diff --git a/__init__.py b/__init__.py
index ad1ded5219dcd98184610046a3fa89f9f53843b8..4b0132c45f452626a336edf603e4ddbd57f34b16 100644
--- a/__init__.py
+++ b/__init__.py
@@ -170,25 +170,26 @@ def searchByUse():
def advancedSearch():
return render_template('advancedSearch.html', version=VERSION, alvisir=URL_ALVISIR)
+# Advanced Search page
+@app.route('/searchTaxon/')
+@app.route('/searchTaxon')
+def searchTaxon():
+ taxon = request.args.get('taxon', None)
+ habitat = request.args.get('habitat', None)
+ qps = request.args.get('qps', None)
+ sources = request.args.getlist("source", None)
+ return render_template('searchByTaxon0.html', taxon=taxon,
+ habitat=habitat,
+ qps=qps,
+ sources=sources,
+ version=VERSION,
+ alvisir=URL_ALVISIR)
+
# Database queries
-@app.route('/_get_list_taxon_habitat')
-def get_list_taxon_habitat():
- return(list_terms(app, conn, "list_taxon"))
-@app.route('/_get_list_habitat_taxon')
-def get_list_habitat_taxon():
- return(list_terms(app, conn, "list_habitat"))
-@app.route('/_get_list_taxon_phenotype')
-def get_list_taxon_phenotype():
- return(list_terms(app, conn, "list_taxon_phenotype"))
-@app.route('/_get_list_phenotype_taxon')
-def get_list_phenotype_taxon():
- return(list_terms(app, conn, "list_phenotype_taxon"))
-@app.route('/_get_list_taxon_use')
-def get_list_taxon_use():
- return(list_terms(app, conn, "list_taxon_use"))
-@app.route('/_get_list_use_taxon')
-def get_list_use_taxon():
- return(list_terms(app, conn, "list_use_taxon"))
+@app.route('/_get_list_term')
+def get_list_term():
+ table = request.args.get('table', None)
+ return(jsonify(list_terms(app, conn, table)))
@app.route('/_get_path')
def get_path():
diff --git a/database.py b/database.py
index 586c7bab3a41e37b3cdb77a0b314517e9e458b9d..013ab5c64214ade3690dd526e277b38c8e83f79f 100644
--- a/database.py
+++ b/database.py
@@ -503,7 +503,7 @@ def search_join_relations_by_ontobiotope_aggregate(app, conn, source, qps, leftt
# List of scientific name or class (taxon, habitat, phenotype, use)
def list_terms(app, conn, table):
- query = "SELECT name, path FROM " + table
+ query = 'SELECT name, path FROM ' + table + ' ORDER BY "name" ASC'
conn = get_db(app)
if conn != None:
cursor = conn.cursor()
@@ -511,9 +511,12 @@ def list_terms(app, conn, table):
cursor.execute(query)
except Exception as err:
print_psycopg2_exception(err)
- results = {}
+ results = []
for row in cursor.fetchall():
- results[row[0]] = row[1]
+ tmp = {}
+ tmp["name"] = row[0]
+ tmp["path"] = row[1].split("/")[-1]
+ results.append(tmp)
cursor.close()
return results
diff --git a/static/css/additional.css b/static/css/additional.css
index a47cf85658262cd8e06d38ee827cbeb8ea7329b5..33b8d00d478661573fad441ecd6c15d2c9f3f848 100644
--- a/static/css/additional.css
+++ b/static/css/additional.css
@@ -14,6 +14,19 @@
# limitations under the License.
*/
+.button-select {
+ background-color: #21517A;
+ border-color: #21517A;
+ color: #fff;
+ height: 34px;
+}
+
+.button-select-filter {
+ height: 34px;
+ align-items: center;
+ display: flex;
+}
+
/* Mimic .fa */
.glyphicon {
display: inline-block !important;
diff --git a/static/css/selectize.boostrap3.css b/static/css/selectize.boostrap3.css
index c5efd323e009c6c67d00e093bf581e519397b720..5323e9e02c0d61c638b44047b6fb10140d68ba17 100644
--- a/static/css/selectize.boostrap3.css
+++ b/static/css/selectize.boostrap3.css
@@ -1 +1,208 @@
-.selectize-control.plugin-drag_drop.multi>.selectize-input>div.ui-sortable-placeholder{visibility:visible !important;background:#f2f2f2 !important;background:rgba(0,0,0,.06) !important;border:0 none !important;box-shadow:inset 0 0 12px 4px #fff}.selectize-control.plugin-drag_drop .ui-sortable-placeholder::after{content:"!";visibility:hidden}.selectize-control.plugin-drag_drop .ui-sortable-helper{box-shadow:0 2px 5px rgba(0,0,0,.2)}.selectize-control .dropdown-header{position:relative;padding:6px 12px;border-bottom:1px solid #d0d0d0;background:#f8f8f8;border-radius:4px 4px 0 0}.selectize-control .dropdown-header-close{position:absolute;right:12px;top:50%;color:#333;opacity:.4;margin-top:-12px;line-height:20px;font-size:20px !important}.selectize-control .dropdown-header-close:hover{color:#000}.selectize-dropdown.plugin-optgroup_columns .selectize-dropdown-content{display:flex}.selectize-dropdown.plugin-optgroup_columns .optgroup{border-right:1px solid #f2f2f2;border-top:0 none;flex-grow:1;flex-basis:0;min-width:0}.selectize-dropdown.plugin-optgroup_columns .optgroup:last-child{border-right:0 none}.selectize-dropdown.plugin-optgroup_columns .optgroup:before{display:none}.selectize-dropdown.plugin-optgroup_columns .optgroup-header{border-top:0 none}.selectize-control.plugin-remove_button .item{display:inline-flex;align-items:center;padding-right:0 !important}.selectize-control.plugin-remove_button .item .remove{color:inherit;text-decoration:none;vertical-align:middle;display:inline-block;padding:1px 5px;border-left:1px solid rgba(0,0,0,0);border-radius:0 2px 2px 0;box-sizing:border-box;margin-left:5px}.selectize-control.plugin-remove_button .item .remove:hover{background:rgba(0,0,0,.05)}.selectize-control.plugin-remove_button .item.active .remove{border-left-color:rgba(0,0,0,0)}.selectize-control.plugin-remove_button .disabled .item .remove:hover{background:none}.selectize-control.plugin-remove_button .disabled .item .remove{border-left-color:rgba(77,77,77,0)}.selectize-control.plugin-remove_button .remove-single{position:absolute;right:0;top:0;font-size:23px}.selectize-control{position:relative}.selectize-dropdown,.selectize-input,.selectize-input input{color:#333;font-family:inherit;font-size:inherit;line-height:20px;font-smoothing:inherit}.selectize-input,.selectize-control.single .selectize-input.input-active{background:#fff;cursor:text;display:inline-block}.selectize-input{border:1px solid #ccc;padding:6px 12px;display:inline-block;width:100%;overflow:hidden;position:relative;z-index:1;box-sizing:border-box;box-shadow:none;border-radius:4px}.selectize-control.multi .selectize-input.has-items{padding:calc( 6px - 1px - 0 ) 12px calc( 6px - 1px - 3px - 0 )}.selectize-input.full{background-color:#fff}.selectize-input.disabled,.selectize-input.disabled *{cursor:default !important}.selectize-input.focus{box-shadow:inset 0 1px 2px rgba(0,0,0,.15)}.selectize-input.dropdown-active{border-radius:4px 4px 0 0}.selectize-input>*{vertical-align:baseline;display:inline-block;zoom:1}.selectize-control.multi .selectize-input>div{cursor:pointer;margin:0 3px 3px 0;padding:1px 5px;background:#efefef;color:#333;border:0 solid rgba(0,0,0,0)}.selectize-control.multi .selectize-input>div.active{background:#337ab7;color:#fff;border:0 solid rgba(0,0,0,0)}.selectize-control.multi .selectize-input.disabled>div,.selectize-control.multi .selectize-input.disabled>div.active{color:gray;background:#fff;border:0 solid rgba(77,77,77,0)}.selectize-input>input{display:inline-block !important;padding:0 !important;min-height:0 !important;max-height:none !important;max-width:100% !important;margin:0 !important;text-indent:0 !important;border:0 none !important;background:none !important;line-height:inherit !important;user-select:auto !important;box-shadow:none !important}.selectize-input>input::-ms-clear{display:none}.selectize-input>input:focus{outline:none !important}.selectize-input>input[placeholder]{box-sizing:initial}.selectize-input.has-items>input{margin:0 4px !important}.selectize-input::after{content:" ";display:block;clear:left}.selectize-input.dropdown-active::before{content:" ";display:block;position:absolute;background:#fff;height:1px;bottom:0;left:0;right:0}.selectize-dropdown{position:absolute;top:100%;left:0;width:100%;z-index:10;border:1px solid #d0d0d0;background:#fff;margin:-1px 0 0 0;border-top:0 none;box-sizing:border-box;box-shadow:0 1px 3px rgba(0,0,0,.1);border-radius:0 0 4px 4px}.selectize-dropdown [data-selectable]{cursor:pointer;overflow:hidden}.selectize-dropdown [data-selectable] .highlight{background:rgba(255,237,40,.4);border-radius:1px}.selectize-dropdown .option,.selectize-dropdown .optgroup-header,.selectize-dropdown .no-results,.selectize-dropdown .create{padding:3px 