diff options
| -rw-r--r-- | qc_app/db/averaging.py | 23 | ||||
| -rw-r--r-- | qc_app/db/datasets.py | 33 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/create-probe-dataset-success.html | 60 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-probeset-dataset.html | 82 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 65 |
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, |