aind-data-transfer-service 1.12.0__py3-none-any.whl

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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.4/jquery.min.js"></script>
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+ <meta charset="UTF-8">
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+ <title>{% block title %} {% endblock %} AIND Data Transfer Service</title>
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+ <style>
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+ body {
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+ margin: 20px;
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+ font-family: arial, sans-serif;
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+ }
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+ fieldset {
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+ display:inline
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+ }
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+ table {
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+ border-collapse: collapse;
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+ width: 75%;
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+ }
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+ td, th {
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+ border: 1px solid #dddddd;
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+ text-align: left;
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+ padding: 8px;
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+ }
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+ th, tr:hover {
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+ background-color: #E8EAF6;
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+ color: #3F51B5;
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+ }
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+ #submit {
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+ border: none;
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+ border-radius: 6px;
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+ color: #ffffff;
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+ padding: 8px;
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+ width: 80px;
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+ font-size: medium;
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+ background-color: #5065df;
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+ &:hover { background-color: #3f51b5; }
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+ }
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+ #message {
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+ margin-top: 20px;
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+ &.success { color: green; }
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+ &.error { color: red; }
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+ }
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+ </style>
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+ </head>
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+ <body>
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+ <nav>
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+ <a href="/">Submit Jobs</a> |
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+ <a href="/jobs">Job Status</a> |
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+ <a href="/job_params">Job Parameters</a> |
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+ <a title="Download job template as .xslx" href= "/api/job_upload_template" download>Job Submit Template</a> |
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+ <a title="List of project names" href= "{{ project_names_url }}" target="_blank" >Project Names</a> |
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+ <a title="For more information click here" href="https://aind-data-transfer-service.readthedocs.io" target="_blank" >Help</a>
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+ </nav>
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+ <br>
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+ <div>
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+ <p1>For instructions on how to submit jobs click on the Help tab</p1>
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+ </div>
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+ <h2>Submit Jobs</h2>
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+ <div>
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+ <fieldset>
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+ <legend>Mail Notifications (optional)</legend><br>
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+ <div>
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+ <label for="email" title="Optionally provide an allen institute email address to receive upload job status notifications">Allen Institute email:</label>
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+ <input type="email" id="email" pattern=".+@alleninstitute\.org" size="30" placeholder="@alleninstitute.org" /><br><br>
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+ </div>
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+ <div>
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+ <input type="checkbox" id="begin" name="begin" />
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+ <label for="begin">BEGIN</label> |
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+ <input type="checkbox" id="end" name="end" />
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+ <label for="end">END</label> |
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+ <input type="checkbox" id="fail" name="fail" checked />
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+ <label for="fail">FAIL</label> |
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+ <input type="checkbox" id="retry" name="retry" />
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+ <label for="retry">RETRY</label> |
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+ <input type="checkbox" id="all" name="all" />
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+ <label for="all">ALL</label>
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+ </div>
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+ </fieldset>
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+ </div><br><br>
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+ <form id="file_form" method="post" enctype="multipart/form-data">
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+ <label for="file">Please select a .csv or .xlsx file:</label>
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+ <input type="file" id="file" name="file" accept=".csv,.xlsx" onchange="validateJobs(this)" onclick="this.value=null"><br><br>
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+ </form>
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+ <button id="submit" type="button" onclick="submitJobs()">Submit</button>
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+ <div id="message"></div><br>
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+ <div id="response"></div>
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+ <script>
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+ var jobs = []
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+ var parsing_errors = []
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+ const msgTypes = {
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+ "validatePending": "Sending...",
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+ "validateSuccess": "Successfully validated jobs from file.",
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+ "validateError": "Error validating jobs from file.",
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+ "submitPending": "Submitting jobs. Please do not refresh or re-submit...",
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+ "submitSuccess": "Successfully submitted jobs.",
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+ "submitError": "Error submitting jobs."
