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LucaCinquiniLucaCinquini
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Fixed heather's requirements
1 parent 2970eda commit 6568fa5

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lines changed

‎INSTALL.rst

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@@ -5,7 +5,7 @@
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To run Labcas's (EDRN's or MCL's) Portal 2.0+, you'll need the following:
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• A Docker environment
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• The Labcas 2.0 code, ``https://github.com/EDRN/labcas-ui.git``
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• The Labcas 2.1 code, ``https://github.com/EDRN/labcas-ui.git``
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• Docker has access to a labcas JWT/Solr API (Currently edrn/mcl/labcas-dev apis
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are available within JPL servers)
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• A public web server (such as Apache HTTPD, NGINX, AWS Elastic Load Balancer,

‎a/index.html

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<link rel="apple-touch-icon" sizes="76x76" href="/labcas-ui/assets/img/apple-icon.png">
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<link rel="icon" type="image/png" href="/labcas-ui/assets/img/favicon.png">
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<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
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<title>Labcas 2.0</title>
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<title>Labcas 2.1</title>
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<meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0, shrink-to-fit=no' name='viewport' />
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<!-- Fonts and icons -->
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<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700,200" rel="stylesheet" />
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U.S. Government Sponsorship Acknowledged.
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</p>
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<p>
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Labcas version 2.0, Licensed under <a href='https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html'>GPLv2</a>.
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Labcas version 2.1, Licensed under <a href='https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html'>GPLv2</a>.
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<a href='https://mcl-labcas.jpl.nasa.gov/ui/static/plupload-2.1.9.zip'>Get Plupload</a>.
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</p>
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‎assets/conf/edrn-environment.cfg

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"collection_header_extend_Team_37_CTIIP_Animal_Models":"Study,DataGroup",
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"dataset_header_extend_MD_Anderson_Pancreas_IPMN_images":"Race,Age,Gender,Diagnosis,SizeOfCyst,Pane1,Panel2,Instrument,FileType",
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"dataset_header_extend_Team_37_CTIIP_Animal_Models":"StudyStatus,Cohort,Sub-Cohort,Experiment,ExperimentStatus,GeneticDescription_1,GeneticDescription_2,Gender,labcas.pathology:NCITDiagnosisCode,labcas.pathology:NCITOrganCode,labcas.pathology:NCITProcedure,labcas.pathology:Stain,FileType",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary,OwnerPrincipal",
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"collection_id_append":"LeadPI,Institution,Organ,Protocol",
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"escape_characters":"+,-,&,|,!,(,),{,},[,],^,\",~,*,?",
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"filters":"Core,Pathology,Aperio",

‎assets/conf/environment.cfg

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@@ -17,7 +17,7 @@
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"collection_header_extend_Team_37_CTIIP_Animal_Models":"Study,DataGroup",
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"dataset_header_extend_MD_Anderson_Pancreas_IPMN_images":"Race,Age,Gender,Diagnosis,SizeOfCyst,Pane1,Panel2,Instrument,FileType",
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"dataset_header_extend_Team_37_CTIIP_Animal_Models":"StudyStatus,Cohort,Sub-Cohort,Experiment,ExperimentStatus,GeneticDescription_1,GeneticDescription_2,Gender,labcas.pathology:NCITDiagnosisCode,labcas.pathology:NCITOrganCode,labcas.pathology:NCITProcedure,labcas.pathology:Stain,FileType",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary,OwnerPrincipal",
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"collection_id_append":"LeadPI,Institution,Organ,Protocol",
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"escape_characters":"+,-,&,|,!,(,),{,},[,],^,\",~,*,?",
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"filters":"Core,Pathology,Aperio",

‎assets/conf/mcl-environment.cfg

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"collection_header_extend_Team_37_CTIIP_Animal_Models":"Study,DataGroup",
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"dataset_header_extend_MD_Anderson_Pancreas_IPMN_images":"Race,Age,Gender,Diagnosis,SizeOfCyst,Pane1,Panel2,Instrument,FileType",
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"dataset_header_extend_Team_37_CTIIP_Animal_Models":"StudyStatus,Cohort,Sub-Cohort,Experiment,ExperimentStatus,GeneticDescription_1,GeneticDescription_2,Gender,labcas.pathology:NCITDiagnosisCode,labcas.pathology:NCITOrganCode,labcas.pathology:NCITProcedure,labcas.pathology:Stain,FileType",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary",
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"collapsible_headers":"CollectionDescription,DataDisclaimer,MethodDetails,ResultsAndConclusionSummary,OwnerPrincipal",
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"collection_id_append":"LeadPI,Institution,Organ,Protocol",
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"escape_characters":"+,-,&,|,!,(,),{,},[,],^,\",~,*,?",
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"filters":"Core,Pathology,Aperio",

