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-rw-r--r--qc_app/db/__init__.py2
-rw-r--r--qc_app/db/datasets.py30
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html17
-rw-r--r--qc_app/templates/rqtl2/select-probeset-study-id.html59
-rw-r--r--qc_app/upload/rqtl2.py132
5 files changed, 199 insertions, 41 deletions
diff --git a/qc_app/db/__init__.py b/qc_app/db/__init__.py
index 270f1a0..36e93e8 100644
--- a/qc_app/db/__init__.py
+++ b/qc_app/db/__init__.py
@@ -5,4 +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
+from .datasets import geno_datasets_by_species_and_population
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 8122cfa..086c103 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -2,7 +2,7 @@
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
-def geno_dataset_by_species_and_population(
+def geno_datasets_by_species_and_population(
conn: mdb.Connection,
speciesid: int,
populationid: int) -> tuple[dict, ...]:
@@ -21,3 +21,31 @@ def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
(dataset_id,))
return dict(cursor.fetchone())
+
+def probeset_studies_by_species_and_population(
+ conn: mdb.Connection,
+ speciesid: int,
+ populationid: int) -> tuple[dict, ...]:
+ """Retrieve all probesets"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute(
+ "SELECT pf.* FROM InbredSet AS iset INNER JOIN ProbeFreeze AS pf "
+ "ON iset.InbredSetId=pf.InbredSetId "
+ "WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
+ {"sid": speciesid, "pid": populationid})
+ return tuple(dict(row) for row in cursor.fetchall())
+
+def probeset_datasets_by_study(conn: mdb.Connection,
+ studyid: int) -> tuple[dict, ...]:
+ """Retrieve all probeset databases by study."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s",
+ (studyid,))
+ return tuple(dict(row) for row in cursor.fetchall())
+
+def probe_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
+ """Retrieve ProbeSet study by ID"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s",
+ (studyid,))
+ return dict(cursor.fetchone())
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
new file mode 100644
index 0000000..c0c6401
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -0,0 +1,17 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
+
+<div class="explainer">
+ <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+ file(s). This data needs to be organised under a dataset..</p>
+ <p>This page gives you the ability to do that.</p>
+</div>
+
+<p style="color: red; font-weight: bold;">Under Construction</p>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
new file mode 100644
index 0000000..bb31fde
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -0,0 +1,59 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Phenotype(ProbeSet) Study</h2>
+
+<div class="explainer">
+ <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
+ file(s). This data needs to be organised under a study.</p>
+ <p>This page gives you the ability to do that.</p>
+</div>
+
+<form method="POST"
+ action="#">
+ <legend class="heading">Select from existing ProbeSet 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}}" />
+ <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+ <fieldset>
+ <label for="select:probe-study">Study</label>
+ <select id="select:probe-study"
+ name="probe-study-id"
+ required="required"
+ {%if studies | length == 0%}disabled="disabled"{%endif%}>
+ <option value="">Select a study</option>
+ {%for study in studies%}
+ <option value={{study.Id}}>
+ {{study.Name}}
+ {%if study.FullName%}
+ -- ({{study.FullName}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+ </fieldset>
+
+ <fieldset>
+ <input type="submit"
+ value="select study"
+ class="btn btn-main form-col-2" />
+ </fieldset>
+</form>
+
+<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+
+<form method="POST"
+ action="#">
+ <legend class="heading">Create new ProbeSet dataset</legend>
+ <strong style="color: red;font-weight:bold;">Under construction</strong>
+</form>
+
+{%endblock%}
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 6ddc83f..3411f98 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -25,7 +25,11 @@ from qc_app.db import (
populations_by_species,
population_by_species_and_id,)
from qc_app.db.datasets import (
- geno_dataset_by_id, geno_dataset_by_species_and_population)
+ geno_dataset_by_id,
+ geno_datasets_by_species_and_population,
+
+ probeset_datasets_by_study,
+ probeset_studies_by_species_and_population)
rqtl2 = Blueprint("rqtl2", __name__)
@@ -199,44 +203,16 @@ def check_errors(conn, *args, **kwargs):
pgsrc="error"),
code=307)
- return None
-
-@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
-
- species = species_by_id(conn, species_id)
- population = population_by_species_and_id(
- conn, species_id, population_id)
- 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-dataset-id")):
- return render_template(
- "rqtl2/select-geno-dataset.html",
- species=species,
- population=population,
- rqtl2_bundle_file=thefile.name,
- datasets=geno_dataset_by_species_and_population(
- conn, species_id, population_id))
-
- geno_dataset = geno_dataset_by_id(
- conn, int(form["geno-dataset-id"]))
+ if ("probe-study-id" in args and
+ not bool(request.form.get("probe-study-id"))):
+ flash("No probeset study was selected!", "alert-error alert-rqtl2")
+ return redirect(url_for("upload.rqtl2.select_probeset_study",
+ species_id=species_id,
+ population_id=population_id,
+ pgsrc="error"),
+ code=307)
- return render_template("rqtl2/summary-info.html",
- species=species,
- population=population,
- geno_dataset=geno_dataset)
+ return None
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
"/rqtl2-bundle/select-geno-dataset"),
@@ -249,7 +225,7 @@ def select_geno_dataset(species_id: int, population_id: int):
if bool(error):
return error
- geno_dset = geno_dataset_by_species_and_population(
+ geno_dset = geno_datasets_by_species_and_population(
conn, species_id, population_id)
if not bool(geno_dset):
flash("No genotype dataset was provided!",
@@ -321,3 +297,81 @@ def create_geno_dataset(species_id: int, population_id: int):
conn, species_id, population_id),
rqtl2_bundle_file=request.form["rqtl2_bundle_file"],
geno_dataset={**new_dataset, "id": cursor.lastrowid})
+
+@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/select-probeset-study"),
+ methods=["POST"])
+def select_probeset_study(species_id: int, population_id: int):
+ """Select or create a probeset study."""
+ with database_connection(app.config["SQL_URI"]) as conn:
+ error = check_errors(
+ conn, "species", "population", "rqtl2_bundle_file", "geno-dataset",
+ "probe-study-id")
+ if bool(error):
+ 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)),
+ code=307)
+ if not bool(probe_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/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
+
+ species = species_by_id(conn, species_id)
+ population = population_by_species_and_id(
+ conn, species_id, population_id)
+ 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-dataset-id")):
+ return render_template(
+ "rqtl2/select-geno-dataset.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ datasets=geno_datasets_by_species_and_population(
+ conn, species_id, population_id))
+ geno_dataset = geno_dataset_by_id(conn, int(form["geno-dataset-id"]))
+
+ if "pheno" in cdata and not bool(form.get("probe-study-id")):
+ return render_template(
+ "rqtl2/select-probeset-study-id.html",
+ species=species,
+ population=population,
+ rqtl2_bundle_file=thefile.name,
+ geno_dataset=geno_dataset,
+ studies=probeset_studies_by_species_and_population(
+ conn, species_id, population_id))
+
+ 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/summary-info.html",
+ species=species,
+ population=population,
+ geno_dataset=geno_dataset)