12px}.selectize-dropdown .option,.selectize-dropdown [data-disabled],.selectize-dropdown [data-disabled] [data-selectable].option{cursor:inherit;opacity:.5}.selectize-dropdown [data-selectable].option{opacity:1;cursor:pointer}.selectize-dropdown .optgroup:first-child .optgroup-header{border-top:0 none}.selectize-dropdown .optgroup-header{color:#777;background:#fff;cursor:default}.selectize-dropdown .active{background-color:#f5f5f5;color:#262626}.selectize-dropdown .active.create{color:#262626}.selectize-dropdown .create{color:rgba(51,51,51,.5)}.selectize-dropdown-content{overflow-y:auto;overflow-x:hidden;max-height:200px;overflow-scrolling:touch}.selectize-dropdown .spinner{display:inline-block;width:30px;height:30px;margin:3px 12px}.selectize-dropdown .spinner:after{content:" ";display:block;width:24px;height:24px;margin:3px;border-radius:50%;border:5px solid #d0d0d0;border-color:#d0d0d0 transparent #d0d0d0 transparent;animation:lds-dual-ring 1.2s linear infinite}@keyframes lds-dual-ring{0%{transform:rotate(0deg)}100%{transform:rotate(360deg)}}.selectize-control.single .selectize-input,.selectize-control.single .selectize-input input{cursor:pointer}.selectize-control.single .selectize-input.input-active,.selectize-control.single .selectize-input.input-active input{cursor:text}.selectize-control.single .selectize-input:after{content:" ";display:block;position:absolute;top:50%;right:17px;margin-top:-3px;width:0;height:0;border-style:solid;border-width:5px 5px 0 5px;border-color:#333 transparent transparent transparent}.selectize-control.single .selectize-input.dropdown-active:after{margin-top:-4px;border-width:0 5px 5px 5px;border-color:transparent transparent #333 transparent}.selectize-control.rtl{text-align:right}.selectize-control.rtl.single .selectize-input:after{left:17px;right:auto}.selectize-control.rtl .selectize-input>input{margin:0 4px 0 -2px !important}.selectize-control .selectize-input.disabled{opacity:.5;background-color:#fff}.selectize-dropdown,.selectize-dropdown.form-control{height:auto;padding:0;margin:2px 0 0 0;z-index:1000;background:#fff;border:1px solid #ccc;border:1px solid rgba(0,0,0,.15);border-radius:4px;box-shadow:0 6px 12px rgba(0,0,0,.175)}.selectize-dropdown .optgroup-header{font-size:12px;line-height:1.428571429}.selectize-dropdown .optgroup:first-child:before{display:none}.selectize-dropdown .optgroup:before{content:" ";display:block;height:1px;margin:9px 0;overflow:hidden;background-color:#e5e5e5;margin-left:-12px;margin-right:-12px}.selectize-dropdown-content{padding:5px 0}.selectize-input{min-height:34px}.selectize-input.dropdown-active{border-radius:4px}.selectize-input.dropdown-active::before{display:none}.selectize-input.focus{border-color:#66afe9;outline:0;box-shadow:inset 0 1px 1px rgba(0,0,0,.075),0 0 8px rgba(102,175,233,.6)}.has-error .selectize-input{border-color:#a94442;box-shadow:inset 0 1px 1px rgba(0,0,0,.075)}.has-error .selectize-input:focus{border-color:#843534;box-shadow:inset 0 1px 1px rgba(0,0,0,.075),0 0 6px #ce8483}.selectize-control.multi .selectize-input.has-items{padding-left:7px;padding-right:7px}.selectize-control.multi .selectize-input>div{border-radius:3px}.form-control.selectize-control{padding:0;height:auto;border:none;background:none;box-shadow:none;border-radius:0}
+.selectize-control.plugin-drag_drop.multi>.selectize-input>div.ui-sortable-placeholder{
+ visibility:visible !important;
+ background:#f2f2f2 !important;
+ background:rgba(0,0,0,.06) !important;
+ border:0 none !important;
+ box-shadow:inset 0 0 12px 4px #fff;
+}
+.selectize-control.plugin-drag_drop .ui-sortable-placeholder::after{
+ content:"!";
+ visibility:hidden;
+}
+.selectize-control.plugin-drag_drop .ui-sortable-helper{
+ box-shadow:0 2px 5px rgba(0,0,0,.2);
+}
+.selectize-control .dropdown-header{
+ position:relative;
+ padding:6px 12px;
+ border-bottom:1px solid #d0d0d0;
+ background:#f8f8f8;
+ border-radius:4px 4px 0 0;
+}
+.selectize-control .dropdown-header-close{
+ position:absolute;
+ right:12px;
+ top:50%;
+ color:#333;
+ opacity:.4;
+ margin-top:-12px;
+ line-height:20px;
+ font-size:20px !important;
+}
+.selectize-control .dropdown-header-close:hover{
+ color:#000;
+}
+.selectize-dropdown.plugin-optgroup_columns .selectize-dropdown-content{
+ display:flex;
+}
+.selectize-dropdown.plugin-optgroup_columns .optgroup{
+ border-right:1px solid #f2f2f2;
+ border-top:0 none;
+ flex-grow:1;
+ flex-basis:0;
+ min-width:0;
+}
+.selectize-dropdown.plugin-optgroup_columns .optgroup:last-child{
+ border-right:0 none;
+}
+.selectize-dropdown.plugin-optgroup_columns .optgroup:before{
+ display:none;
+}
+.selectize-dropdown.plugin-optgroup_columns .optgroup-header{
+ border-top:0 none;
+}
+.selectize-control.plugin-remove_button .item{
+ display:inline-flex;
+ align-items:center;
+ padding-right:0 !important;
+}
+.selectize-control.plugin-remove_button .item .remove{
+ color:inherit;
+ text-decoration:none;
+ vertical-align:middle;
+ display:inline-block;
+ padding:1px 5px;
+ border-left:1px solid rgba(0,0,0,0);
+ border-radius:0 2px 2px 0;
+ box-sizing:border-box;
+ margin-left:5px;
+}
+.selectize-control.plugin-remove_button .item .remove:hover{
+ background:rgba(0,0,0,.05);
+}
+.selectize-control.plugin-remove_button .item.active .remove{
+ border-left-color:rgba(0,0,0,0);
+}
+.selectize-control.plugin-remove_button .disabled .item .remove:hover{
+ background:none;
+}
+.selectize-control.plugin-remove_button .disabled .item .remove{
+ border-left-color:rgba(77,77,77,0);
+}
+.selectize-control.plugin-remove_button .remove-single{
+ position:absolute;
+ right:0;
+ top:0;
+ font-size:23px;
+}
+.selectize-control{
+ position:relative;
+}
+.selectize-dropdown,.selectize-input,.selectize-input input{
+ color:#333;
+ font-family:inherit;
+ font-size:inherit;
+ line-height:20px;
+ font-smoothing:inherit;
+}
+.selectize-input,.selectize-control.single .selectize-input.input-active{
+ background:#fff;
+ cursor:text;
+ display:inline-block;
+}
+.selectize-input{
+ border:1px solid #ccc;
+ padding:6px 12px;
+ display:inline-block;
+ width:100%;
+ overflow:hidden;
+ position:relative;
+ z-index:1;
+ box-sizing:border-box;
+ box-shadow:none;
+ border-radius:4px;
+}
+.selectize-control.multi .selectize-input.has-items{
+ padding:calc( 6px - 1px - 0 ) 12px calc( 6px - 1px - 3px - 0 );
+}
+.selectize-input.full{
+ background-color:#fff;
+}
+.selectize-input.disabled,.selectize-input.disabled *{
+ cursor:default !important;
+}
+.selectize-input.focus{
+ box-shadow:inset 0 1px 2px rgba(0,0,0,.15);
+}
+.selectize-input.dropdown-active{
+ border-radius:4px 4px 0 0;
+}
+.selectize-input>*{
+ vertical-align:baseline;
+ display:inline-block;
+ zoom:1;
+}
+.selectize-control.multi .selectize-input>div{
+ cursor:pointer;
+ margin:0 3px 3px 0;
+ padding:1px 5px;
+ background:#efefef;
+ color:#333;
+ border:0 solid rgba(0,0,0,0);
+}
+.selectize-control.multi .selectize-input>div.active{
+ background:#337ab7;
+ color:#fff;
+ border:0 solid rgba(0,0,0,0);
+}
+.selectize-control.multi .selectize-input.disabled>div,.selectize-control.multi .selectize-input.disabled>div.active{
+ color:gray;
+ background:#fff;
+ border:0 solid rgba(77,77,77,0);
+}
+.selectize-input>input{
+ display:inline-block !important;
+ padding:0 !important;
+ min-height:0 !important;
+ max-height:none !important;
+ max-width:100% !important;
+ margin:0 !important;
+ text-indent:0 !important;
+ border:0 none !important;
+ background:none !important;
+ line-height:inherit !important;
+ user-select:auto !important;
+ box-shadow:none !important;
+}
+.selectize-input>input::-ms-clear{
+ display:none;
+}
+.selectize-input>input:focus{
+ outline:none !important;
+}
+.selectize-input>input[placeholder]{
+ box-sizing:initial;
+}
+.selectize-input.has-items>input{
+ margin:0 4px !important;
+}
+.selectize-input::after{
+ content:" ";
+ display:block;
+ clear:left;
+}
+.selectize-input.dropdown-active::before{
+ content:" ";
+ display:block;
+ position:absolute;
+ background:#fff;
+ height:1px;
+ bottom:0;
+ left:0;
+ right:0;
+}
+.selectize-dropdown{
+ position:absolute;
+ top:100%;
+ left:0;
+ width:100%;
+ z-index:10;