‎assets/js/labcas/authentication.js

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@@ -310,6 +310,8 @@ function fill_collection_details_data(data){
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});
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$('#loading_collection').hide(500);
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}
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function fill_dataset_details_data(data){
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var datasetname = data.response.docs[0].DatasetName;
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}
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$("#children-datasets-section").append(dataset_html);
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}
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function fill_datasets_metadata(data){
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function fill_collection_level_files(data){
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console.log("Metadata size");
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var size = data.response.numFound;
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console.log(size);
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var cpage = data.response.start;
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load_pagination("files",size,cpage);
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$("#files-table tbody").empty();
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var download_list = JSON.parse(localStorage.getItem("download_list"));
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$.each(data.response.docs, function(key, value) {
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var color = "btn-info";
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if(user_data["FavoriteFiles"].includes(value.id)){
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color = "btn-success";
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}
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var thumb = "";
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var filetype = value.FileType ? value.FileType.join(",") : "";
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var site = value.Site ? value.Site.join(",") : "";
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var description = value.Description? value.Description.join(",") : "";
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if ('ThumbnailRelativePath' in value){
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thumb = "<img width='50' height='50' src='/labcas-ui/assets/"+value.ThumbnailRelativePath+"'/>";
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}
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var html_safe_id = encodeURI(escapeRegExp(value.id));
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var filesize = "";
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var filesizenum = 0;
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if (value.FileSize){
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filesize = humanFileSize(value.FileSize, true);
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filesizenum = value.FileSize;
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}
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var checked = "";
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if ( download_list && download_list.includes(html_safe_id) ){
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checked = "checked";
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}
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$("#files-table tbody").append(
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"<tr>"+
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"<td><center><input type='checkbox' class='form-check-input' value='"+html_safe_id+"' "+checked+" data-valuesize='"+filesizenum+"'></center></td>"+
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"<td class='text-left'>"+
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"<a href=\"/labcas-ui/f/index.html?file_id="+
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html_safe_id+"\">"+
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value.FileName+
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"</a>"+
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"</td>"+
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"<td class='text-left'>"+
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site +
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"</td>"+
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"<td class='text-left'>"+
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filetype +
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"</td>"+
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"<td class='text-left'>"+
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description +
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"</td>"+
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"<td class='text-left'>"+
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thumb+
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"</td>"+
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"<td class='text-left'>"+
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filesize+
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"</td>"+
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"<td class=\"td-actions text-right\">"+
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"<button type=\"button\" rel=\"favoritebutton\" title=\"Favorite\" onclick=\"save_favorite('"+value.id+"', 'FavoriteFiles')\" class=\"btn "+color+" btn-simple btn-link\">"+
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"<i class=\"fa fa-star\"></i>"+
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"</button>"+
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"<button type=\"button\" rel=\"downloadbutton\" title=\"Download\" class=\"btn btn-danger btn-simple btn-link\" onclick=\"download_file('"+html_safe_id+"','single')\">"+
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"<i class=\"fa fa-download\"></i>"+
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"</button>"+
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"</td>"+
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"</tr>");
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});
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if (size > 0){
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$("#children-files").show();
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}
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$('#loading_file').hide(500);
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}
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function fill_collection_metadata(data){
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var dataset_metadata_html = '<table class="table" id="metadatadetails-table" style="table-layout: fixed;">';
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$.each(data.response.docs, function(key, value) {
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console.log(key);
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console.log(value.id);
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var html_safe_id = encodeURI(escapeRegExp(value.id));
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console.log(html_safe_id);
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dataset_metadata_html+="<tr>"+
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"<td valign='top' style='padding: 2px 8px;' width='100%'>"+"<center><a href='#' onclick=\"download_file('"+html_safe_id+"','single');\">"+value.FileName+"</a></center>"+"</td>"+
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"<td valign='top' style='padding: 2px 8px;' width='80%'>"+"<center><a href='/labcas-ui/f/index.html?file_id="+html_safe_id+"'>"+value.FileName+"</a></center>"+"</td>"+
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"<td valign='top' style='padding: 2px 8px;' width='20%'>"+"<center><a href='#' onclick=\"download_file('"+html_safe_id+"','single');\">"+"<i class=\"fa fa-download\"></i>"+"</a></center>"+"</td>"+
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"</tr>"
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size += 1;
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});
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var get_var = get_url_vars();
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var metadata_exists = false;
573+
var collection_file_exists = false;
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$.each(data.response.docs, function(key, value) {
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if (value.id.split(/\//)[1] == get_var["collection_id"]){
500-
query_labcas_api(localStorage.getItem('environment')+"/data-access-api/files/select?q=DatasetId:"+value.id+"&wt=json&indent=true", fill_datasets_metadata);
501-
metadata_exists = true;
576+
query_labcas_api(localStorage.getItem('environment')+"/data-access-api/files/select?q=DatasetId:"+value.id+"&wt=json&indent=true", fill_collection_level_files);
577+
collection_file_exists = true;
502578
return;
579+
} else if(value.id.split(/\//)[1].toLowerCase() == "documentation"){
580+
query_labcas_api(localStorage.getItem('environment')+"/data-access-api/files/select?q=DatasetId:"+value.id+"&wt=json&indent=true", fill_collection_metadata);
581+
metadata_exists = true;
503582
}
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var html_safe_id = encodeURI(escapeRegExp(value.id));
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var color = "#0000FF";
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547626
if (!metadata_exists){
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$('#collection_level_files').hide();
549628
}
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if (!collection_file_exists){
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$('#children-files').hide();
631+
}
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if ( dataset_html == "" ){
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$('#datasets_in_collection').hide();
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}

