diff options
| -rw-r--r-- | wqflask/wqflask/oauth2/data.py | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/oauth2/data-list-phenotype.html | 128 |
2 files changed, 97 insertions, 48 deletions
diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py index 432ca3b9..73ed171b 100644 --- a/wqflask/wqflask/oauth2/data.py +++ b/wqflask/wqflask/oauth2/data.py @@ -1,6 +1,9 @@ """Handle linking data to groups.""" +from urllib.parse import urljoin + from flask import ( - flash, request, url_for, redirect, Response, Blueprint, render_template) + flash, request, url_for, redirect, Response, Blueprint, render_template, + current_app as app) from .request_utils import process_error from .client import oauth2_get, oauth2_post @@ -26,11 +29,13 @@ def list_data_by_species_and_dataset( 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)) - traits = oauth2_get( - (f"search/?type={dataset_type}&per_page={per_page}&query=" - f"species:{species_name}")).either( - lambda err: {"traits_error": process_error(er)}, + 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))}) @@ -38,7 +43,7 @@ def list_data_by_species_and_dataset( return __render_template__( templates[dataset_type], **roles, **traits, species_name=species_name, dataset_type=dataset_type, per_page=per_page, - query=request.args.get("query", "")) + query=query, search_endpoint=urljoin(app.config["GN_SERVER_URL"], "search/")) @data.route("/list", methods=["GET", "POST"]) def list_data(): diff --git a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html b/wqflask/wqflask/templates/oauth2/data-list-phenotype.html index 3c58f275..5212a146 100644 --- a/wqflask/wqflask/templates/oauth2/data-list-phenotype.html +++ b/wqflask/wqflask/templates/oauth2/data-list-phenotype.html @@ -24,9 +24,10 @@ </div> <div class="row"> - <form id="frm-select-datatype" + <form id="frm-search-traits" action="#" method="POST"> + {{search_endpoint}} {%if dataset_type == "mrna"%} <legend>mRNA: Search</legend> {%else%} @@ -34,16 +35,20 @@ {{dataset_type}}: Search </legend> {%endif%} - <input type="hidden" value="{{species_name}}" name="species" /> - <input type="hidden" value="{{dataset_type}}" name="dataset_type" /> - <input type="hidden" value="{{per_page}}" name="per_page" /> + <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">Search</label> <div class="input-group"> - <span class="input-group-addon">species:{{species_name}}</span> + <span class="input-group-addon">species:{{species_name}} AND (</span> <input type="text" id="txt-query" name="query" class="form-control" value="{{query}}"/> + <span class="input-group-addon">)</span> </div> </div> </form> @@ -83,42 +88,81 @@ src="/static/new/javascript/create_datatable.js"></script> <script language="javascript" type="text/javascript"> - var traits = {{traits | list | tojson}}; - create_table( - tableId="tbl-phenotypes", tableData=traits, - columnDefs=[ - {"data": null, "render": function(data) { - return ( - '<input type="checkbox" name="pheno_traits" ' + - 'class="checkbox" value="' + - data.dataset + '::' + data.name + - '" />'); - }}, - {"title": "Index", "data": "index"}, - {"title": "Dataset", "data": "dataset_fullname"}, - {"title": "Group", "data": "group"}, - {"title": "Record", "data": null, "render": function(data) { - return ( - '<a target="_blank" href="/show_trait?trait_id=' + - data.name + '&dataset=' + data.dataset + - '">' + data.name + "</a>"); - }}, - {"title": "Description", "data": "description"}, - {"title": "Authors", "data": "authors"}, - {"title": "Year", "data": null, render: function(data) { - return ( - '<a target="_blank" href="' + data.pubmed_link + - '" >' + data.year + '</a>'); - }}, - {"title": "LRS", "data": null, "render": function(data) { - console.debug(data); - return data.lrs ? data.lrs.toFixed(4) : "N/A"; - }}, - {"title": "Peak Location", "data": null, "render": function(data) { - return 'Chr' + data.geno_chr + ': ' + data.geno_mb; - }}, - {"title": "Additive Effects", "data": null, "render": function(data) { - return data.additive ? data.additive.toFixed(4) : "N/A"; - }}]); + function init_table(traits) { + create_table( + tableId="tbl-phenotypes", tableData=traits, + columnDefs=[ + {"data": null, "render": function(data) { + return ( + '<input type="checkbox" name="pheno_traits" ' + + 'class="checkbox" value="' + + data.dataset + '::' + data.name + + '" />'); + }}, + {"title": "Index", "data": "index"}, + {"title": "Dataset", "data": "dataset_fullname"}, + {"title": "Group", "data": "group"}, + {"title": "Record", "data": null, "render": function(data) { + return ( + '<a target="_blank" href="/show_trait?trait_id=' + + data.name + '&dataset=' + data.dataset + + '">' + data.name + "</a>"); + }}, + {"title": "Description", "data": "description"}, + {"title": "Authors", "data": "authors"}, + {"title": "Year", "data": null, render: function(data) { + return ( + '<a target="_blank" href="' + data.pubmed_link + + '" >' + data.year + '</a>'); + }}, + {"title": "LRS", "data": null, "render": function(data) { + return data.lrs ? data.lrs.toFixed(4) : "N/A"; + }}, + {"title": "Peak Location", "data": null, "render": function(data) { + return 'Chr' + data.geno_chr + ': ' + data.geno_mb; + }}, + {"title": "Additive Effects", "data": null, "render": function(data) { + return data.additive ? data.additive.toFixed(4) : "N/A"; + }}]); + } + + function add_index(item, index) { + return {"index": index, ...item}; + } + + function do_search() { + /*vent.preventDefault();*/ + user_query = $("#txt-query").val(); + dataset_type = $("#txt-dataset-type").val(); + per_page = $("#txt-per-page").val(); + species = $("#txt-species").val(); + query = "species:" + species; + if (user_query.length > 2) { + query = query + " AND (" + user_query + ")"; + } + $.get( + ("{{search_endpoint}}?" + "type=" + dataset_type + "&" + "per_page=" + + per_page + "&query=" + query), + function (data, status) { + init_table(data.map(add_index)); + }); + } + + function debounced_search() { + var timeout; + return function search(event) { + clearTimeout(timeout); + timeout = setTimeout(do_search, 500); + }; + } + + $(document).ready(function() { + $("#frm-search-traits").submit(function(event) { + event.preventDefault(); + return false; + }); + $("#txt-query").keyup(debounced_search()) + init_table({{traits | list | tojson}}); + }); </script> {%endblock%} |