+ border:1px solid #d0d0d0;
+ background:#fff;
+ margin:-1px 0 0 0;
+ border-top:0 none;
+ box-sizing:border-box;
+ box-shadow:0 1px 3px rgba(0,0,0,.1);
+ border-radius:0 0 4px 4px;
+}
+.selectize-dropdown [data-selectable]{cursor:pointer;overflow:hidden}.selectize-dropdown [data-selectable] .highlight{background:rgba(255,237,40,.4);border-radius:1px}.selectize-dropdown .option,.selectize-dropdown .optgroup-header,.selectize-dropdown .no-results,.selectize-dropdown .create{padding:3px 12px}.selectize-dropdown .option,.selectize-dropdown [data-disabled],.selectize-dropdown [data-disabled] [data-selectable].option{cursor:inherit;opacity:.5}.selectize-dropdown [data-selectable].option{opacity:1;cursor:pointer}.selectize-dropdown .optgroup:first-child .optgroup-header{border-top:0 none}.selectize-dropdown .optgroup-header{color:#777;background:#fff;cursor:default}.selectize-dropdown .active{background-color:#f5f5f5;color:#262626}.selectize-dropdown .active.create{color:#262626}.selectize-dropdown .create{color:rgba(51,51,51,.5)}.selectize-dropdown-content{overflow-y:auto;overflow-x:hidden;max-height:200px;overflow-scrolling:touch}.selectize-dropdown .spinner{display:inline-block;width:30px;height:30px;margin:3px 12px}.selectize-dropdown .spinner:after{content:" ";display:block;width:24px;height:24px;margin:3px;border-radius:50%;border:5px solid #d0d0d0;border-color:#d0d0d0 transparent #d0d0d0 transparent;animation:lds-dual-ring 1.2s linear infinite}@keyframes lds-dual-ring{0%{transform:rotate(0deg)}100%{transform:rotate(360deg)}}.selectize-control.single .selectize-input,.selectize-control.single .selectize-input input{cursor:pointer}.selectize-control.single .selectize-input.input-active,.selectize-control.single .selectize-input.input-active input{cursor:text}.selectize-control.single .selectize-input:after{content:" ";display:block;position:absolute;top:50%;right:17px;margin-top:-3px;width:0;height:0;border-style:solid;border-width:5px 5px 0 5px;border-color:#333 transparent transparent transparent}.selectize-control.single .selectize-input.dropdown-active:after{margin-top:-4px;border-width:0 5px 5px 5px;border-color:transparent transparent #333 transparent}.selectize-control.rtl{text-align:right}.selectize-control.rtl.single .selectize-input:after{left:17px;right:auto}.selectize-control.rtl .selectize-input>input{margin:0 4px 0 -2px !important}.selectize-control .selectize-input.disabled{opacity:.5;background-color:#fff}.selectize-dropdown,.selectize-dropdown.form-control{height:auto;padding:0;margin:2px 0 0 0;z-index:1000;background:#fff;border:1px solid #ccc;border:1px solid rgba(0,0,0,.15);border-radius:4px;box-shadow:0 6px 12px rgba(0,0,0,.175)}.selectize-dropdown .optgroup-header{font-size:12px;line-height:1.428571429}.selectize-dropdown .optgroup:first-child:before{display:none}.selectize-dropdown .optgroup:before{content:" ";display:block;height:1px;margin:9px 0;overflow:hidden;background-color:#e5e5e5;margin-left:-12px;margin-right:-12px}.selectize-dropdown-content{padding:5px 0}.selectize-input{min-height:34px}.selectize-input.dropdown-active{border-radius:4px}.selectize-input.dropdown-active::before{display:none}.selectize-input.focus{border-color:#66afe9;outline:0;box-shadow:inset 0 1px 1px rgba(0,0,0,.075),0 0 8px rgba(102,175,233,.6)}.has-error .selectize-input{border-color:#a94442;box-shadow:inset 0 1px 1px rgba(0,0,0,.075)}.has-error .selectize-input:focus{border-color:#843534;box-shadow:inset 0 1px 1px rgba(0,0,0,.075),0 0 6px #ce8483}.selectize-control.multi .selectize-input.has-items{padding-left:7px;padding-right:7px}.selectize-control.multi .selectize-input>div{border-radius:3px}.form-control.selectize-control{padding:0;height:auto;border:none;background:none;box-shadow:none;border-radius:0}
diff --git a/static/js/searchByHabitat.js b/static/js/searchByHabitat.js
index dcd356c029f9f16b79b17d22039d6455d905468c..edf4156a64d446806ab5f12d4f7d83301818b080 100644
--- a/static/js/searchByHabitat.js
+++ b/static/js/searchByHabitat.js
@@ -18,34 +18,56 @@ import { format_docs } from './utils.js';
$("#searchByHabitat.nav-item").addClass( "active" );
-// List Habitat
-if ( sessionStorage.getItem("list_habitat_taxon") === null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_habitat_taxon',
- function success(list_habitat_taxon) {
- sessionStorage.setItem("list_habitat_taxon", JSON.stringify(Object.keys(list_habitat_taxon).sort()));
- autocomplete_taxon_habitat();
+$('#spinner_habitat_taxon').show();
+$('#spinner_habitat_taxon2').show();
+
+// Habitat selection
+var $select = $('#search_habitat').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. soy milk',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_habitat"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_habitat_taxon').hide();
+ $('#spinner_habitat_taxon2').hide();
+ $('#search_habitat option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(ontobiotopeid){
+ if (ontobiotopeid != "") {
+
+ // Tree event
+ $('#habitattree').data('simpleTree').clearSelection();
+ $('#habitattree').data('simpleTree').collapseAll();
+ var node = $('#habitattree').data('simpleTree').getNodeFromValue(ontobiotopeid);
+ $('#habitattree').data('simpleTree').setSelectedNode(node);
+ }
+ }
});
-}
-else {
- autocomplete_taxon_habitat();
-}
+var selectize = $select[0].selectize;
-// Tree Options
+// Tree
var options = {
searchBox: $('#searchtreehabitat'),
searchMinInputLength: 4
};
-// Tree
$.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_habitat', function(data) {
$('#habitattree').simpleTree(options, data);
// URL: habitat
if ( habitat !== null ) {
- $('#spinner_habitat_taxon').show();
- $('#spinner_habitat_taxon2').show();
-
- $("#relationTaxonByHabitat").val(habitat);
- $('#filter_habitat_taxon').removeAttr('disabled');
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: habitat, table: 'list_habitat'},
@@ -57,7 +79,6 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_habitat', function(data) {
// Tree event
var node = $('#habitattree').data('simpleTree').getNodeFromValue(ontobiotopeid);
$('#habitattree').data('simpleTree').setSelectedNode(node);
- $('#searchtreehabitat').val(habitat);
}});
}
@@ -76,101 +97,30 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_habitat', function(data) {
$('input.column_filter').val(taxon);
}
});
-
-// Tree event
$('#habitattree').on('simpleTree:change', function(event){
- $('#treeModalHabitat').modal('hide');
+ if ( $('#habitattree').data('simpleTree').getSelectedNode() != undefined ) {
- $('#habitattree').data('simpleTree').collapseAll();
- $('#habitattree').data('simpleTree').expandTo($('#habitattree').data('simpleTree').getSelectedNode());
+ selectize.clear(false);
+ selectize.setValue($('#habitattree').data('simpleTree').getSelectedNode().value, true);
- $('#spinner_habitat_taxon').show();
- $('#spinner_habitat_taxon2').show();
-
- $("#relationTaxonByHabitat").val($('#habitattree').data('simpleTree').getSelectedNode().label);
- $('#filter_habitat_taxon').removeAttr('disabled');
-
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: $('#habitattree').data('simpleTree').getSelectedNode().label, table: 'list_habitat'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
+ $('#spinner_habitat_taxon').show();
+ $('#spinner_habitat_taxon2').show();
- // Tree event
- var node = $('#habitattree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#habitattree').data('simpleTree').setSelectedNode(node);
- createTable(ontobiotopeid);
- }
- else {
- alert("No result for " + $('#habitattree').data('simpleTree').getSelectedNode().label);
- // Spinner off
- $('#spinner_habitat_taxon').hide();
- $('#spinner_habitat_taxon2').hide();
- // Clear oracle
- $("#relationTaxonByHabitat").val("");
- $('#filter_habitat_taxon').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
- });
+ $('#searchtreehabitat').val($('#habitattree').data('simpleTree').getSelectedNode().label);
+ createTable($('#habitattree').data('simpleTree').getSelectedNode().value);
+ $("#search_habitat option:selected").text();
+ $("#search_habitat option:selected").text($('#habitattree').data('simpleTree').getSelectedNode().label);