‎assets/js/labcas/utils.js

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}
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function checkSize(filecount, filesize, threshold){
455-
$('#sizeHTML').html("There are <B><font color='red'>"+filecount+"</font></B> files with total size of <B><font color='red'>"+filesize+"</font></B>. This is more than the <B><font color='red'>"+threshold+"</font></B> recommended download size from a web browser. If you'd like to proceed, the browser will initiate a series of download, please ensure to keep your browser and internet connection open over the duration of the download. Alternatively, you may download the below script (requires curl pre-installed) that can be run through your command prompt/terminal instead with minimal interferance.");
455+
$('#sizeHTML').html("There are <B><font color='red'>"+filecount+"</font></B> files with total size of <B><font color='red'>"+filesize+"</font></B>. This is more than the <B><font color='red'>"+threshold+"</font></B> recommended download size from a web browser. If you'd like to proceed, the browser will initiate a series of downloads, please keep your browser and internet connection open for the duration of the download. Alternatively, you may download the below script that can be run through your command prompt/terminal instead with minimal interferance.");
456456
$('#sizeModal').modal({backdrop: 'static', keyboard: false});
457457
$('#sizeModal').modal('show');
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}
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554554
document.body.removeChild(element);
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556556
localStorage.setItem("download_list",JSON.stringify([]));
557-
window.location.reload();
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$('#download_list_link').hide();
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//window.location.reload();
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}
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‎c/index.html

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</div>
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</div>
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</div>
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<div id='children-files' style="display: none" class="col-md-12 ml-auto mr-auto">
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<div class="card card-tasks">
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<div class="card-header ">
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<h4 class="card-title" id="files-title">Files in this Collection</h4>
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</div>
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<div class="card-body">
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<button type="submit" onclick="download_files('files-table');" class="btn btn-primary">Download Selected</button>
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<button type="submit" onclick="download_dataset(dataset_id)" class="btn btn-primary">Download All</button>
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<ul class="pagination pagination-no-border" id='files_pagination_top' style="float: right;"></ul>
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<div class="table-full-width">
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<table class="table" id="files-table">
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<thead>
104+
<th>Select</th>
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<th>Name</th>
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<th>Site</th>
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<th>Type</th>
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<th>Description</th>
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<th>Thumbnail</th>
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<th>Size</th>
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<th>Action</th>
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</thead>
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<tbody>
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<center><img id="loading_file" class="collapse show" height="50px" width="50px" src="/labcas-ui/assets/img/loading.gif"></center>
115+
</tbody>
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</table>
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</div>
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</div>
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<div class="card-footer ">
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<hr>
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<div class="stats">
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<i class="now-ui-icons loader_refresh spin"></i>
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<ul class="pagination pagination-no-border" id='files_pagination_bottom' style="float: right;"></ul>
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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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<!--<script src="/labcas-ui/assets/js/demo.js"></script>-->
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<script src="/labcas-ui/assets/js/plugins/js.cookie.js"></script>
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<script src="/labcas-ui/assets/js/labcas/labcas-sidebar.js"></script>
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<script src="/labcas-ui/assets/js/labcas/authentication.js?109"></script>
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<script src="/labcas-ui/assets/js/labcas/authentication.js?112"></script>
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<script src="/labcas-ui/assets/js/labcas/utils.js?101"></script>
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<script src="/labcas-ui/assets/js/labcas/search.js?100"></script>
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<script type="text/javascript">

