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-rw-r--r--qc_app/db/averaging.py23
-rw-r--r--qc_app/db/datasets.py33
-rw-r--r--qc_app/templates/rqtl2/create-probe-dataset-success.html60
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html82
-rw-r--r--qc_app/upload/rqtl2.py65
5 files changed, 260 insertions, 3 deletions
diff --git a/qc_app/db/averaging.py b/qc_app/db/averaging.py
new file mode 100644
index 0000000..62bbe67
--- /dev/null
+++ b/qc_app/db/averaging.py
@@ -0,0 +1,23 @@
+"""Functions for db interactions for averaging methods"""
+from typing import Optional
+
+import MySQLdb as mdb
+from MySQLdb.cursors import DictCursor
+
+def averaging_methods(conn: mdb.Connection) -> tuple[dict, ...]:
+ """Fetch all available averaging methods"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM AvgMethod")
+ return tuple(dict(row) for row in cursor.fetchall())
+
+def averaging_method_by_id(
+ conn: mdb.Connection, averageid: int) -> Optional[dict]:
+ """Fetch the averaging method by its ID"""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ cursor.execute("SELECT * FROM AvgMethod WHERE Id=%s",
+ (averageid,))
+ result = cursor.fetchone()
+ if bool(result):
+ return dict(result)
+
+ return None
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py
index 5f6a2d5..5816146 100644
--- a/qc_app/db/datasets.py
+++ b/qc_app/db/datasets.py
@@ -85,3 +85,36 @@ def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-argume
cursor.execute("UPDATE ProbeFreeze SET ProbeFreezeId=%s",
(studyid,))
return {**studydata, "studyid": studyid}
+
+def probeset_create_dataset(conn: mdb.Connection,#pylint: disable=[too-many-arguments]
+ studyid: int,
+ averageid: int,
+ datasetname: str,
+ datasetfullname: str,
+ datasetshortname: str="",
+ public: bool = True,
+ datascale="log2") -> dict:
+ """Create a new ProbeSet dataset."""
+ with conn.cursor(cursorclass=DictCursor) as cursor:
+ dataset = {
+ "studyid": studyid,
+ "averageid": averageid,
+ "name2": datasetname,
+ "fname": datasetfullname,
+ "name": datasetshortname,
+ "sname": datasetshortname,
+ "today": date.today().isoformat(),
+ "public": 2 if public else 0,
+ "datascale": datascale
+ }
+ cursor.execute(
+ """
+ insert into ProbeSetFreeze(
+ ProbeFreezeId, AvgId, Name, Name2, FullName, ShortName,
+ CreateTime, public, DataScale)
+ VALUES(
+ %(studyid)s, %(averageid)s, %(name)s, %(name2)s, %(fname)s,
+ %(sname)s, %(today)s, %(public)s, %(datascale)s)
+ """,
+ dataset)
+ return {**dataset, "datasetid": cursor.lastrowid}
diff --git a/qc_app/templates/rqtl2/create-probe-dataset-success.html b/qc_app/templates/rqtl2/create-probe-dataset-success.html
new file mode 100644
index 0000000..33612c4
--- /dev/null
+++ b/qc_app/templates/rqtl2/create-probe-dataset-success.html
@@ -0,0 +1,60 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Create ProbeSet Dataset</h2>
+
+<div class="explainer">
+ <p>You successfully created the ProbeSet dataset with the following
+ information.
+ <dl>
+ <dt>Averaging Method</dt>
+ <dd>{{avgmethod.Name}}</dd>
+
+ <dt>ID</dt>
+ <dd>{{dataset.datasetid}}</dd>
+
+ <dt>Name</dt>
+ <dd>{{dataset.name2}}</dd>
+
+ <dt>Full Name</dt>
+ <dd>{{dataset.fname}}</dd>
+
+ <dt>Short Name</dt>
+ <dd>{{dataset.sname}}</dd>
+
+ <dt>Created On</dt>
+ <dd>{{dataset.today}}</dd>
+
+ <dt>DataScale</dt>
+ <dd>{{dataset.datascale}}</dd>
+ </dl>
+ </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">
+ <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="{{study.Id}}" />
+ <input type="hidden" name="probe-dataset-id" value="{{dataset.datasetid}}" />
+
+ <fieldset>
+ <input type="submit"
+ value="continue"
+ class="btn btn-main form-col-2" />
+ </fieldset>
+</form>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index 8b9e5ed..3e160fd 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -14,6 +14,7 @@
{{flash_all_messages()}}
+{%if datasets | length > 0%}
<form method="POST"
action="{{url_for('upload.rqtl2.select_probeset_dataset',
species_id=species.SpeciesId, population_id=population.Id)}}"
@@ -53,6 +54,85 @@
</fieldset>
</form>
-<p style="color: red; font-weight: bold;">Under Construction</p>
+<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+{%endif%}
+
+<form method="POST"
+ action="{{url_for('upload.rqtl2.create_probeset_dataset',
+ species_id=species.SpeciesId, population_id=population.Id)}}"
+ id="frm:create-probeset-dataset">
+ <legend class="heading">Create a new 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}}" />
+
+ <fieldset>
+ <label for="select:average">averaging method</label>
+ <select id="select:average"
+ name="averageid"
+ required="required">
+ <option value="">Select averaging method</option>