+ $("#search_habitat option:selected").val($('#habitattree').data('simpleTree').getSelectedNode().value);
+ selectize.setTextboxValue("");
+ selectize.setTextboxValue($('#habitattree').data('simpleTree').getSelectedNode().label);
+ $('#filter_habitat_taxon').removeAttr('disabled');
+ $('#treeModalHabitat').modal('hide');
+ }
});
-// Search by habitat (autocompletion)
-function autocomplete_taxon_habitat() {
- $( "#relationTaxonByHabitat" ).autocomplete({
- source: JSON.parse(sessionStorage.getItem("list_habitat_taxon")),
- minLength: 3,
- select: function( event, ui ) {
- $('#filter_habitat_taxon').removeAttr('disabled');
-
- $('#spinner_habitat_taxon').show();
- $('#spinner_habitat_taxon2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: ui.item.value, table: 'list_habitat'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
-
- createTable(ontobiotopeid);
-
- // Tree event
- $('#habitattree').data('simpleTree').clearSelection();
- var node = $('#habitattree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#habitattree').data('simpleTree').setSelectedNode(node);
- $('#searchtreehabitat').val(ui.item.value);
- }
- }
- );
- }
- });
-}
-
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'habitat');
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (habitat)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
-
-var thtable = $('#results_habitat_taxon').DataTable();
-
// Datatable
+var thtable = $('#results_habitat_taxon').DataTable();
function createTable(ontobiotopeid) {
$.getJSON($SCRIPT_ROOT + '/_get_list_relations',
@@ -312,36 +262,17 @@ function createTable(ontobiotopeid) {
]
});
- if ( $('#taxon_ht').val() != '' ) { filterColumnTaxon(3); }
- if ( $('#sources_ht').val() != '' ) { filterSourceColumn(5); }
- if ( $('input[name=qps_ht]').is(':checked') == true ) { filterColumnCheck(4); }
+ if ( $('#taxon_ht').val() != '' ) { filterColumnTaxon(3); }
+ if ( $('#sources_ht').val() != '' ) { filterSourceColumn(5); }
+ if ( $('input[name=qps_ht]').is(':checked') == true ) { filterColumnCheck(4); }
- $('#spinner_habitat_taxon').hide();
- $('#spinner_habitat_taxon2').hide();
+ $('#spinner_habitat_taxon').hide();
+ $('#spinner_habitat_taxon2').hide();
- checkURL();
+ checkURL();
});
}
-// Click on table row
-// $('#results_habitat_taxon tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// console.log("TR : ", tr);
-// var row = thtable.row( tr );
-// console.log("ROW : ", row);
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - Taxon
function filterColumnTaxon(i) {
$('#results_habitat_taxon').DataTable().column(i).search(
@@ -381,8 +312,8 @@ $('input:checkbox').on('change', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationTaxonByHabitat").val() !== '' ) {
- url += "?habitat=" + $("#relationTaxonByHabitat").val();
+ if ( $("#search_habitat option:selected").text() !== '' ) {
+ url += "?habitat=" + $("#search_habitat option:selected").text();
}
if ( $("#taxon_ht").val() !== '' ) {
url += "&taxon=" + $("#taxon_ht").val();
diff --git a/static/js/searchByPhenotype.js b/static/js/searchByPhenotype.js
index e2612aa1ccdf48c190eb35fb8ef452f0c1c165ee..c51c5bd90192a091c8337ee029dd7ea72848b7c3 100644
--- a/static/js/searchByPhenotype.js
+++ b/static/js/searchByPhenotype.js
@@ -18,35 +18,56 @@ import { format_docs } from './utils.js';
$("#searchByPhenotype.nav-item").addClass( "active" );
-// List Phenotype
-if ( sessionStorage.getItem("list_phenotype_taxon") === null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_phenotype_taxon',
- function success(list_phenotype_taxon) {
- sessionStorage.setItem("list_phenotype_taxon", JSON.stringify(Object.keys(list_phenotype_taxon).sort()));
- autocomplete_taxon_phenotype();
+$('#spinner_phenotype_taxon').show();
+$('#spinner_phenotype_taxon2').show();
+
+// Phenotype selection
+var $select = $('#search_phenotype').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. thermophile',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_phenotype_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_phenotype_taxon').hide();
+ $('#spinner_phenotype_taxon2').hide();
+ $('#search_phenotype option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(ontobiotopeid){
+ if (ontobiotopeid != "") {
+
+ // Tree event
+ $('#phenotypetree').data('simpleTree').clearSelection();
+ $('#phenotypetree').data('simpleTree').collapseAll();
+ var node = $('#phenotypetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
+ $('#phenotypetree').data('simpleTree').setSelectedNode(node);
+ }
+ }
});
-}
-else {
- autocomplete_taxon_phenotype();
-}
+var selectize = $select[0].selectize;
-// Tree Options
+// Tree
var options = {
searchBox: $('#searchtreephenotype'),
searchMinInputLength: 4
};
-// Tree
$.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_phenotype', function(data) {
$('#phenotypetree').simpleTree(options, data);
// URL : phenotype
if ( phenotype !== null ) {
- $('#spinner_phenotype_taxon').show();
- $('#spinner_phenotype_taxon2').show();
-
- $("#relationTaxonByPhenotype").val(phenotype);
- $('#filter_phenotype_taxon').removeAttr('disabled');
-
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: phenotype, table: 'list_phenotype_taxon'},
function success(path) {
@@ -57,7 +78,6 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_phenotype', function(data) {
// Tree event
var node = $('#phenotypetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
$('#phenotypetree').data('simpleTree').setSelectedNode(node);
- $('#searchtreephenotype').val(phenotype);
}
});
}
@@ -72,100 +92,30 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_phenotype', function(data) {
$('input.column_filter').val(taxon);
}
});
-
-// Tree event
$('#phenotypetree').on('simpleTree:change', function(event){
- $('#treeModalPhenotype').modal('hide');
-
- $('#phenotypetree').data('simpleTree').collapseAll();
- $('#phenotypetree').data('simpleTree').expandTo($('#phenotypetree').data('simpleTree').getSelectedNode());
-
- $('#spinner_phenotype_taxon').show();
- $('#spinner_phenotype_taxon2').show();
+ if ( $('#phenotypetree').data('simpleTree').getSelectedNode() != undefined ) {
- $("#relationTaxonByPhenotype").val($('#phenotypetree').data('simpleTree').getSelectedNode().label);
- $('#filter_phenotype_taxon').removeAttr('disabled');
+ selectize.clear(false);
+ selectize.setValue($('#phenotypetree').data('simpleTree').getSelectedNode().value, true);
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: $('#phenotypetree').data('simpleTree').getSelectedNode().label, table: 'list_phenotype_taxon'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
+ $('#spinner_phenotype_taxon').show();
+ $('#spinner_phenotype_taxon2').show();
- // Tree event
- var node = $('#phenotypetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#phenotypetree').data('simpleTree').setSelectedNode(node);
- createTable(ontobiotopeid);
- }
- else {
- alert("No result for " + phenotype);
- // Spinner off
- $('#spinner_phenotype_taxon').hide();
- $('#spinner_phenotype_taxon2').hide();
- // Clear oracle
- $("#relationTaxonByPhenotype").val("");
- $('#filter_phenotype_taxon').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
- });
+ $('#searchtreephenotype').val($('#phenotypetree').data('simpleTree').getSelectedNode().label);
+ createTable($('#phenotypetree').data('simpleTree').getSelectedNode().value);
+ $("#search_phenotype option:selected").text();
+ $("#search_phenotype option:selected").text($('#phenotypetree').data('simpleTree').getSelectedNode().label);
+ $("#search_phenotype option:selected").val($('#phenotypetree').data('simpleTree').getSelectedNode().value);
+ selectize.setTextboxValue("");
+ selectize.setTextboxValue($('#phenotypetree').data('simpleTree').getSelectedNode().label);
+ $('#filter_phenotype_taxon').removeAttr('disabled');
+ $('#treeModalPhenotype').modal('hide');
+ }
})
-// Search by phenotype (autocompletion)
-function autocomplete_taxon_phenotype() {
- $( "#relationTaxonByPhenotype" ).autocomplete({
- source: JSON.parse(sessionStorage.getItem("list_phenotype_taxon")),
- minLength: 3,
- select: function( event, ui ) {
- $('#filter_phenotype_taxon').removeAttr('disabled');