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+ }
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+ setMessage = function(msgType) {
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+ $("#message").removeClass("success");
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+ $("#message").removeClass("error");
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+ $("#message").html(msgType);
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+ if (msgType == msgTypes.validateSuccess || msgType == msgTypes.submitSuccess) {
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+ $("#message").addClass("success");
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+ } else if (msgType == msgTypes.validateError || msgType == msgTypes.submitError) {
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+ $("#message").addClass("error");
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+ }
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+ };
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+ addTableRow = function(data, table, tr, td, isHeader) {
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+ tr = document.createElement('tr');
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+ for (var d of data) {
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+ td = document.createElement(isHeader ? 'th' : 'td');
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+ td.innerHTML = d.value ?? d;
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+ if (d.rowspan) {
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+ td.setAttribute("rowspan", d.rowspan);
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+ }
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+ tr.append(td);
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+ }
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+ table.appendChild(tr);
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+ };
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+ validateJobs = function(fileElement) {
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+ if (fileElement.files.length != 1) {
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+ // File attach was cancelled by user
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+ return;
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+ }
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+ if (![".csv", ".xlsx"].some(ext => fileElement.files[0].name.endsWith(ext))) {
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+ fileElement.value = null;
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+ alert("Invalid file type. Please attach a .csv or .xlsx file.");
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+ return;
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+ }
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+ var formData = new FormData(document.getElementById("file_form"));
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+ $.ajax({
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+ url: "/api/v1/validate_csv",
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+ type: "POST",
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+ data: formData,
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+ cache: false,
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+ contentType: false,
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+ processData: false,
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+ beforeSend: function() {
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+ setMessage(msgTypes.validatePending);
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+ $("#response").html("");
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+ },
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+ success: function(data) {
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+ setMessage(msgTypes.validateSuccess);
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+ jobs = data["data"]["jobs"];
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+ parsing_errors = []
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+ let jobsLength = jobs.length;
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+ var table = document.createElement('table'), tr, td, row;
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+ addTableRow(
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+ [ "project_name", "process_capsule_id", "input_data_mount", "s3_bucket", "platform", "subject_id", "acq_datetime", "metadata_dir", "modality", "modality.source" ],
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+ table, tr, td, true
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+ );
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+ for (row = 0; row < jobsLength; row++) {
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+ let job = jobs[row];
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+ let modalities = job.modalities;
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+ let modalitiesLength = modalities.length;
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+ addTableRow(
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+ [ { value: job.project_name, rowspan: modalitiesLength },
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+ { value: job.process_capsule_id ?? "", rowspan: modalitiesLength },
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+ { value: job.input_data_mount ?? "", rowspan: modalitiesLength },
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+ { value: job.s3_bucket, rowspan: modalitiesLength },
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+ { value: job.platform.abbreviation, rowspan: modalitiesLength },
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+ { value: job.subject_id, rowspan: modalitiesLength },
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+ { value: job.acq_datetime, rowspan: modalitiesLength },
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+ { value: job.metadata_dir ?? "", rowspan: modalitiesLength },
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+ modalities ? modalities[0].modality.abbreviation : "",
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+ modalities ? modalities[0].source : ""
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+ ], table, tr, td, false
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+ );
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+ for (mRow = 1; mRow < modalitiesLength; mRow++) {
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+ let modality = modalities[mRow]
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+ addTableRow(
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+ [ modality.modality.abbreviation, modality.source ],
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+ table, tr, td, false
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+ );
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+ }
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+ }
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+ $("#response").html(table);
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+ },
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+ error: function(data) {
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+ jobs = []
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+ parsing_errors = data.responseJSON["data"]["errors"]
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+ setMessage(msgTypes.validateError);
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+ $("#response").html(parsing_errors.map((err) => {
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+ return `<li>${err}</li>`
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+ }));
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+ }
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+ });
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+ };
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+ submitJobs = function() {
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+ if(jobs.length > 0 && parsing_errors.length == 0){
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+ let job_settings = {};
