diff options
| -rw-r--r-- | wqflask/wqflask/oauth2/data.py | 46 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list-genotype.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list-mrna.html | 166 |
3 files changed, 207 insertions, 7 deletions
diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py index 03fde15f..6804dafa 100644 --- a/wqflask/wqflask/oauth2/data.py +++ b/wqflask/wqflask/oauth2/data.py @@ -20,7 +20,20 @@ def __render_template__(templatepath, **kwargs): templatepath, **kwargs, user_privileges=user_privileges) def __search_mrna__(query, template, **kwargs): - return __render_template__(template, **kwargs) + species_name = kwargs["species_name"] + search_uri = urljoin(app.config["GN_SERVER_URL"], "oauth2/data/search") + print(f"SEARCHING FOR mrna") + datasets = oauth2_get( + "oauth2/data/search", + json = { + "query": query, + "dataset_type": "mrna", + "species_name": species_name, + "selected": __selected_datasets__() + }).either( + lambda err: {"datasets_error": process_error(err)}, + lambda datasets: {"datasets": datasets}) + return __render_template__(template, search_uri=search_uri, **datasets, **kwargs) def __selected_datasets__(): if bool(request.json): @@ -70,12 +83,7 @@ def __search_phenotypes__(query, template, **kwargs): def json_search_genotypes() -> Response: def __handle_error__(err): error = process_error(err) - print(f"THE ERROR: {error}") return jsonify(error), error["status_code"] - - print(f"===============================================") - print(request.json) - print(f"===============================================") return oauth2_get( "oauth2/data/search", @@ -213,3 +221,29 @@ def link_genotype_data(): "selected": tuple(json.loads(dataset) for dataset in form.getlist("selected")) }).either(lambda err: __link_error__(process_error(err)), __link_success__) + + +@data.route("/link/mrna", methods=["POST"]) +def link_mrna_data(): + """Link mrna data to a group.""" + form = request.form + link_source_url = redirect(url_for("oauth2.data.list_data")) + if bool(form.get("species_name")): + link_source_url = redirect(url_for( + "oauth2.data.list_data_by_species_and_dataset", + species_name=form["species_name"], dataset_type="mrna")) + + def __link_error__(err): + flash(f"{err['error']}: {err['error_description']}", "alert-danger") + return link_source_url + + def __link_success__(success): + flash(success["description"], "alert-success") + return link_source_url + + return oauth2_post("oauth2/data/link/mrna", json={ + "species_name": form.get("species_name"), + "group_id": form.get("group_id"), + "selected": tuple(json.loads(dataset) for dataset + in form.getlist("selected")) + }).either(lambda err: __link_error__(process_error(err)), __link_success__) diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html index 47c21079..30ee0d27 100644 --- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html +++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html @@ -25,7 +25,7 @@ <div class="row"> <form id="frm-link-genotypes" method="POST" action="{{url_for('oauth2.data.link_genotype_data')}}"> - <legend>Link Genotype Traits to Group</legend> + <legend>Link Genotype Datasets to Group</legend> <input type="hidden" name="species_name" value="{{species_name}}" /> diff --git a/wqflask/wqflask/templates/oauth2/data-list-mrna.html b/wqflask/wqflask/templates/oauth2/data-list-mrna.html new file mode 100644 index 00000000..1c22f65c --- /dev/null +++ b/wqflask/wqflask/templates/oauth2/data-list-mrna.html @@ -0,0 +1,166 @@ +{%extends "base.html"%} +{%from "oauth2/profile_nav.html" import profile_nav%} +{%from "oauth2/display_error.html" import display_error%} + +{%block title%}Link Data: Genotype{%endblock%} + +{%block css%} +<link rel="stylesheet" type="text/css" + href="/css/DataTables/css/jquery.dataTables.css" /> +<link rel="stylesheet" type="text/css" + href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" /> +<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> +{%endblock%} + +{%block