‎download.html

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<link rel="apple-touch-icon" sizes="76x76" href="/labcas-ui/assets/img/apple-icon.png">
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<link rel="icon" type="image/png" href="/labcas-ui/assets/img/favicon.png">
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<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
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<title>Labcas 2.0</title>
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<title>Labcas 2.1</title>
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<meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0, shrink-to-fit=no' name='viewport' />
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<!-- Fonts and icons -->
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<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700,200" rel="stylesheet" />
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101101
<div id="fileHTML"></div>
102102
</div>
103103
<div class="modal-footer">
104-
<center><button type="button" class="btn btn-link btn-simple" onclick='download_script_files("data_download.ps1",);' data-dismiss="modal">Download Script File List</button></center>
104+
<center><button type="button" id="download_list_link" class="btn btn-link btn-simple" onclick='download_script_files("data_download.ps1",);' >Download Script File List</button></center>
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<center><button type="button" class="btn btn-link btn-simple" onclick='window.location.reload();' data-dismiss="modal">Done</button></center>
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</div>
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</div>
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</div>

‎index.html

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<link rel="apple-touch-icon" sizes="76x76" href="img/apple-icon.png">
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<link rel="icon" type="image/png" href="img/favicon.png">
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<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
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<title>Labcas 2.0</title>
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<title>Labcas 2.1</title>
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<meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0, shrink-to-fit=no' name='viewport' />
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<!-- Fonts and icons -->
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<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700,200" rel="stylesheet" />
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<nav class="navbar navbar-expand-lg navbar-transparent navbar-absolute">
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<div class="container">
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<div class="navbar-wrapper">
59-
<a class="navbar-brand" href="#pablo">Labcas 2.0</a>
59+
<a class="navbar-brand" href="#pablo">Labcas 2.1</a>
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<button class="navbar-toggler navbar-toggler-right" type="button" data-toggle="collapse" aria-controls="navigation-index" aria-expanded="false" aria-label="Toggle navigation">
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<span class="navbar-toggler-bar burger-lines"></span>
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<span class="navbar-toggler-bar burger-lines"></span>

‎notes.rst

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Assets
2020
------
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assets/conf contains json configuration files specific for each environment the
22-
labcas-ui 2.0 portal is deployed in. EDRN, MCL, and Labcas-dev are the three versions
22+
labcas-ui 2.1 portal is deployed in. EDRN, MCL, and Labcas-dev are the three versions
2323
currently deployed which displays each consortium's relevant data within the portal.
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Configurations include base url links, sort/show/hide fields for each of the three
2525
hierarchical detail pages (collection, dataset, file), search filter fields, and

‎p/index.html

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<link rel="apple-touch-icon" sizes="76x76" href="/labcas-ui/assets/img/apple-icon.png">
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<link rel="icon" type="image/png" href="/labcas-ui/assets/img/favicon.png">
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<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
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<title>Labcas 2.0</title>
9+
<title>Labcas 2.1</title>
1010
<meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0, shrink-to-fit=no' name='viewport' />
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<!-- Fonts and icons -->
1212
<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700,200" rel="stylesheet" />
@@ -167,7 +167,7 @@
167167
U.S. Government Sponsorship Acknowledged.
168168
</p>
169169
<p>
170-
Labcas version 2.0, Licensed under <a href='https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html'>GPLv2</a>.
170+
Labcas version 2.1, Licensed under <a href='https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html'>GPLv2</a>.
171171
<a href='https://mcl-labcas.jpl.nasa.gov/ui/static/plupload-2.1.9.zip'>Get Plupload</a>.
172172
</p>
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