-
- $('#spinner_phenotype_taxon').show();
- $('#spinner_phenotype_taxon2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: ui.item.value, table: 'list_phenotype_taxon'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
-
- createTable(ontobiotopeid);
-
- // Tree event
- var node = $('#phenotypetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#phenotypetree').data('simpleTree').setSelectedNode(node);
- $('#searchtreephenotype').val(ui.item.value);
- }
- });
- }
- });
-}
-
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'phenotype');
-//
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (phenotype)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
-
-var thtable = $('#results_phenotype_taxon').DataTable();
-
// Data table
+var thtable = $('#results_phenotype_taxon').DataTable();
function createTable(ontobiotopeid) {
$.getJSON($SCRIPT_ROOT + '/_get_list_relations',
@@ -315,22 +265,6 @@ function createTable(ontobiotopeid) {
});
}
-// $('#results_phenotype_taxon tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// var row = thtable.row(tr);
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - Taxon
function filterColumnTaxon(i) {
$('#results_phenotype_taxon').DataTable().column(i).search(
@@ -359,8 +293,8 @@ $('input:checkbox').on('change', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationTaxonByPhenotype").val() !== '' ) {
- url += "?phenotype=" + $("#relationTaxonByPhenotype").val();
+ if ( $("#search_phenotype option:selected").text() !== '' ) {
+ url += "?phenotype=" + $("#search_phenotype option:selected").text();
}
if ( $("#taxon_pt").val() !== '' ) {
url += "&taxon=" + $("#taxon_pt").val();
diff --git a/static/js/searchByTaxon.js b/static/js/searchByTaxon.js
index e9501876c08c631ba0e1f755eab9248a19077fa3..785b7b37a4d9a312e6655e0ef3153fa5e17a9d74 100644
--- a/static/js/searchByTaxon.js
+++ b/static/js/searchByTaxon.js
@@ -21,25 +21,50 @@ $("#searchByTaxon.nav-item").addClass( "active" );
// Spinner
$('#spinner_taxon_habitat').show();
$('#spinner_taxon_habitat2').show();
-$('#relationHabitatByTaxon').prop('disabled', true);
+// $('#relationHabitatByTaxon').prop('disabled', true);
-$.getJSON($SCRIPT_ROOT + '/_get_list_taxon_habitat',
- function success(list_taxon_habitat) {
- autocomplete_taxon_habitat(Object.keys(list_taxon_habitat).sort());
- $('#spinner_taxon_habitat').hide();
- $('#spinner_taxon_habitat2').hide();
- $('#relationHabitatByTaxon').prop('disabled', false);
-});
+var $select = $('#search').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Bacillus subtilis',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_habitat').hide();
+ $('#spinner_taxon_habitat2').hide();
+ $('#search option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+ createTable(value);
+ }
+ }
+ });
+
+var selectize = $select[0].selectize;
// URL: taxon
if ( taxon !== null ) {
$('#spinner_taxon_habitat').show();
$('#spinner_taxon_habitat2').show();
-
- $("#relationHabitatByTaxon").val(taxon);
+ selectize.setTextboxValue(taxon);
+ $("#search option:selected").text(taxon);
+ $("#search option:selected").val(taxon);
$('#filter_taxon_habitat').removeAttr('disabled');
- createTable(taxon);
+ createTable_old(taxon);
}
// URL: qps
if ( qps !== null ) {
@@ -54,45 +79,179 @@ if ( habitat !== null ) {
$('input.column_filter').val(habitat);
}
-// Search by taxon (autocompletion)
-function autocomplete_taxon_habitat(json_data) {
- $( "#relationHabitatByTaxon" ).autocomplete({
- source: json_data,
- minLength: 5,
- select: function( event, ui ) {
- $('#filter_taxon_habitat').removeAttr('disabled');
- $('#spinner_taxon_habitat').show();
- $('#spinner_taxon_habitat2').show();
+var thtable = $('#results_taxon_habitat').DataTable();
- createTable(ui.item.value);
- }
- });
-}
+// Datatable
+function createTable(path) {
+ if ( path != '' ) {
+ let l_path = path.split('/');
+ let taxonid = l_path[l_path.length-1];
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'habitat');
-//
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (habitat)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
+ $('#filter_taxon_habitat').removeAttr('disabled');
+ $('#spinner_taxon_habitat').show();
+ $('#spinner_taxon_habitat2').show();
-var thtable = $('#results_taxon_habitat').DataTable();
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: 'habitat'
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#results_taxon_habitat').DataTable().destroy();
+ thtable = $('#results_taxon_habitat').DataTable(
+ {
+ dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function ( data, type, row, meta ) {
+ let taxa = row[1].split(', ');
+ let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ return taxon;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[3].split(',')[0];
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ for ( let i = 1; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ for ( let i = 1; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
-// Datatable
-function createTable(taxon) {
+ if ( $('#habitat_th').val() != '' ) { filterColumnHabitat(3); }
+ if ( $('#sources_th').val() != '' ) { filterSourceColumn(5); }
+ if ( $('input[name=qps_th]').is(':checked') == true ) { filterColumnCheck(4); }
+
+ $('#spinner_taxon_habitat').hide();
+ $('#spinner_taxon_habitat2').hide();
+
+ checkURL();
+ });
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_habitat').hide();
+ $('#spinner_taxon_habitat2').hide();
+ // Clear oracle
+ $("#relationHabitatByTaxon").val("");
+ $('#filter_taxon_habitat').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+}
+
+function createTable_old(taxon) {
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: taxon, table: 'list_taxon'},
function success(path) {
@@ -261,22 +420,6 @@ function createTable(taxon) {
});
}
-// $('#results_taxon_habitat tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// var row = thtable.row( tr );
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - Habitat
function filterColumnHabitat(i) {
$('#results_taxon_habitat').DataTable().column(i).search(
@@ -316,8 +459,8 @@ $('input.column_source').on( 'keyup click', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationHabitatByTaxon").val() !== '' ) {
- url += "?taxon=" + $("#relationHabitatByTaxon").val();
+ if ( $("#search option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search option:selected").text();
}
if ( $("#habitat_th").val() !== '' ) {
url += "&habitat=" + $("#habitat_th").val();
diff --git a/static/js/searchByTaxonForPhenotype.js b/static/js/searchByTaxonForPhenotype.js
index 3ceee8a8d28b3e42563bf90ccd742e04e648dfae..b084de7131d39d20e6c6a7f863e99094e7278674 100644
--- a/static/js/searchByTaxonForPhenotype.js
+++ b/static/js/searchByTaxonForPhenotype.js
@@ -18,27 +18,51 @@ import { format_docs } from './utils.js';
$("#searchByTaxonForPhenotype.nav-item").addClass( "active" );
-// List Taxon
-if ( sessionStorage.getItem("list_taxon_phenotype") === null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_taxon_phenotype',
- function success(list_taxon_phenotype) {
- sessionStorage.setItem("list_taxon_phenotype", JSON.stringify(Object.keys(list_taxon_phenotype).sort()));
- autocomplete_taxon_phenotype();
+$('#spinner_taxon_phenotype').show();
+$('#spinner_taxon_phenotype2').show();
+
+var $select = $('#search_taxon_phenotype').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Bacillus subtilis',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_taxon_phenotype"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_phenotype').hide();
+ $('#spinner_taxon_phenotype2').hide();
+ $('#search_taxon_phenotype option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+ createTable(value);
+ }
+ }
});
-}
-else {
- autocomplete_taxon_phenotype();
-}
+
+var selectize = $select[0].selectize;
// URL: taxon
if ( taxon !== null ) {
$('#spinner_taxon_phenotype').show();
$('#spinner_taxon_phenotype2').show();
-
- $("#relationPhenotypeByTaxon").val(taxon);
+ selectize.setTextboxValue(taxon);
+ $("#search_taxon_phenotype option:selected").text(taxon);
+ $("#search_taxon_phenotype option:selected").val(taxon);
$('#filter_taxon_phenotype').removeAttr('disabled');
