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-rw-r--r--qc_app/db/__init__.py1
-rw-r--r--qc_app/db/datasets.py16
-rw-r--r--qc_app/files.py5
-rw-r--r--qc_app/static/css/styles.css7
-rw-r--r--qc_app/templates/rqtl2/select-geno-dataset.html55
-rw-r--r--qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html36
-rw-r--r--qc_app/upload/rqtl2.py73
7 files changed, 190 insertions, 3 deletions
diff --git a/qc_app/db/__init__.py b/qc_app/db/__init__.py
index 0b48461..270f1a0 100644
--- a/qc_app/db/__init__.py
+++ b/qc_app/db/__init__.py
@@ -5,3 +5,4 @@ from .populations import (
population_by_id,
populations_by_species,
population_by_species_and_id)
+from .datasets import geno_dataset_by_species_and_population
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
new file mode 100644
index 0000000..3a27706
--- /dev/null
+++ b/qc_app/db/datasets.py
@@ -0,0 +1,16 @@
+"""Functions for accessing the database relating to datasets."""
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def geno_dataset_by_species_and_population(
+ conn: mdb.Connection,
+ speciesid: int,
+ populationid: int) -> tuple[dict, ...]:
+ """Retrieve all genotypes datasets by species and population"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT gf.* FROM InbredSet AS iset INNER JOIN GenoFreeze AS gf "
+ "ON iset.InbredSetId=gf.InbredSetId "
+ "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
+ {"sid": speciesid, "pid": populationid})
+ return tuple(dict(row) for row in cursor.fetchall())
diff --git a/qc_app/files.py b/qc_app/files.py
index 205a39c..baac5ec 100644
--- a/qc_app/files.py
+++ b/qc_app/files.py
@@ -3,6 +3,7 @@ import hashlib
from pathlib import Path
from typing import Union
from datetime import datetime
+from flask import current_app
from werkzeug.utils import secure_filename
from werkzeug.datastructures import FileStorage
@@ -21,3 +22,7 @@ def save_file(fileobj: FileStorage, upload_dir: Path) -> Union[Path, bool]:
filepath = Path(upload_dir, filename)
fileobj.save(filepath)
return filepath
+
+def fullpath(filename: str):
+ """Get a file's full path. This makes use of `flask.current_app`."""
+ return Path(current_app.config["UPLOAD_FOLDER"], filename).absolute()
diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css
index f4112d1..af5281e 100644
--- a/qc_app/static/css/styles.css
+++ b/qc_app/static/css/styles.css
@@ -71,6 +71,11 @@ fieldset {
background-color: #AAEEAA;
}
+.alert-warning {
+ background-color: #F9FAB6;
+ border-color: #E8E9C5;
+}
+
table {
margin-left: 1em;
border-collapse: collapse;
@@ -130,7 +135,7 @@ form fieldset:nth-child(odd) {
@media(min-width: 1250px) {
form {
- width: 40%;
+ width: 65ch;
}
.explainer {
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
new file mode 100644
index 0000000..c8623b3
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-geno-dataset.html
@@ -0,0 +1,55 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Genotypes Dataset</h2>
+
+<div class="explainer">
+ <p>Your R/qtl2 files bundle contains a "geno" specification. You will
+ therefore need to select from one of the existing Genotype datasets or
+ create a new one.</p>
+ <p>This is the dataset where your data will be organised under.</p>
+</div>
+
+<form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.rqtl2.select_geno_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ <legend class="heading">select from existing genotype datasets</legend>
+
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+
+ {{flash_messages("error-rqtl2")}}
+
+ <fieldset>
+ <legend>Datasets</legend>
+ <label for="select:geno-datasets">Dataset</label>
+ <select id="select:geno-datasets"
+ name="geno-datasets"
+ required="required"
+ {%if datasets | length == 0%}
+ disabled="disabled"
+ {%endif%}>
+ <option value="">Select dataset</option>
+ {%for dset in datasets%}
+ <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
+ {%endfor%}
+ </select>
+ </fieldset>
+
+ <fieldset>
+ <input type="submit"
+ value="select dataset"
+ class="btn btn-main form-col-2" />
+ </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
new file mode 100644
index 0000000..9269a3c
--- /dev/null
+++ b/qc_app/templates/rqtl2/upload-rqtl2-bundle-step-02.html
@@ -0,0 +1,36 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Upload R/qtl2 Bundle</h2>
+
+<div class="explainer">
+ <p>You have successfully uploaded the zipped bundle of R/qtl2 files.</p>
+ <p>The next step is to select the various extra information we need to figure
+ out what to do with the data. You will select/create the relevant studies
+ and/or datasets to organise the data in the steps that follow.</p>
+ <p>Click "Continue" below to proceed.</p>
+</div>
+
+<form id="frm-upload-rqtl2-bundle"
+ action="{{url_for('upload.rqtl2.select_dataset_info',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+ <input type="hidden" name="population_id"
+ value="{{population.InbredSetId}}" />
+ <input type="hidden" name="rqtl2_bundle_file"
+ value="{{rqtl2_bundle_file}}" />
+
+ {{flash_messages("error-rqtl2")}}
+
+ <fieldset>
+ <input type="submit" value="continue" class="btn btn-main form-col-2" />
+ </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 0eca6ae..e020d5a 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -1,5 +1,6 @@
"""Module to handle uploading of R/qtl2 bundles."""
