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-rw-r--r--qc_app/db/datasets.py15
-rw-r--r--qc_app/templates/rqtl2/summary-info.html28
-rw-r--r--qc_app/upload/rqtl2.py25
3 files changed, 66 insertions, 2 deletions
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 5816146..448db18 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -1,5 +1,6 @@
"""Functions for accessing the database relating to datasets."""
from datetime import date
+from typing import Optional
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
@@ -109,7 +110,7 @@ def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-argu
}
cursor.execute(
"""
- insert into ProbeSetFreeze(
+ INSERT INTO ProbeSetFreeze(
ProbeFreezeId, AvgId, Name, Name2, FullName, ShortName,
CreateTime, public, DataScale)
VALUES(
@@ -118,3 +119,15 @@ def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-argu
""",
dataset)
return {**dataset, "datasetid": cursor.lastrowid}
+
+def probeset_dataset_by_id(
+ conn: mdb.Connection, datasetid: int) -> Optional[dict]:
+ """Fetch a ProbeSet dataset by its ID"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM ProbeSetFreeze WHERE Id=%s",
+ (datasetid,))
+ result = cursor.fetchone()
+ if bool(result):
+ return dict(result)
+
+ return None
diff --git a/qc_app/templates/rqtl2/summary-info.html b/qc_app/templates/rqtl2/summary-info.html
index c3a2ac0..3882c9c 100644
--- a/qc_app/templates/rqtl2/summary-info.html
+++ b/qc_app/templates/rqtl2/summary-info.html
@@ -21,6 +21,34 @@
<dt>Genotype Dataset</dt>
<dd>{{geno_dataset.Name}} ({{geno_dataset.FullName}})</dd>
+
+ <dt>ProbeSet Study</dt>
+ <dd>{{probe_study.Name}} ({{probe_study.FullName}})</dd>
+
+ <dt>ProbeSet Dataset</dt>
+ <dd>{{probe_dataset.Name2}} ({{probe_dataset.FullName}})</dd>
</dl>
+<form id="frm:confirm-rqtl2bundle-details"
+ action="{{url_for('upload.rqtl2.confirm_bundle_details',
+ species_id=species.SpeciesId,
+ population_id=population.InbredSetId)}}"
+ method="POST"
+ enctype="multipart/form-data">
+ <legend class="heading">Create ProbeSet dataset</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}}" />
+ <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+ <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
+ <input type="hidden" name="probe-dataset-id" value="{{probe_dataset.Id}}" />
+
+ <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 0b446ac..7609fa9 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -34,6 +34,7 @@ from qc_app.db.datasets import (
probeset_study_by_id,
probeset_create_study,
+ probeset_dataset_by_id,
probeset_create_dataset,
probeset_datasets_by_study,
probeset_studies_by_species_and_population)
@@ -512,8 +513,30 @@ def select_dataset_info(species_id: int, population_id: int):
datasets=probeset_datasets_by_study(
conn, int(form["probe-study-id"])),
avgmethods=averaging_methods(conn))
+ probeset_study = probeset_study_by_id(
+ conn, int(form["probe-study-id"]))
+ probeset_dataset = probeset_dataset_by_id(
+ conn, int(form["probe-dataset-id"]))
return render_template("rqtl2/summary-info.html",
species=species,
population=population,
- geno_dataset=geno_dataset)
+ geno_dataset=geno_dataset,
+ probe_study=probeset_study,
+ probe_dataset=probeset_dataset)
+
+
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/confirm-bundle-details"),
+ methods=["POST"])
+def confirm_bundle_details(species_id: int, population_id: int):
+ """Confirm the details and trigger R/qtl2 bundle processing..."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(
+ conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+ "probe-study-id", "probe-dataset-id")
+ if bool(error):
+ return error
+
+ raise NotImplementedError