- createTable(taxon);
+ createTable_old(taxon);
}
// URL: qps
if ( qps !== null ) {
@@ -49,45 +73,172 @@ if ( phenotype !== null ) {
$('input.column_filter').val(phenotype);
}
-// Search by taxon (autocompletion)
-function autocomplete_taxon_phenotype() {
- $( "#relationPhenotypeByTaxon" ).autocomplete({
- source: JSON.parse(sessionStorage.getItem("list_taxon_phenotype")),
- minLength: 5,
- select: function( event, ui ) {
- $('#filter_taxon_phenotype').removeAttr('disabled');
- $('#spinner_taxon_phenotype').show();
- $('#spinner_taxon_phenotype2').show();
+var thtable = $('#results_taxon_phenotype').DataTable();
- createTable(ui.item.value);
- }
- });
-}
+// Datatable
+function createTable(path) {
+ if ( path != '' ) {
+ let l_path = path.split('/');
+ let taxonid = l_path[l_path.length-1];
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: 'phenotype'
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#results_taxon_phenotype').DataTable().destroy();
+ thtable = $('#results_taxon_phenotype').DataTable(
+ {dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function ( data, type, row, meta ) {
+ let taxa = row[1].split(', ');
+ let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ return taxon;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[3].split(',')[0];
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ for ( let i = 1; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ for ( let i = 1; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'phenotype');
-//
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (phenotype)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
+ if ( $('#phenotype_tp').val() != '' ) { filterColumnphenotype(3); }
+ if ( $('input[name=qps_tp]').is(':checked') == true ) { filterColumnCheck(4); }
-var thtable = $('#results_taxon_phenotype').DataTable();
+ $('#spinner_taxon_phenotype').hide();
+ $('#spinner_taxon_phenotype2').hide();
-// Datatable
-function createTable(taxon) {
+ checkURL();
+ });
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_phenotype').hide();
+ $('#spinner_taxon_phenotype2').hide();
+ // Clear oracle
+ $("#relationPhenotypeByTaxon").val("");
+ $('#filter_taxon_phenotype').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+}
+function createTable_old(taxon) {
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: taxon, table: 'list_taxon_phenotype'},
function success(path) {
@@ -325,22 +476,6 @@ function createTable(taxon) {
});
}
-// $('#results_taxon_phenotype tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// var row = thtable.row( tr );
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - phenotype
function filterColumnphenotype(i) {
$('#results_taxon_phenotype').DataTable().column(i).search(
@@ -369,8 +504,8 @@ $('input:checkbox').on('change', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationPhenotypeByTaxon").val() !== '' ) {
- url += "?taxon=" + $("#relationPhenotypeByTaxon").val();
+ if ( $("#search_taxon_phenotype option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search_taxon_phenotype option:selected").text();
}
if ( $("#phenotype_tp").val() !== '' ) {
url += "&phenotype=" + $("#phenotype_tp").val();
diff --git a/static/js/searchByTaxonForUse.js b/static/js/searchByTaxonForUse.js
index 753539518fdfbbb5161b8ec39c0ef82619b40cc9..868964caf2eeb4e98f584eed065dd27fc57efa68 100644
--- a/static/js/searchByTaxonForUse.js
+++ b/static/js/searchByTaxonForUse.js
@@ -18,27 +18,50 @@ import { format_docs } from './utils.js';
$("#searchByTaxonForUse.nav-item").addClass( "active" );
-// List Taxon
-if ( sessionStorage.getItem("list_taxon_use") === null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_taxon_use',
- function success(list_taxon_use) {
- sessionStorage.setItem("list_taxon_use", JSON.stringify(Object.keys(list_taxon_use).sort()));
- autocomplete_taxon_use();
+$('#spinner_taxon_use').show();
+$('#spinner_taxon_use2').show();
+
+var $select = $('#search_taxon_use').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. Bacillus subtilis',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_taxon_use"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_taxon_use').hide();
+ $('#spinner_taxon_use2').hide();
+ $('#search_taxon_use').prop('disabled', false);
+ });
+ },
+ onChange:function(value){
+ if (value != "") {
+ createTable(value);
+ }
+ }
});
-}
-else {
- autocomplete_taxon_use();
-}
+
+var selectize = $select[0].selectize;
// URL: taxon
if ( taxon !== null ) {
$('#spinner_taxon_use').show();
$('#spinner_taxon_use2').show();
-
- $("#relationUseByTaxon").val(taxon);
+ selectize.setTextboxValue(taxon);
+ $("#search_taxon_use option:selected").text(taxon);
+ $("#search_taxon_use option:selected").val(taxon);
$('#filter_taxon_use').removeAttr('disabled');
-
- createTable(taxon);
+ createTable_old(taxon);
}
// URL: qps
if ( qps !== null ) {
@@ -49,45 +72,172 @@ if ( use !== null ) {
$('input.column_filter').val(use);
}
-// Search by taxon (autocompletion)
-function autocomplete_taxon_use() {
- $( "#relationUseByTaxon" ).autocomplete({
- source: JSON.parse(sessionStorage.getItem("list_taxon_use")),
- minLength: 5,
- select: function( event, ui ) {
- $('#filter_taxon_use').removeAttr('disabled');
- $('#spinner_taxon_use').show();
- $('#spinner_taxon_use2').show();
+var thtable = $('#results_taxon_use').DataTable();
- createTable(ui.item.value);
- }
- });
-}
+// Data table
+function createTable(path) {
+ if ( path != '' ) {
+ let l_path = path.split('/');
+ let taxonid = l_path[l_path.length-1];
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'use');
-//
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (use)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
+ $.getJSON($SCRIPT_ROOT + '/_get_list_relations',
+ { taxonid: taxonid,
+ type: 'use'
+ },
+ function success(relations) {
+ $('#hide').css( 'display', 'block' );
+ $('#results_taxon_use').DataTable().destroy();
+ thtable = $('#results_taxon_use').DataTable(
+ {dom: 'lifrtBp', // 'Bfrtip'
+ data: relations,
+ buttons: [
+ {
+ extend: 'copyHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'csvHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'excelHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ else { return $('#' + table_id).DataTable().column( idx ).visible(); } }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ {
+ extend: 'pdfHtml5',
+ exportOptions: { columns: function ( idx, data, node ) {
+ var table_id = node.getAttribute('aria-controls');
+ if ( idx == 0 ) { return false; } // Never Source Text
+ else if ( idx == 6 ) { return true; } // Always Full Source Text
+ return $('#' + table_id).DataTable().column( idx ).visible(); }
+ },
+ title: 'Omnicrobe_V_'+version
+ },
+ 'colvis'
+ ],
+ columns: [
+ {"render": function(data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ let docs = "";
+ if ( data.includes(', ') ) { docs = data.split(', '); }
+ else { docs = data.split(','); }
+ let docs_f = "";
+ if ( docs.length > 2 ) { // 3
+ docs_f = docids.split(", ").slice(0,2).join(', ') + ", ..."; // 0,3
+ }
+ else {
+ docs_f = docids;
+ }
+ return docs_f;
+ }},
+ {"render": function ( data, type, row, meta ) {
+ let taxa = row[1].split(', ');
+ let taxon = taxa[0];
+ if ( row[9].includes("ncbi") ) {
+ taxon = "<a target='_blank' class='doc' href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id="+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ else if ( row[9].includes("bd") ) {
+ taxon = "<a target='_blank' class='doc' href='https://bacdive.dsmz.de/strain/"+row[9].replace(/.+:/ig, '')+"'>"+taxa[0]+"</a>";
+ }
+ return taxon;
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[2];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[3].split(',')[0];
+ }},
+ {"orderable": false, "render": function (data, type, row, meta) {
+ return row[4];
+ }},
+ {"render": function (data, type, row, meta) {
+ return row[5];
+ }},
+ {"render": function (data, type, row, meta) {
+ let taxs = row[1].split(', ');
+ let forms = "";
+ for ( let i = 1; i < taxs.length ; i++ ) {
+ forms += taxs[i]
+ if ( i != taxs.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let elts = row[3].split(', ');
