diff options
| -rw-r--r-- | qc_app/templates/rqtl2/select-probeset-dataset.html | 45 | ||||
| -rw-r--r-- | qc_app/upload/rqtl2.py | 44 |
2 files changed, 81 insertions, 8 deletions
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html index c0c6401..8b9e5ed 100644 --- a/qc_app/templates/rqtl2/select-probeset-dataset.html +++ b/qc_app/templates/rqtl2/select-probeset-dataset.html @@ -1,5 +1,5 @@ {%extends "base.html"%} -{%from "flash_messages.html" import flash_messages%} +{%from "flash_messages.html" import flash_all_messages%} {%block title%}Upload R/qtl2 Bundle{%endblock%} @@ -8,10 +8,51 @@ <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> + file(s). This data needs to be organised under a dataset.</p> <p>This page gives you the ability to do that.</p> </div> +{{flash_all_messages()}} + +<form method="POST" + action="{{url_for('upload.rqtl2.select_probeset_dataset', + species_id=species.SpeciesId, population_id=population.Id)}}" + id="frm:select-probeset-dataset"> + <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}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <fieldset> + <label for="select:probe-dataset">Dataset</label> + <select id="select:probe-dataset" + name="probe-dataset-id" + required="required" + {%if datasets | length == 0%}disabled="disabled"{%endif%}> + <option value="">Select a dataset</option> + {%for dataset in datasets%} + <option value={{dataset.Id}}> + {{dataset.Name}} + {%if dataset.FullName%} + -- ({{dataset.FullName}}) + {%endif%} + </option> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <input type="submit" + value="select dataset" + class="btn btn-main form-col-2" /> + </fieldset> +</form> + <p style="color: red; font-weight: bold;">Under Construction</p> {%endblock%} diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py index 0d80776..fc4e0e8 100644 --- a/qc_app/upload/rqtl2.py +++ b/qc_app/upload/rqtl2.py @@ -172,7 +172,7 @@ def upload_rqtl2_bundle(species_id: int, population_id: int): flash("".join(exc.args), "alert-error alert-rqtl2") return this_page_with_errors -def check_errors(conn, *args, **kwargs): +def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements] """Check for select errors in the forms and return a page to redirect to.""" species_id = kwargs.get("species_id") or request.form.get("species_id") population_id = (kwargs.get("population_id") @@ -208,14 +208,21 @@ def check_errors(conn, *args, **kwargs): pgsrc="error"), code=307) + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + population_id=population_id, + pgsrc="error"), + code=307) + 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 summary_page + + if ("probe-dataset-id" in args and + not bool(request.form.get("probe-dataset-id"))): + flash("No probeset dataset was selected!", "alert-error alert-rqtl2") + return summary_page return None @@ -326,6 +333,28 @@ def select_probeset_study(species_id: int, population_id: int): return summary_page @rqtl2.route(("/upload/species/<int:species_id>/population/<int:population_id>" + "/rqtl2-bundle/select-probeset-dataset"), + methods=["POST"]) +def select_probeset_dataset(species_id: int, population_id: int): + """Select or create a 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", "probe-dataset-id") + if bool(error): + return error + + summary_page = redirect(url_for("upload.rqtl2.select_dataset_info", + species_id=species_id, + 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") + 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): @@ -409,6 +438,8 @@ def select_dataset_info(species_id: int, population_id: int): conn, species_id, population_id), platforms=platforms_by_species(conn, species_id), tissues=all_tissues(conn)) + probeset_study = probeset_study_by_id( + conn, int(form["probe-study-id"])) if "pheno" in cdata and not bool(form.get("probe-dataset-id")): return render_template( @@ -417,6 +448,7 @@ def select_dataset_info(species_id: int, population_id: int): population=population, rqtl2_bundle_file=thefile.name, geno_dataset=geno_dataset, + probe_study=probeset_study, datasets=probeset_datasets_by_study( conn, int(form["probe-study-id"]))) |