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[ALS-5208] Remove Open Access from Authorized BDC (#257)
* [ALS-5208] Remove Open Access from Authorized BDC * [ALS-5208] Remove top panel from Data Access Dashboard
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77 changes: 77 additions & 0 deletions
77
biodatacatalyst-ui/src/main/webapp/picsureui/studyAccess/study-utility.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| define(["jquery", "backbone", "handlebars", "text!studyAccess/studies-data.json"], | ||
| function ($, bb, hbs, studyAccessConfiguration) { | ||
| function getStudyAccessConfiguration() { | ||
| return JSON.parse(studyAccessConfiguration); | ||
| } | ||
|
|
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| function groupRecordsByAccess() { | ||
| // extract the consent identifiers from the query template | ||
| let session = JSON.parse(sessionStorage.getItem("session")); | ||
| let validConsents = []; | ||
| if (session.queryTemplate) { | ||
| let temp = JSON.parse(session.queryTemplate); | ||
|
|
||
| if (temp && temp.categoryFilters && temp.categoryFilters["\\_consents\\"]) { | ||
| validConsents = temp.categoryFilters["\\_consents\\"]; | ||
| } | ||
| } | ||
|
|
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| // process the study data into permission granted or not groups | ||
| let records = { | ||
| permitted: [], | ||
| denied: [], | ||
| na: [] | ||
| }; | ||
| let configurationData = JSON.parse(studyAccessConfiguration); | ||
| for (let groupid in configurationData) { | ||
| for (idx = 0; idx < configurationData[groupid].length; idx++) { | ||
| // determine if logged in user is permmited access | ||
| let tmpStudy = configurationData[groupid][idx]; | ||
| const cvc = parseInt(tmpStudy["clinical_variable_count"]).toLocaleString(); | ||
| tmpStudy["clinical_variable_count"] = cvc == '-1' || cvc == 'NaN' ? 'N/A' : cvc; | ||
| const css = parseInt(tmpStudy["clinical_sample_size"]).toLocaleString(); | ||
| tmpStudy["clinical_sample_size"] = css == '-1' || cvc == 'NaN' ? 'N/A' : css; | ||
| const gsc = parseInt(tmpStudy["genetic_sample_size"]).toLocaleString(); | ||
| tmpStudy["genetic_sample_size"] = gsc == '-1' || gsc == 'NaN' ? 'N/A' : gsc; | ||
|
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| let studyConsent = tmpStudy["study_identifier"] + (tmpStudy["consent_group_code"] && tmpStudy["consent_group_code"] != "" ? "." + tmpStudy["consent_group_code"] : ""); | ||
| tmpStudy['accession'] = tmpStudy["consent_group_code"] ? | ||
| tmpStudy["study_identifier"] + "." + tmpStudy["study_version"] + "." + tmpStudy["study_phase"] + "." + tmpStudy["consent_group_code"] : | ||
| ""; // Show empty string if no consent group code (open dataset) | ||
| if (validConsents.includes(studyConsent)) { | ||
| tmpStudy['isGranted'] = true; | ||
| records.permitted.push(tmpStudy); | ||
| } else { | ||
| if (!tmpStudy['authZ']) { | ||
| tmpStudy['isSuspended'] = true; | ||
| } | ||
| if (tmpStudy["consent_group_code"] == "c0") { | ||
| tmpStudy['isGranted'] = false; | ||
| records.na.push(tmpStudy); | ||
| } else { | ||
| records.denied.push(tmpStudy); | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| // sort by "consent group" then "abbreviated name" | ||
| var funcSort = function (a, b) { | ||
| if (a["abbreviated_name"] == b["abbreviated_name"]) { | ||
| return (a["study_identifier"].localeCompare(b["study_identifier"])); | ||
| } else { | ||
| return (a["abbreviated_name"].localeCompare(b["abbreviated_name"])); | ||
| } | ||
| }; | ||
| records.permitted.sort(funcSort); | ||
| records.denied.sort(funcSort); | ||
| records.na.sort(funcSort); | ||
|
|
||
| return records; | ||
| } | ||
|
|
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| return { | ||
| getStudyAccessConfiguration: getStudyAccessConfiguration, | ||
| groupRecordsByAccess: groupRecordsByAccess | ||
| }; | ||
| }); |
89 changes: 4 additions & 85 deletions
89
biodatacatalyst-ui/src/main/webapp/picsureui/studyAccess/studyAccess.hbs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,97 +1,16 @@ | ||
| <div class="center-panel"> | ||
| <div class="panel panel-outline explor-panel"> | ||
| <div class="panel-heading no-border center-panel"> | ||