+ let forms = "";
+ for ( let i = 1; i < elts.length ; i++ ) {
+ forms += elts[i]
+ if ( i != elts.length - 1 ) { forms += ", " }
+ }
+ return forms;
+ }},
+ {"render": function (data, type, row, meta) {
+ let rtype = '';
+ if ( row[2] == 'Lives in' || row[2] == 'Contains' ) { rtype = 'habitat'; }
+ else if ( row[2] == 'Studied for' || row[2] == 'Involves' ) { rtype = 'use'; }
+ else if ( row[2] == 'Exhibits' || row[2] == 'Is exhibited by' ) { rtype = 'phenotype'; }
+ var docids = format_docs(row, alvisir, rtype);
+ return docids;
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[9];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[7];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[8];
+ }},
+ {"visible": false, "render": function (data, type, row, meta) {
+ return row[6];
+ }}
+ ]
+ });
-var thtable = $('#results_taxon_use').DataTable();
+ if ( $('#use_tu').val() != '' ) { filterColumnuse(3); }
+ if ( $('input[name=qps_tu]').is(':checked') == true ) { filterColumnCheck(4); }
-// Data table
-function createTable(taxon) {
+ $('#spinner_taxon_use').hide();
+ $('#spinner_taxon_use2').hide();
+
+ checkURL();
+ });
+ }
+ else {
+ alert("No result for " + taxon);
+ // Spinner off
+ $('#spinner_taxon_use').hide();
+ $('#spinner_taxon_use2').hide();
+ // Clear oracle
+ $("#relationUseByTaxon").val("");
+ $('#filter_taxon_use').attr('disabled', 'disabled');
+ // Change URL
+ window.location.replace(window.location.pathname);
+ }
+}
+function createTable_old(taxon) {
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: taxon, table: 'list_taxon_use'},
function success(path) {
@@ -254,22 +404,6 @@ function createTable(taxon) {
});
}
-// $('#results_taxon_use tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// var row = thtable.row( tr );
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - use
function filterColumnuse(i) {
$('#results_taxon_use').DataTable().column(i).search(
@@ -298,8 +432,8 @@ $('input:checkbox').on('change', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationUseByTaxon").val() !== '' ) {
- url += "?taxon=" + $("#relationUseByTaxon").val();
+ if ( $("#search_taxon_use option:selected").text() !== '' ) {
+ url += "?taxon=" + $("#search_taxon_use option:selected").text();
}
if ( $("#use_tu").val() !== '' ) {
url += "&use=" + $("#use_tu").val();
diff --git a/static/js/searchByUse.js b/static/js/searchByUse.js
index 05b05f411439192d75f48f13c39850fb2693a514..178df597221a0b5228a80126386523ad24e40ecd 100644
--- a/static/js/searchByUse.js
+++ b/static/js/searchByUse.js
@@ -18,35 +18,61 @@ import { format_docs } from './utils.js';
$("#searchByUse.nav-item").addClass( "active" );
-// List Use
-if ( sessionStorage.getItem("list_use_taxon") === null ) {
- $.getJSON($SCRIPT_ROOT + '/_get_list_use_taxon',
- function success(list_use_taxon) {
- sessionStorage.setItem("list_use_taxon", JSON.stringify(Object.keys(list_use_taxon).sort()));
- autocomplete_taxon_use();
+$('#spinner_use_taxon').show();
+$('#spinner_use_taxon2').show();
+
+// Use selection
+var $select = $('#search_use').selectize({
+ valueField: 'path',
+ labelField: 'name',
+ searchField: 'name',
+ sortField: 'name',
+ placeholder: 'e.g. acidification',
+ openOnFocus: false,
+ create: false,
+ maxItems: 1,
+ onInitialize: function() {
+ var that = this;
+
+ $.getJSON($SCRIPT_ROOT + '/_get_list_term',
+ { table: "list_use_taxon"},
+ function(data) {
+ data.forEach(function(item) {
+ that.addOption(item);
+ });
+ $('#spinner_use_taxon').hide();
+ $('#spinner_use_taxon2').hide();
+ $('#search_use option:selected').prop('disabled', false);
+ });
+ },
+ onChange:function(ontobiotopeid){
+ if (ontobiotopeid != "") {
+
+ // Tree event
+ $('#usetree').data('simpleTree').clearSelection();
+ $('#usetree').data('simpleTree').collapseAll();
+ var node = $('#usetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
+ $('#usetree').data('simpleTree').setSelectedNode(node);
+ }
+ }
});
-}
-else {
- autocomplete_taxon_use();
-}
+var selectize = $select[0].selectize;
-// Tree Options
+// Tree
var options = {
searchBox: $('#searchtreeuse'),
searchMinInputLength: 4
};
-
-// Tree
$.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_use', function(data) {
$('#usetree').simpleTree(options, data);
// URL: use
if ( use !== null ) {
- $('#spinner_use_taxon').show();
- $('#spinner_use_taxon2').show();
-
- $("#relationTaxonByUse").val(use);
- $('#filter_use_taxon').removeAttr('disabled');
+ // $('#spinner_use_taxon').show();
+ // $('#spinner_use_taxon2').show();
+ //
+ // $("#relationTaxonByUse").val(use);
+ // $('#filter_use_taxon').removeAttr('disabled');
$.getJSON($SCRIPT_ROOT + '/_get_path',
{name: use, table: 'list_use_taxon'},
@@ -58,7 +84,7 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_use', function(data) {
// Tree event
var node = $('#usetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
$('#usetree').data('simpleTree').setSelectedNode(node);
- $('#searchtreeuse').val(use);
+ // $('#searchtreeuse').val(use);
}
});
@@ -75,100 +101,30 @@ $.getJSON($SCRIPT_ROOT + '/_get_ontobiotope_use', function(data) {
$('input.column_filter').val(taxon);
}
});
-
-// Tree event
$('#usetree').on('simpleTree:change', function(event){
- $('#treeModalUse').modal('hide');
-
- $('#usetree').data('simpleTree').collapseAll();
- $('#usetree').data('simpleTree').expandTo($('#usetree').data('simpleTree').getSelectedNode());
-
- $('#spinner_use_taxon').show();
- $('#spinner_use_taxon2').show();
+ if ( $('#usetree').data('simpleTree').getSelectedNode() != undefined ) {
- $("#relationTaxonByUse").val($('#usetree').data('simpleTree').getSelectedNode().label);
- $('#filter_use_taxon').removeAttr('disabled');
+ selectize.clear(false);
+ selectize.setValue($('#usetree').data('simpleTree').getSelectedNode().value, true);
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: $('#usetree').data('simpleTree').getSelectedNode().label, table: 'list_use_taxon'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
+ $('#spinner_use_taxon').show();
+ $('#spinner_use_taxon2').show();
- // Tree event
- var node = $('#usetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#usetree').data('simpleTree').setSelectedNode(node);
- createTable(ontobiotopeid);
- }
- else {
- alert("No result for " + use);
- // Spinner off
- $('#spinner_use_taxon').hide();
- $('#spinner_use_taxon2').hide();
- // Clear oracle
- $("#relationTaxonByUse").val("");
- $('#filter_use_taxon').attr('disabled', 'disabled');
- // Change URL
- window.location.replace(window.location.pathname);
- }
- });
+ $('#searchtreeuse').val($('#usetree').data('simpleTree').getSelectedNode().label);
+ createTable($('#usetree').data('simpleTree').getSelectedNode().value);
+ $("#search_use option:selected").text();
+ $("#search_use option:selected").text($('#usetree').data('simpleTree').getSelectedNode().label);
+ $("#search_use option:selected").val($('#usetree').data('simpleTree').getSelectedNode().value);
+ selectize.setTextboxValue("");
+ selectize.setTextboxValue($('#usetree').data('simpleTree').getSelectedNode().label);
+ $('#filter_use_taxon').removeAttr('disabled');
+ $('#treeModalUse').modal('hide');
+ }
})
-// Search by use (autocompletion)
-function autocomplete_taxon_use() {
- $( "#relationTaxonByUse" ).autocomplete({
- source: JSON.parse(sessionStorage.getItem("list_use_taxon")),
- minLength: 3,
- select: function( event, ui ) {
- $('#filter_use_taxon').removeAttr('disabled');
-
- $('#spinner_use_taxon').show();
- $('#spinner_use_taxon2').show();
-
- $.getJSON($SCRIPT_ROOT + '/_get_path',
- {name: ui.item.value, table: 'list_use_taxon'},
- function success(path) {
- if ( path != '' ) {
- let l_path = path[0].split('/');
- let ontobiotopeid = l_path[l_path.length-1];
-
- createTable(ontobiotopeid);
-
- // Tree event
- var node = $('#usetree').data('simpleTree').getNodeFromValue(ontobiotopeid);
- $('#usetree').data('simpleTree').setSelectedNode(node);
- $('#searchtreeuse').val(ui.item.value);
- }
- });
- }
- });
-}
-
-// function format(d) {
-//
-// var docids = format_docs(d, alvisir, 'use');
-//
-// return '<table cellpadding="5" cellspacing="0" border="0" style="padding-left:50px;">'+