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+ let mail_user = $("#email").val();
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+ if (mail_user !== "" && mail_user !== undefined) {
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+ job_settings["user_email"] = mail_user;
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+ };
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+ let mail_type = [];
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+ if ($("#all").is(":checked")) {
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+ mail_type = ["all"];
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+ };
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+ if ($("#begin").is(":checked")) {
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+ mail_type.push("begin");
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+ };
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+ if ($("#end").is(":checked")) {
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+ mail_type.push("end");
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+ };
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+ if ($("#fail").is(":checked")) {
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+ mail_type.push("fail");
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+ };
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+ if ($("#retry").is(":checked")) {
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+ mail_type.push("retry");
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+ };
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+ job_settings["email_notification_types"] = mail_type
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+ job_settings["upload_jobs"] = jobs
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+ $.ajax({
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+ url: "/api/v1/submit_jobs",
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+ type: "POST",
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+ data: JSON.stringify(job_settings),
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+ contentType: 'application/json; charset=utf-8',
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+ beforeSend: function() {
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+ setMessage(msgTypes.submitPending);
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+ $("#response").html("");
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+ },
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+ success: function (data) {
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+ jobs = []
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+ parsing_errors = []
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+ setMessage(msgTypes.submitSuccess);
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+ $("#response").html(data);
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+ },
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+ error: function(data) {
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+ jobs = []
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+ setMessage(msgTypes.submitError);
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+ parsing_errors = data.responseJSON["data"]["errors"]
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+ $("#response").html(parsing_errors.map((errStr) => {
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+ return `<li>${errStr}</li>`
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+ }));
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+ }
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+ });
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+ } else if (jobs.length == 0) {
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+ alert("No valid jobs to submit. Please attach a .csv or .xlsx file with valid jobs.");
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+ return;
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+ }
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+ };
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+ </script>
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+ </body>
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+ </html>
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta charset="UTF-8">
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+ <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet">
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+ <link href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-icons/1.8.1/font/bootstrap-icons.min.css" rel="stylesheet">
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+ <link rel="stylesheet" href="https://cdn.datatables.net/2.1.8/css/dataTables.dataTables.css" />
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+ <link rel="stylesheet" href="https://cdn.datatables.net/searchpanes/2.3.3/css/searchPanes.dataTables.css" />
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+ <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
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+ <script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.29.3/moment.min.js"></script>
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+ <script type="text/javascript" src="https://cdn.jsdelivr.net/jquery/latest/jquery.min.js"></script>
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+ <script src="https://cdn.datatables.net/2.1.8/js/dataTables.js"></script>
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+ <script src="https://cdn.datatables.net/searchpanes/2.3.3/js/dataTables.searchPanes.js"></script>
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+ <script src="https://cdn.datatables.net/select/3.0.0/js/dataTables.select.js"></script>
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+ <title>{% block title %} {% endblock %} AIND Data Transfer Service Job Parameters</title>
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+ <style>
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+ body {
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+ margin: 20px;
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+ font-family: arial, sans-serif;
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+ }
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+ nav {
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+ height: 40px;
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+ }
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+ .modal-body {
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+ max-height: calc(100vh - 200px);
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+ overflow: auto;
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+ }
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+ </style>
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+ </head>
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+ <body>
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+ <nav>
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+ <a href="/">Submit Jobs</a> |
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+ <a href="/jobs">Job Status</a> |
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+ <a href="/job_params">Job Parameters</a> |
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+ <a title="Download job template as .xslx" href= "/api/job_upload_template" download>Job Submit Template</a> |
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+ <a title="List of project names" href= "{{ project_names_url }}" target="_blank" >Project Names</a> |
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+ <a title="For more information click here" href="https://aind-data-transfer-service.readthedocs.io" target="_blank" >Help</a>
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+ </nav>
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+ <div class="content">
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+ <h4 class="mb-2">
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+ <!-- dropdown to switch version -->
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+ <div id="version-dropdown" class="btn-group mb-2">