from pathlib import Path
+from typing import Optional
from zipfile import ZipFile, is_zipfile
from flask import (
@@ -7,6 +8,7 @@ from flask import (
request,
url_for,
redirect,
+ Response,
Blueprint,
render_template,
current_app as app)
@@ -14,14 +16,15 @@ from flask import (
from r_qtl import r_qtl2
from r_qtl.errors import InvalidFormat
-from qc_app.files import save_file
+from qc_app.files import save_file, fullpath
from qc_app.dbinsert import species as all_species
from qc_app.db_utils import with_db_connection, database_connection
from qc_app.db import (
species_by_id,
save_population,
populations_by_species,
- population_by_species_and_id)
+ population_by_species_and_id,
+ geno_dataset_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@@ -158,3 +161,69 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
except (InvalidFormat, __RequestError__) as exc:
flash("".join(exc.args), "alert-error alert-danger error-rqtl2")
return this_page_with_errors
+
+def check_errors(conn, *args, **kwargs) -> Optional[Response]:
+ """Check for select errors in the forms and return a page to redirect to."""
+ species_id = kwargs.get("species_id") or request.form.get("species_id")
+ population_id = (kwargs.get("population_id")
+ or request.form.get("population_id"))
+ species = species_by_id(conn, species_id)
+ population = population_by_species_and_id(conn, species_id, population_id)
+
+ if "species" in args and not bool(species):
+ flash("Invalid species!", "alert-error error-rqtl2")
+ return redirect(url_for("upload.rqtl2.select_species"))
+
+ if "population" in args and not bool(population):
+ flash("Invalid Population!", "alert-error error-rqtl2")
+ return redirect(
+ url_for("upload.rqtl2.select_population", pgsrc="error"),
+ code=307)
+
+ if ("rqtl2_bundle_file" in args
+ and not bool(request.form.get("rqtl2_bundle_file"))):
+ flash("There is no file to process.",
+ "alert-error alert-danger error-rqtl2")
+ return redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
+ species_id=species_id,
+ population_id=population_id,
+ pgsrc="error"),
+ code=307)
+
+ return False
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/dataset-info"),
+ methods=["POST"])
+def select_dataset_info(species_id: int, population_id: int):
+ """
+ If `geno` files exist in the R/qtl2 bundle, prompt user to provide the
+ dataset the genotypes belong to.
+ """
+ form = request.form
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error_page = check_errors(conn, "species", "population", "rqtl2_bundle_file")
+ if bool(error_page):
+ return error_page
+
+ thefile = fullpath(form["rqtl2_bundle_file"])
+ with ZipFile(str(thefile), "r") as zfile:
+ cdata = r_qtl2.control_data(zfile)
+ if "geno" in cdata and not bool(form.get("geno_datasetid")):
+ return render_template(
+ "rqtl2/select-geno-dataset.html",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id),
+ rqtl2_bundle_file=thefile.name,
+ datasets=geno_dataset_by_species_and_population(
+ conn, species_id, population_id))
+
+ return "All data points collected. Should proceed to launching the job."
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/select-geno-dataset"),
+ methods=["POST"])
+def select_geno_dataset(species_id: int, population_id: int) -> Response:
+ """Select from existing geno datasets."""
+ return "IMPLEMENT THIS!!!"