-// '<tr>'+
-// '<td><b>Full source text</b></td>'+
-// '<td align="justify">'+docids+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (use)</b></td>'+
-// '<td align="justify">'+d[3].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '<tr>'+
-// '<td><b>Occurrence in text (taxon)</b></td>'+
-// '<td align="justify">'+d[1].split(", ").slice(1,).join(', ')+'</td>'+
-// '</tr>'+
-// '</table>';
-// }
-
-var thtable = $('#results_use_taxon').DataTable();
-
// Datatable
+var thtable = $('#results_use_taxon').DataTable();
function createTable(ontobiotopeid) {
$.getJSON($SCRIPT_ROOT + '/_get_list_relations',
@@ -318,22 +274,6 @@ function createTable(ontobiotopeid) {
});
}
-// $('#results_use_taxon tbody').on('click', 'td.details-control', function () {
-// var tr = $(this).closest('tr');
-// var row = thtable.row(tr);
-//
-// if ( row.child.isShown() ) {
-// // This row is already open - close it
-// row.child.hide();
-// tr.removeClass('shown');
-// }
-// else {
-// // Open this row
-// row.child( format(row.data())).show();
-// tr.addClass('shown');
-// }
-// } );
-
// Filter - Taxon
function filterColumnTaxon(i) {
$('#results_use_taxon').DataTable().column(i).search(
@@ -362,8 +302,8 @@ $('input:checkbox').on('change', function () {
// Check url
function checkURL() {
var url = window.location.pathname;
- if ( $("#relationTaxonByUse").val() !== '' ) {
- url += "?use=" + $("#relationTaxonByUse").val();
+ if ( $("#search_use option:selected").text() !== '' ) {
+ url += "?use=" + $("#search_use option:selected").text();
}
if ( $("#taxon_ut").val() !== '' ) {
url += "&taxon=" + $("#taxon_ut").val();
diff --git a/templates/searchByHabitat.html b/templates/searchByHabitat.html
index fdf5aac58e29ce1ae9132db768b043223b549d97..fca570c9173e78bb6821885c4179390bfa70e2ff 100644
--- a/templates/searchByHabitat.html
+++ b/templates/searchByHabitat.html
@@ -32,6 +32,11 @@
</script>
<link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByHabitat.js') }}"></script>
@@ -53,9 +58,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationTaxonByHabitat">Search relations by habitat</label>
- <input type="text" class="form-control" id="relationTaxonByHabitat" placeholder="e.g. cheese">
- <button id="filter_habitat_taxon" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonByHabitat">Search relations by habitat</label>
+ <select class="form-select" id="search_habitat"></select>
+ <button id="filter_habitat_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
diff --git a/templates/searchByPhenotype.html b/templates/searchByPhenotype.html
index 9f052181e775b462e4ceb1700897191abfae86a8..6d03456902c4e1b10c105ed34c3348ca59cdc50c 100644
--- a/templates/searchByPhenotype.html
+++ b/templates/searchByPhenotype.html
@@ -30,7 +30,11 @@
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
- <link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet"><link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByPhenotype.js') }}"></script>
@@ -52,9 +56,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationTaxonByPhenotype">Search relations by phenotype</label>
- <input type="text" class="form-control" id="relationTaxonByPhenotype" placeholder="e.g. thermophile">
- <button id="filter_phenotype_taxon" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonByPhenotype">Search relations by phenotype</label>
+ <select class="form-select" id="search_phenotype"></select>
+ <button id="filter_phenotype_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
diff --git a/templates/searchByTaxon.html b/templates/searchByTaxon.html
index bc847c76eeb99a95ae42bde7ec34acefc7a7ef75..95b66d14a8b2cba0dba87262620bb585d1b004a2 100644
--- a/templates/searchByTaxon.html
+++ b/templates/searchByTaxon.html
@@ -31,6 +31,11 @@
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByTaxon.js') }}"></script>
<div style="margin:30px 0;"></div>
@@ -48,10 +53,10 @@
<div class="container">
<div class="row justify-content-center">
<div class="col-8">
- <div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationHabitatByTaxon">Search relations by taxon</label>
- <input type="text" class="form-control" id="relationHabitatByTaxon" placeholder="e.g. Bacillus subtilis">
- <button id="filter_taxon_habitat" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <div class="input-group mb-3">
+ <label class="button-select input-group-text" for="relationHabitatByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search"></select>
+ <button id="filter_taxon_habitat" type="button" class="btn btn-info button-select-filter" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
diff --git a/templates/searchByTaxonForPhenotype.html b/templates/searchByTaxonForPhenotype.html
index 4b690bc350b19f181d7ed73b143265c6cab56b7d..a35c6507b377b10271a098ed1c125c8b15fd26f9 100644
--- a/templates/searchByTaxonForPhenotype.html
+++ b/templates/searchByTaxonForPhenotype.html
@@ -30,6 +30,11 @@
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByTaxonForPhenotype.js') }}"></script>
<div style="margin:30px 0;"></div>
@@ -49,9 +54,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationPhenotypeByTaxon">Search relations by taxon</label>
- <input type="text" class="form-control" id="relationPhenotypeByTaxon" placeholder="e.g. Bacillus subtilis">
- <button id="filter_taxon_phenotype" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationPhenotypeByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search_taxon_phenotype"></select>
+ <button id="filter_taxon_phenotype" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
diff --git a/templates/searchByTaxonForUse.html b/templates/searchByTaxonForUse.html
index ce033dfd3b2511b8e1b8e0174e1849a0729db61d..930eceb8639bb5cfe572ea9850053c514f152cc8 100644
--- a/templates/searchByTaxonForUse.html
+++ b/templates/searchByTaxonForUse.html
@@ -30,6 +30,11 @@
var alvisir = JSON.parse('{{ alvisir | tojson | safe }}');
</script>
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByTaxonForUse.js') }}"></script>
<div style="margin:30px 0;"></div>
@@ -49,9 +54,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationUseByTaxon">Search relations by taxon</label>
- <input type="text" class="form-control" id="relationUseByTaxon" placeholder="e.g. Bacillus subtilis">
- <button id="filter_taxon_use" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationUseByTaxon">Search relations by taxon</label>
+ <select class="form-select" id="search_taxon_use"></select>
+ <button id="filter_taxon_use" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>
diff --git a/templates/searchByUse.html b/templates/searchByUse.html
index 4a7d21f92e9ec6a871efbcc9eb89e2f83eab678c..09a9d11507d3ea6ae5e0e4ecf5806c71996a151b 100644
--- a/templates/searchByUse.html
+++ b/templates/searchByUse.html
@@ -31,6 +31,11 @@
</script>
<link href="{{ url_for('static', filename='css/simpleTree.css') }}" rel="stylesheet">
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/selectize.boostrap3.css') }}" />
+ <link rel="stylesheet" href="{{ url_for('static', filename='css/additional.css') }}" />
+
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/selectize.js/0.12.1/js/standalone/selectize.js"></script>
<script src="{{ url_for('static', filename='js/lib/simpleTree.js') }}"></script>
<script type="module" src="{{ url_for('static', filename='js/searchByUse.js') }}"></script>
@@ -53,9 +58,9 @@
<div class="row justify-content-center">
<div class="col-8">
<div class="input-group">
- <label style="background-color: #21517A; border-color: #21517A; color: #fff;" class="input-group-text" for="relationTaxonByUse">Search relations by use</label>
- <input type="text" class="form-control" id="relationTaxonByUse" placeholder="e.g. pigmentation">
- <button id="filter_use_taxon" type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
+ <label class="button-select input-group-text" for="relationTaxonByUse">Search relations by use</label>
+ <select class="form-select" id="search_use"></select>
+ <button id="filter_use_taxon" type="button" class="button-select-filter btn btn-info" data-toggle="collapse" data-target="#demo" disabled>Filter selection</button>
</div>
</div>
</div>