + +@popbp.route("//create-population/", methods=["GET", "POST"]) +@require_login +def create_population(species_id: int): + """Create a new population.""" + with database_connection(app.config["SQL_URI"]) as conn: + species = species_by_id(conn, species_id) + + if request.method == "GET": + return render_template( + "populations/create-population.html", + species=species, + continue_to=request.args.get("continue_uri")) + + error = False + + if not bool(species): + flash("You must select a species.", "alert-danger") + error = True + + population_name = request.form.get("population_name", "").strip() + if not bool(population_name): + flash("You must provide a name for the population!", "alert-danger") + error = True + + if not valid_population_name(population_name): + flash("The population name can only contain letters, numbers, " + "hyphens and underscores.", + "alert-danger") + error = True + + population_fullname = request.form.get("inbredset_fullname", "").strip() + if not bool(population_fullname): + flash("You MUST provide a Full Name for the population." + "alert-danger") + error = True + + if error: + return redirect(url_for("populations.create_population", + **dict(request.args))) + + new_population = save_population(conn, { + "SpeciesId": species["SpeciesId"], + "Name": population_name, + "InbredSetName": population_fullname, + "FullName": population_fullname, + "Family": request.form.get("inbredset_family") or None, + "Description": request.form.get("description") or None + }) + + return redirect(url_for("populations.view_population", + species_id=species["SpeciesId"], + population_id=new_population["InbredSetId"])) + + +@popbp.route("//populations/", + methods=["GET"]) +@require_login +def view_population(species_id: int, population_id: int): + """View the details of a population.""" + raise NotImplementedError("Please implement this too …") diff --git a/uploader/static/css/styles.css b/uploader/static/css/styles.css index 4aa776e..6d95fe6 100644 --- a/uploader/static/css/styles.css +++ b/uploader/static/css/styles.css @@ -7,7 +7,7 @@ body { grid-gap: 20px; font-family: Georgia, Garamond, serif; - font-style: normal;. + font-style: normal; } #header { diff --git a/uploader/templates/base.html b/uploader/templates/base.html index 7431767..fd6010b 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -45,6 +45,7 @@ diff --git a/uploader/templates/populations/base.html b/uploader/templates/populations/base.html new file mode 100644 index 0000000..1033927 --- /dev/null +++ b/uploader/templates/populations/base.html @@ -0,0 +1,12 @@ +{%extends "base.html"%} + +{%block breadcrumbs%} +
  • + Populations +
    • +{%block lvl3_breadcrumbs%}{%endblock%} +{%endblock%} diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html new file mode 100644 index 0000000..14cf547 --- /dev/null +++ b/uploader/templates/populations/index.html @@ -0,0 +1,16 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + + +{%block contents%} +
    + To continue, you need to select the species: + + {{select_species_form(url_for("populations.index"), species)}} +
    +{%endblock%} diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html new file mode 100644 index 0000000..bf6cf98 --- /dev/null +++ b/uploader/templates/populations/list-populations.html @@ -0,0 +1,87 @@ +{%extends "populations/base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "species/macro-select-species.html" import select_species_form%} + +{%block title%}Populations{%endblock%} + +{%block pagetitle%}Populations{%endblock%} + +{%block lvl3_breadcrumbs%} +
  • + List +
    • +{%endblock%} + + +{%block contents%} +
    +

    + The following populations/groups exist for the '{{species.FullName}}' + species. +

    +

    + Click on the population's name to select and continue using the population. +

    +
    + +
    +

    + If the population you need for the species '{{species.FullName}}' does not + exist, click on the "Create Population" button below to create a new one. +

    +

    + + Create Population + +

    +
    + +
    + + + + + + + + + + + + {%for population in populations%} + + + + + + {%else%} + + + + {%endfor%} + +
    Populations for {{species.FullName}}
    NameFull NameDescription
    + + {{population.Name}} + + {{population.FullName}}{{population.Description}}
    +

    + + There were no populations found for {{species.FullName}}! +

    +
    +
    +{%endblock%} + +{%block sidebarcontents%} +… maybe provide species details here, perhaps? … +{%endblock%} diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html index a0eb54b..0a3b0dd 100644 --- a/uploader/templates/species/view-species.html +++ b/uploader/templates/species/view-species.html @@ -60,7 +60,8 @@ title="Upload genotypes for {{species.FullName}}">Upload Genotypes
  • - Manage populations
    • -- cgit v1.2.3