| <div class="side-border heading-space"> | ||
| <div> | ||
| <h4 class="access-title">Authorized Access</h4> | ||
| <button type="button" data-href="/picsureui/queryBuilder" aria-label="Explore Authorized Access" | ||
| {{#if authorizedAccess}}class="btn btn-primary btn-blue clickable-button"{{/if}} | ||
| {{#unless authorizedAccess}}class="btn btn-primary btn-grey"{{/unless}} | ||
| {{#unless authorizedAccess}}disabled="disabled"{{/unless}}> | ||
| Explore Now | ||
| </button> | ||
| </div> | ||
| <div class="participants-container"> | ||
| <h4 class="">{{auth_studies_cnt}} Studies</h4> | ||
| <h5 class="" id="authorized-participants"></h5> | ||
| <div id="authorized-participants-spinner"></div> | ||
| </div> | ||
| </div> | ||
| <div class="heading-space"> | ||
| <div> | ||
| <h4 class="access-title">Open Access</h4> | ||
| <button type="button" class="btn btn-primary btn-blue clickable-button" data-href="/picsureui/openAccess" aria-label="Explore Open Access">Explore Now</button> | ||
| </div> | ||
| <div class="participants-container"> | ||
| <h4 id="open-studies-count" class=""></h4> | ||
| <h5 id="open-participants" class=""></h5> | ||
| <div id="open-participants-spinner"></div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <div class="panel-body" style="display: flex;"> | ||
| <div class="body-space side-border"> | ||
| <ul class="plain-list"> | ||
| <li style="display: flex; flex-direction:row"> | ||
| <i class="fa-regular fa-address-card" aria-hidden="true"></i> | ||
| <i class="fa-solid fa-dna" aria-hidden="true"></i> | ||
| <span>Authorized Phenotypic and Genomic Datasets</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa fa-users" aria-hidden="true"></i> | ||
| <span>Aggregate Counts</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa-regular fa-user" aria-hidden="true"></i> | ||
| <span>Participant-level Data</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa fa-pie-chart" aria-hidden="true"></i> | ||
| <span>Visualizations</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa-solid fa-laptop-code" aria-hidden="true"></i> | ||
| <span>R and Python API Access</span> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| <div class="body-space"> | ||
| <ul class="plain-list"> | ||
| <li> | ||
| <i class="fa-regular fa-circle-check" aria-hidden="true"></i> | ||
| <span>No Authorization Required</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa-regular fa-address-card" aria-hidden="true"></i> | ||
| <span>All Phenotypic Datasets Available in PIC-SURE</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa fa-users" aria-hidden="true"></i> | ||
| <span>Aggregate Counts Only</span> | ||
| </li> | ||
| <li> | ||
| <i class="fa-solid fa-laptop-code" aria-hidden="true"></i> | ||
| <span>R and Python API Access</span> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
|
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| <div id="studies-access"> | ||
| <div class="space-out"> | ||
| <div> | ||
| <h2 class="studies-title">Data Access Table</h2> | ||
| <h4 class="studies-sub-title">View all studies and associated information available in PIC-SURE separated by consent group. Check personalized authorization for available studies in the "Access" column.</h4> | ||
| <h4 class="studies-sub-title">View all studies and associated information available in PIC-SURE separated by | ||
| consent group. Check personalized authorization for available studies in the "Access" column.</h4> | ||
| </div> | ||
| <div class="freeze-message"> | ||
| <div>{{freeze_msg}}</div> | ||
| </div> | ||
| </div> | ||
| <div class="flex-col table-responsive" style="overflow-x: visible !important;"> | ||
| <table id="data-access-table" style="width:100%" class="table table-striped row-border hover" role="region" aria-label="A table showing infomation about studies included in Pic-sure. Use the first column to request access to studies."></table> | ||
| <table id="data-access-table" style="width:100%" class="table table-striped row-border hover" role="region" | ||
| aria-label="A table showing infomation about studies included in Pic-sure. Use the first column to request access to studies."></table> | ||
| </div> | ||
| </div> |
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