diff options
| -rw-r--r-- | wqflask/wqflask/oauth2/client.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/oauth2/data.py | 68 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list-genotype.html | 167 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list-phenotype.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list.html | 2 |
5 files changed, 221 insertions, 23 deletions
diff --git a/wqflask/wqflask/oauth2/client.py b/wqflask/wqflask/oauth2/client.py index 70cdfbe2..999bbfc8 100644 --- a/wqflask/wqflask/oauth2/client.py +++ b/wqflask/wqflask/oauth2/client.py @@ -15,14 +15,15 @@ def oauth2_client(): scope=SCOPE, token_endpoint_auth_method="client_secret_post", token=session.get("oauth2_token")) -def oauth2_get(uri_path: str) -> Either: +def oauth2_get(uri_path: str, data: dict = {}) -> Either: token = session.get("oauth2_token") config = app.config client = OAuth2Session( config["OAUTH2_CLIENT_ID"], config["OAUTH2_CLIENT_SECRET"], token=token, scope=SCOPE) resp = client.get( - urljoin(config["GN_SERVER_URL"], uri_path)) + urljoin(config["GN_SERVER_URL"], uri_path), + data=data) if resp.status_code == 200: return Right(resp.json()) diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py index 963ab547..96acb2c2 100644 --- a/wqflask/wqflask/oauth2/data.py +++ b/wqflask/wqflask/oauth2/data.py @@ -18,6 +18,44 @@ def __render_template__(templatepath, **kwargs): return render_template( templatepath, **kwargs, user_privileges=user_privileges) +def __search_mrna__(query, template, **kwargs): + return __render_template__(template, **kwargs) + +def __search_genotypes__(query, template, **kwargs): + species_name = kwargs["species_name"] + datasets = oauth2_get( + "oauth2/data/search", + data = { + "query": query, + "dataset_type": "genotype", + "species_name": species_name + }).either( + lambda err: {"datasets_error": process_error(err)}, + lambda datasets: {"datasets": tuple({ + "index": idx, **dataset + } for idx,dataset in enumerate(datasets, start=1))}) + return __render_template__(template, **datasets, **kwargs) + +def __search_phenotypes__(query, template, **kwargs): + per_page = int(request.args.get("per_page", 500)) + species_name = kwargs["species_name"] + search_uri = (f"search/?type=phenotype&per_page={per_page}&query=" + f"species:{species_name}") + ( + f" AND ({query})" if bool(query) else "") + traits = oauth2_get(search_uri).either( + lambda err: {"traits_error": process_error(err)}, + lambda trts: {"traits": tuple({ + "index": idx, **trait + } for idx, trait in enumerate(trts, start=1))}) + + selected_traits = request.form.getlist("selected_traits") + + return __render_template__( + template, **traits, per_page=per_page, query=query, + selected_traits=selected_traits, + search_endpoint=urljoin(app.config["GN_SERVER_URL"], "search/"), + **kwargs) + @data.route("/<string:species_name>/<string:dataset_type>/list", methods=["GET", "POST"]) def list_data_by_species_and_dataset( @@ -25,31 +63,23 @@ def list_data_by_species_and_dataset( templates = { "mrna": "oauth2/data-list-mrna.html", "genotype": "oauth2/data-list-genotype.html", - "phenotype": "oauth2/data-list-phenotype.html"} + "phenotype": "oauth2/data-list-phenotype.html" + } + search_fns = { + "mrna": __search_mrna__, + "genotype": __search_genotypes__, + "phenotype": __search_phenotypes__ + } roles = oauth2_get("oauth2/user/roles").either( lambda err: {"roles_error": process_error(err)}, lambda roles: {"roles": roles}) - query = request.args.get("query", "") - per_page = int(request.args.get("per_page", 500)) - search_uri = (f"search/?type={dataset_type}&per_page={per_page}&query=" - f"species:{species_name}") + ( - f" AND ({query})" if bool(query) else "") - traits = oauth2_get(search_uri).either( - lambda err: {"traits_error": process_error(err)}, - lambda trts: {"traits": tuple({ - "index": idx, **trait - } for idx, trait in enumerate(trts, start=1))}) groups = oauth2_get("oauth2/group/list").either( lambda err: {"groups_error": process_error(err)}, lambda grps: {"groups": grps}) - - selected_traits = request.form.getlist("selected_traits") - - return __render_template__( - templates[dataset_type], **roles, **traits, **groups, - species_name=species_name, dataset_type=dataset_type, per_page=per_page, - query=query, selected_traits=selected_traits, - search_endpoint=urljoin(app.config["GN_SERVER_URL"], "search/")) + query = request.args.get("query", "") + return search_fns[dataset_type]( + query, templates[dataset_type], **roles, **groups, + species_name=species_name, dataset_type=dataset_type) @data.route("/list", methods=["GET", "POST"]) def list_data(): diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html new file mode 100644 index 00000000..6dbcbd38 --- /dev/null +++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html @@ -0,0 +1,167 @@ +{%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="min-width: 