diff options
Diffstat (limited to 'qc_app')
| -rw-r--r-- | qc_app/db/datasets.py | 38 | ||||
| -rw-r--r-- | qc_app/db/platforms.py | 25 | ||||
| -rw-r--r-- | qc_app/db/tissues.py | 22 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/create-probe-study-success.html | 53 | ||||
| -rw-r--r-- | qc_app/templates/rqtl2/select-probeset-study-id.html | 79 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 75 |
6 files changed, 272 insertions, 20 deletions
diff --git a/qc_app/db/datasets.py b/qc_app/db/datasets.py index 086c103..5f6a2d5 100644 --- a/qc_app/db/datasets.py +++ b/qc_app/db/datasets.py @@ -1,4 +1,6 @@ """Functions for accessing the database relating to datasets.""" +from datetime import date + import MySQLdb as mdb from MySQLdb.cursors import DictCursor @@ -43,9 +45,43 @@ def probeset_datasets_by_study(conn: mdb.Connection, (studyid,)) return tuple(dict(row) for row in cursor.fetchall()) -def probe_study_by_id(conn: mdb.Connection, studyid: int) -> dict: +def probeset_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()) + +def probeset_create_study(conn: mdb.Connection,#pylint: disable=[too-many-arguments] + populationid: int, + platformid: int, + tissueid: int, + studyname: str, + studyfullname: str = "", + studyshortname: str = ""): + """Create a new ProbeSet study.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + studydata = { + "platid": platformid, + "tissueid": tissueid, + "name": studyname, + "fname": studyfullname or studyname, + "sname": studyshortname, + "today": date.today().isoformat(), + "popid": populationid + } + cursor.execute( + """ + INSERT INTO ProbeFreeze( + ChipId, TissueId, Name, FullName, ShortName, CreateTime, + InbredSetId + ) VALUES ( + %(platid)s, %(tissueid)s, %(name)s, %(fname)s, %(sname)s, + %(today)s, %(popid)s + ) + """, + studydata) + studyid = cursor.lastrowid + cursor.execute("UPDATE ProbeFreeze SET ProbeFreezeId=%s", + (studyid,)) + return {**studydata, "studyid": studyid} diff --git a/qc_app/db/platforms.py b/qc_app/db/platforms.py new file mode 100644 index 0000000..cb527a7 --- /dev/null +++ b/qc_app/db/platforms.py @@ -0,0 +1,25 @@ +"""Handle db interactions for platforms.""" +from typing import Optional + +import MySQLdb as mdb +from MySQLdb.cursors import DictCursor + +def platforms_by_species( + conn: mdb.Connection, speciesid: int) -> tuple[dict, ...]: + """Retrieve platforms by the species""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM GeneChip WHERE SpeciesId=%s " + "ORDER BY GeneChipName ASC", + (speciesid,)) + return tuple(dict(row) for row in cursor.fetchall()) + +def platform_by_id(conn: mdb.Connection, platformid: int) -> Optional[dict]: + """Retrieve a platform by its ID""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM GeneChip WHERE Id=%s", + (platformid,)) + result = cursor.fetchone() + if bool(result): + return dict(result) + + return None diff --git a/qc_app/db/tissues.py b/qc_app/db/tissues.py new file mode 100644 index 0000000..ebf24fd --- /dev/null +++ b/qc_app/db/tissues.py @@ -0,0 +1,22 @@ +"""Handle db interactions for tissue.""" +from typing import Optional + +import MySQLdb as mdb +from MySQLdb.cursors import DictCursor + +def all_tissues(conn: mdb.Connection) -> tuple[dict, ...]: + """All available tissue.""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM Tissue ORDER BY TissueName") + return tuple(dict(row) for row in cursor.fetchall()) + +def tissue_by_id(conn: mdb.Connection, tissueid: int) -> Optional[dict]: + """Retrieve a tissue by its ID""" + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute("SELECT * FROM Tissue WHERE Id=%s", + (tissueid,)) + result = cursor.fetchone() + if bool(result): + return dict(result) + + return None diff --git a/qc_app/templates/rqtl2/create-probe-study-success.html b/qc_app/templates/rqtl2/create-probe-study-success.html new file mode 100644 index 0000000..1b85d0c --- /dev/null +++ b/qc_app/templates/rqtl2/create-probe-study-success.html @@ -0,0 +1,53 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Create ProbeSet Study</h2> + +<div class="explainer"> + <p>You successfully created the ProbeSet study with the following + information. + <dl> + <dt>ID</dt> + <dd>{{study.id}}</dd> + + <dt>Name</dt> + <dd>{{study.name}}</dd> + + <dt>Full Name</dt> + <dd>{{study.fname}}</dd> + + <dt>Short Name</dt> + <dd>{{study.sname}}</dd> + + <dt>Created On</dt> + <dd>{{study.today}}</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 study</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.studyid}}" /> + + <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-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html index bb31fde..34aa54e 100644 --- a/qc_app/templates/rqtl2/select-probeset-study-id.html +++ b/qc_app/templates/rqtl2/select-probeset-study-id.html @@ -1,5 +1,5 @@ {%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} +{%from "flash_messages.html" import flash_messages, flash_all_messages%} {%block title%}Upload R/qtl2 Bundle{%endblock%} @@ -12,9 +12,13 @@ <p>This page gives you the ability to do that.</p> </div> +{{flash_all_messages()}} + <form method="POST" - action="#"> - <legend class="heading">Select from existing ProbeSet datasets</legend> + action="{{url_for('upload.rqtl2.select_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-study"> + <legend class="heading">Select from existing ProbeSet studies</legend> <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> <input type="hidden" name="population_id" @@ -51,9 +55,72 @@ <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> + action="{{url_for('upload.rqtl2.create_probeset_study', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:create-probeset-study"> + <legend class="heading">Create new ProbeSet study</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:platform">Platform</label> + <select id="select:platform" + name="platformid" + required="required" + {%if platforms | length == 0%}disabled="disabled"{%endif%}> + <option value="">Select a platform</option> + {%for platform in platforms%} + <option value="{{platform.GeneChipId}}"> + {{platform.GeneChipName}} ({{platform.Name}}) + </option> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <label for="select:tissue">Tissue</label> + <select id="select:tissue" + name="tissueid" + required="required" + {%if tissues | length == 0%}disabled="disabled"{%endif%}> + <option value="">Select tissue</option> + {%for tissue in tissues%} + <option value="{{tissue.Id}}"> + {{tissue.TissueName}} ({{tissue.Short_Name}}) + </option> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <label for="txt:studyname">Study name</label> + <input type="text" id="txt:studyname" name="studyname" + placeholder="Name of the study. (Required)" + required="required" /> + </fieldset> + + <fieldset> + <label for="txt:studyfullname">Study name</label> + <input type="text" id="txt:studyfullname" name="studyfullname" + placeholder="Longer name of the study. (Optional)" /> + </fieldset> + + <fieldset> + <label for="txt:studyshortname">Study name</label> + <input type="text" id="txt:studyshortname" name="studyshortname" + placeholder="Shorter name of the study. (Optional)" /> + </fieldset> + + <fieldset> + <input type="submit" + value="create study" + 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 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, |