+ {%for avgmethod in avgmethods%}
+ <option value="{{avgmethod.Id}}">
+ {{avgmethod.Name}}
+ {%if avgmethod.Normalization%}
+ ({{avgmethod.Normalization}})
+ {%endif%}
+ </option>
+ {%endfor%}
+ </select>
+ </fieldset>
+
+ <fieldset>
+ <label for="txt:datasetname">Name</label>
+ <input type="text" id="txt:datasetname" name="datasetname"
+ required="required"
+ title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" />
+ </fieldset>
+
+ <fieldset>
+ <label for="txt:datasetfullname">Full Name</label>
+ <input type="text" id="txt:datasetfullname" name="datasetfullname"
+ required="required"
+ title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" />
+ </fieldset>
+
+ <fieldset>
+ <label for="txt:datasetshortname">Short Name</label>
+ <input type="text" id="txt:datasetshortname" name="datasetshortname"
+ title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" />
+ </fieldset>
+
+ <fieldset>
+ <input type="checkbox" id="chk:public" name="datasetpublic"
+ checked="checked"
+ title="Whether or not the dataset is accessible by the general public." />
+ <label for="chk:datasetpublic">Public?</label>
+ </fieldset>
+
+ <fieldset>
+ <label for="select:datasetdatascale">Data Scale</label>
+ <select id="select:datasetdatascale"
+ name="datasetdatascale"
+ required="required">
+ <option value="log2" selected="selected">log2</option>
+ <option value="z_score">z_score</option>
+ <option value="log2_ratio">log2_ratio</option>
+ <option value="linear">linear</option>
+ <option value="linear_positive">linear_positive</option>
+ </select>
+ </fieldset>
+
+ <fieldset>
+ <input type="submit"
+ value="create dataset"
+ 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 fc4e0e8..0b446ac 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -22,6 +22,7 @@ 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.averaging import averaging_methods, averaging_method_by_id
from qc_app.db import (
species_by_id,
save_population,
@@ -33,6 +34,7 @@ from qc_app.db.datasets import (
probeset_study_by_id,
probeset_create_study,
+ probeset_create_dataset,
probeset_datasets_by_study,
probeset_studies_by_species_and_population)
@@ -349,7 +351,7 @@ def select_probeset_dataset(species_id: int, population_id: int):
population_id=population_id),
code=307)
if not bool(probeset_study_by_id(conn, int(request.form["probe-study-id"]))):
- flash("Invalid dataset selected!", "alert-error alert-rqtl2")
+ flash("Invalid study selected!", "alert-error alert-rqtl2")
return summary_page
return summary_page
@@ -398,6 +400,64 @@ def create_probeset_study(species_id: int, population_id: int):
study=study)
@rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>"
+ "/rqtl2-bundle/create-probeset-dataset"),
+ methods=["POST"])
+def create_probeset_dataset(species_id: int, population_id: int):#pylint: disable=[too-many-return-statements]
+ """Create a new probeset dataset."""
+ 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
+
+ form = request.form
+ summary_page = redirect(url_for("upload.rqtl2.select_dataset_info",
+ species_id=species_id,
+ population_id=population_id),
+ code=307)
+ if not bool(form.get("averageid")):
+ flash("Averaging method not selected!", "alert-error alert-rqtl2")
+ return summary_page
+ if not bool(form.get("datasetname")):
+ flash("Dataset name not provided!", "alert-error alert-rqtl2")
+ return summary_page
+ if not bool(form.get("datasetfullname")):
+ flash("Dataset full name not provided!", "alert-error alert-rqtl2")
+ return summary_page
+
+ study = probeset_study_by_id(conn, int(form["probe-study-id"]))
+ if not bool(study):
+ flash("Invalid ProbeSet study provided!", "alert-error alert-rqtl2")
+ return summary_page
+
+ avgmethod = averaging_method_by_id(conn, int(form["averageid"]))
+ if not bool(avgmethod):
+ flash("Invalid averaging method provided!", "alert-error alert-rqtl2")
+ return summary_page
+
+ dset = probeset_create_dataset(conn,
+ int(form["probe-study-id"]),
+ int(form["averageid"]),
+ form["datasetname"],
+ form["datasetfullname"],
+ form["datasetshortname"],
+ form["datasetpublic"] == "on",
+ form.get("datasetdatascale", "log2"))
+ return render_template(
+ "rqtl2/create-probe-dataset-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,
+ avgmethod=avgmethod,
+ dataset=dset)
+
+@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):
@@ -450,7 +510,8 @@ def select_dataset_info(species_id: int, population_id: int):
geno_dataset=geno_dataset,
probe_study=probeset_study,
datasets=probeset_datasets_by_study(
- conn, int(form["probe-study-id"])))
+ conn, int(form["probe-study-id"])),
+ avgmethods=averaging_methods(conn))
return render_template("rqtl2/summary-info.html",
species=species,