1250px;"> + {{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-genotypes"> + <legend>Link Genotype Traits to Group</legend> + + <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> + + <table id="tbl-link-genotypes" class="table-hover table-striped cell-border"> + <tbody> + <tr> + <td colspan="100%" align="center" style="text-align: center;"> + <br/><b><font size="4"> + <span class="glyphicon glyphicon-info-sign text-info"></span> + + There are no selected genotype datasets to link to the group. + </font></b><br /> + </td> + </tr> + </tbody> + </table> + + {%if groups | length > 0%} + <input type="submit" value="Link Selected" class="btn btn-primary" /> + {%else%} + <input type="submit" value="No group to link to" class="btn btn-warning" + disabled="disabled" /> + {%endif%} + </form> + </div> + + <div class="row"> + <span id="search-messages" class="alert-danger" style="display:none"></span> + <form id="frm-search-traits" + action="#" + method="POST"> + <legend>Search: Genotype</legend> + <input type="hidden" value="{{species_name}}" name="species" + id="txt-species" /> + <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"> + <table id="tbl-genotypes" class="table-hover table-striped cell-border"> + <tbody> + <tr> + <td colspan="100%" align="center"> + <br><b><font size="15">Loading...</font></b><br> + </td> + </tr> + </table> + </div> + + +</div> +{%endblock%} + +{%block js%} +<script language="javascript" type="text/javascript" + src="/js/DataTables/js/jquery.dataTables.min.js"></script> + +<script language="javascript" type="text/javascript" + src="/js/DataTablesExtensions/plugins/sorting/natural.js"></script> + +<script language="javascript" type="text/javascript" + src="/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js"> +</script> + +<script language="javascript" type="text/javascript" + src="/js/DataTablesExtensions/colResize/dataTables.colResize.js"> +</script> + +<script language="javascript" type="text/javascript" + src="/static/new/javascript/create_datatable.js"></script> + +<script language="javascript" type="text/javascript"> + var common_column_definitions = [ + {"title": "Index", "data": "index"}, + {"title": "Group", "data": "InbredSetName"}, + {"title": "Dataset", "data": "dataset_name"}, + {"title": "Dataset FullName", "data": "dataset_fullname"}, + {"title": "Dataset ShortName", "data": "dataset_shortname"} + ]; + + var search_column_definitions = [{"data": null, "render": function(data) { + return ( + '<input type="checkbox" name="geno_datasets" ' + + 'class="checkbox" value="' + + JSON.stringify(data) + '" />'); + }},].concat(common_column_definitions); + + var selected_column_definitions = [{"data": null, "render": function(data) { + return ( + '<input type="checkbox" name="selected_datasets" ' + + 'class="checkbox" value="' + + data.name + ':' + data.dataset + + '" />'); + }},].concat(common_column_definitions); + + var table_settings = { + "scrollY": "40vh", + "language": { + "emptyTable": "No datasets to display!", + "info": "Showing _START_ to _END_ of _TOTAL_ entries", + "infoEmpty": "No entries to show", + "loadingRecords": "Loading entries ..." + } + } + + $(document).ready(function() { + $("#frm-search-traits").submit(function(event) { + event.preventDefault(); + return false; + }); + /* $("#txt-query").keyup(debounced_search()); */ + create_table(tableId="tbl-genotypes", + tableData={{datasets | list | tojson}}, + columnDefs=search_column_definitions, + customSettings=table_settings); + create_table(tableId="tbl-link-genotypes", + tableData={{selected_datasets | list | tojson}}, + columnDefs=selected_column_definitions, + customSettings=table_settings); + }); +</script> +{%endblock%} diff --git a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html b/wqflask/wqflask/templates/oauth2/data-list-phenotype.html index 0e94bcfa..53c6ce8c 100644 --- a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html +++ b/wqflask/wqflask/templates/oauth2/data-list-phenotype.html @@ -2,7 +2,7 @@ {%from "oauth2/profile_nav.html" import profile_nav%} {%from "oauth2/display_error.html" import display_error%} -{%block title%}View User{%endblock%} +{%block title%}Link Data: Phenotype{%endblock%} {%block css%} <link rel="stylesheet" type="text/css" diff --git a/wqflask/wqflask/templates/oauth2/data-list.html b/wqflask/wqflask/templates/oauth2/data-list.html index b7c526c6..8a8f6694 100644 --- a/wqflask/wqflask/templates/oauth2/data-list.html +++ b/wqflask/wqflask/templates/oauth2/data-list.html @@ -1,7 +1,7 @@ {%extends "base.html"%} {%from "oauth2/profile_nav.html" import profile_nav%} {%from "oauth2/display_error.html" import display_error%} -{%block title%}View User{%endblock%} +{%block title%}Link Data{%endblock%} {%block content%} <div class="container" style="min-width: 1250px;"> {{profile_nav("data", user_privileges)}} |