content%} +<div class="container" style="width: 98%;"> + {{profile_nav("data", user_privileges)}} + + {{flash_me()}} + + <div class="row"> + <noscript>This page needs javascript to work correctly</noscript> + </div> + + <div class="row"> + <form id="frm-link-mrna" method="POST" + action="{{url_for('oauth2.data.link_mrna_data')}}"> + <legend>Link mRNA Assay Datasets to Group</legend> + + <input type="hidden" name="species_name" value="{{species_name}}" /> + + <div class="form-group"> + <label for="select-group">Group</label> + <select id="select-group" name="group_id" required="required" + class="form-control"> + <option value="">Select group</option> + {%for group in groups%} + <option value="{{group.group_id}}">{{group.group_name}}</option> + {%endfor%} + </select> + </div> + + <div class="form-group"> + <table id="tbl-link-mrna" + class="table-hover table-striped cell-border dataTable no-footer" + data-selected-datasets='{{selected_datasets | list | tojson}}'> + <thead> + <tr> + <th>Deselect</th> + <th>Group</th> + <th>Dataset Name</th> + <th>Dataset FullName</th> + <th>Dataset ShortName</th> + </tr> + </thead> + <tbody> + {%for dataset in selected_datasets%} + <tr> + <td> + <input type="checkbox" class="checkbox checkbox-selected" + name="selected" + value='{{dataset | tojson}}' /> + </td> + <td>{{dataset.dataset_name}}</td> + <td>{{dataset.dataset_fullname}}</td> + <td>{{dataset.dataset_shortname}}</td> + </tr> + {%else%} + <tr> + <td colspan="100%" align="center"> + <span class="glyphicon glyphicon-info-sign text-info"></span> +   + No datasets selected for linking. + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> + + <div class="form-group text-center"> + <input type="submit" value="Link Selected" + class="btn btn-primary" + style="border-top: 0.3em;" + {%if groups | length <= 0 or selected_datasets | length <= 0%} + disabled="disabled" + {%endif%} /> + </div> + </form> + </div> + + <div class="row"> + <span id="search-messages" class="alert-danger" style="display:none"></span> + <form id="frm-search" + action="{{search_uri}}" + method="POST"> + <legend>Search: mRNA Assay</legend> + <input type="hidden" value="{{species_name}}" name="species" + id="txt-species-name" /> + <input type="hidden" value="{{dataset_type}}" name="dataset_type" + id="txt-dataset-type" /> + <input type="hidden" value="{{per_page}}" name="per_page" + id="txt-per-page" /> + + <div class="form-group"> + <label for="txt-query">Dataset Search String</label> + <input type="text" id="txt-query" name="query" class="form-control" + value="{{query}}"/> + </div> + </form> + </div> + + <div class="row"> + <div id="search-error" class="text-danger" style="display: none;"> + <span class="glyphicon glyphicon-exclamation-sign"></span> +   + <span id="search-error-text"></span> + </div> + <table id="tbl-search" + class="table-hover table-striped cell-border dataTable no-footer" + data-datasets='{{datasets | list | tojson}}'> + <thead> + <tr> + <th>Select</th> + <th>Group</th> + <th>Study Name</th> + <th>Dataset Name</th> + <th>Dataset FullName</th> + <th>Dataset ShortName</th> + </tr> + </thead> + <tbody> + {%for dataset in datasets:%} + <tr> + <td> + <input type="checkbox" class="checkbox checkbox-search" + name="search_datasets" + value='{{dataset | tojson}}' /> + </td> + <td>{{dataset.InbredSetName}}</td> + <td>{{dataset.StudyName}}</td> + <td>{{dataset.dataset_name}}</td> + <td>{{dataset.dataset_fullname}}</td> + <td>{{dataset.dataset_shortname}}</td> + </tr> + {%else%} + <tr> + <td colspan="100%" align="center"> + <span class="glyphicon glyphicon-info-sign text-info"></span> +   + No datasets available for selection. + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> + + +</div> +{%endblock%} + +{%block js%} +<script src="/static/new/javascript/auth/search_mrna.js" + language="javascript" type="text/javascript"></script> +{%endblock%} |