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-rw-r--r--qc_app/upload/rqtl2.py75
1 files changed, 62 insertions, 13 deletions
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 3411f98..0d80776 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -19,6 +19,9 @@ from r_qtl.errors import InvalidFormat
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.tissues import all_tissues, tissue_by_id
+from qc_app.db.platforms import platform_by_id, platforms_by_species
from qc_app.db import (
species_by_id,
save_population,
@@ -28,6 +31,8 @@ from qc_app.db.datasets import (
geno_dataset_by_id,
geno_datasets_by_species_and_population,
+ probeset_study_by_id,
+ probeset_create_study,
probeset_datasets_by_study,
probeset_studies_by_species_and_population)
@@ -311,17 +316,59 @@ def select_probeset_study(species_id: int, population_id: int):
return error
summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
- species=species_by_id(conn, species_id),
- population=population_by_species_and_id(
- conn, species_id, population_id)),
+ species_id=species_id,
+ population_id=population_id),
code=307)
- if not bool(probe_study_by_id(conn, int(request.form["probe-study-id"]))):
+ if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
flash("Invalid study selected!", "alert-error alert-rqtl2")
return summary_page
return summary_page
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/create-probeset-study"),
+ methods=["POST"])
+def create_probeset_study(species_id: int, population_id: int):
+ """Create a new probeset study."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(
+ conn, "species", "population", "rqtl2_bundle_file", "geno-dataset")
+ if bool(error):
+ return error
+
+ form = request.form
+ select_study_page = redirect(
+ url_for("upload.rqtl2.select_probeset_study",
+ species_id=species_id,
+ population_id=population_id),
+ code=307)
+
+ if not (bool(form.get("platformid")) and
+ bool(platform_by_id(conn, int(form["platformid"])))):
+ flash("Invalid platform selected.", "alert-error alert-rqtl2")
+ return select_study_page
+
+ if not (bool(form.get("tissueid")) and
+ bool(tissue_by_id(conn, int(form["tissueid"])))):
+ flash("Invalid tissue selected.", "alert-error alert-rqtl2")
+ return select_study_page
+
+ study = probeset_create_study(
+ conn, population_id, int(form["platformid"]), int(form["tissueid"]),
+ form["studyname"], form.get("studyfullname") or "",
+ form.get("studyshortname") or "")
+ return render_template(
+ "rqtl2/create-probe-study-success.html",
+ species=species_by_id(conn, species_id),
+ population=population_by_species_and_id(
+ conn, species_id, population_id),
+ rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
+ geno_dataset=geno_dataset_by_id(
+ conn,
+ int(request.form["geno-dataset-id"])),
+ study=study)
+
+@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):
@@ -359,17 +406,19 @@ def select_dataset_info(species_id: int, population_id: int):
rqtl2_bundle_file=thefile.name,
geno_dataset=geno_dataset,
studies=probeset_studies_by_species_and_population(
- conn, species_id, population_id))
+ conn, species_id, population_id),
+ platforms=platforms_by_species(conn, species_id),
+ tissues=all_tissues(conn))
if "pheno" in cdata and not bool(form.get("probe-dataset-id")):
- return render_template(
- "rqtl2/select-probeset-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- geno_dataset=geno_dataset,
- datasets=probeset_datasets_by_study(
- conn, int(form["probe-study-id"])))
+ return render_template(
+ "rqtl2/select-probeset-dataset.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ geno_dataset=geno_dataset,
+ datasets=probeset_datasets_by_study(
+ conn, int(form["probe-study-id"])))
return render_template("rqtl2/summary-info.html",
species=species,