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+ <button id="version-button" type="button" class="btn btn-primary dropdown-toggle" data-bs-toggle="dropdown">
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+ {{default_version}}
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+ </button>
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+ <ul class="dropdown-menu">
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+ {% for v in versions %}
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+ <button class="dropdown-item" type="button">{{ v }}</button>
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+ {% endfor %}
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+ </ul>
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+ </div>
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+ <span>Job Parameters</span>
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+ </h4>
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+ <!-- job params table -->
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+ <div>
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+ <table id="job-params-table" class="display compact table table-bordered table-sm" style="font-size: small">
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+ <thead>
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+ <tr>
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+ <th>Job Type</th>
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+ <th>Task ID</th>
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+ <th>Modality</th>
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+ <th>Parameter Name</th>
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+ <th>Last Modified</th>
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+ </tr>
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+ </thead>
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+ </table>
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+ <!-- modal for displaying param value as json -->
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+ <div class="modal fade" id="param-modal" tabindex="-1" aria-labelledby="param-modal-label" aria-hidden="true">
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+ <div class="modal-dialog modal-xl">
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+ <div class="modal-content">
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+ <div class="modal-header">
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+ <h5 class="modal-title" id="param-modal-label"></h5>
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+ <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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+ </div>
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+ <div class="modal-body">
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+ <pre id="param-modal-content" class="bg-light p-1 border rounded"></pre>
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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>
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+ $(document).ready(function() {
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+ createJobParamsTable();
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+ // Event listeners for param value modal
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+ $('#param-modal').on('show.bs.modal', function(event) {
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+ var button = $(event.relatedTarget);
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+ var paramName = button.data('bs-param-name');
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+ var jobType = button.data('bs-job-type');
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+ var taskId = button.data('bs-task-id');
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+ var modality = button.data('bs-modality');
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+ // update the modal label and contents
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+ var modal = $(this);
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+ modal.find('#param-modal-label').text(paramName);
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+ var version = $('#version-button').text().trim();
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+ var getParameterUrl = `/api/${version}/parameters/job_types/${jobType}/tasks/${taskId}`;
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+ if (modality) {
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+ getParameterUrl += `/${modality}`;
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+ }
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+ $.ajax({
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+ url: getParameterUrl,
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+ type: 'GET',
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+ success: function(response) {
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+ jsonStr = JSON.stringify(response.data, null, 3);
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+ modal.find('#param-modal-content').text(jsonStr);
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+ },
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+ error: function(xhr, status, error) {
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+ modal.find('#param-modal-content').text(error);
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+ }
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+ });
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+ });
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+ $('#param-modal').on('hidden.bs.modal', function() {
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+ $(this).find('#param-modal-label').text('');
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+ $(this).find('#param-modal-content').text('');
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+ });
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+ // Event listener for version dropdown
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+ $('#version-dropdown .dropdown-item').on('click', function() {
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+ var version = $(this).text();
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+ if (version != $('#version-button').text().trim()) {
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+ $('#version-button').text(version);
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+ $('#job-params-table').DataTable().ajax.url(`/api/${version}/parameters`).load();
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+ }
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+ });
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+ });
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+ // Create DataTable for job params table
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+ function createJobParamsTable() {
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+ $('#job-params-table').DataTable({
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+ ajax: {
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+ url: "/api/{{default_version}}/parameters",
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+ dataSrc: 'data'
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+ },
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+ processing: true,
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+ columns: [
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+ { data: 'job_type', searchPanes: {show: true} },
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+ { data: 'task_id', searchPanes: {show: true} },
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+ { data: 'modality', searchPanes: {show: false} },
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+ { data: 'name', render: renderParameterButton },
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+ { data: 'last_modified', render: renderDatetime },
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+ ],
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+ order: [0, 'asc'],
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+ // preselect "default" job_type
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+ searchPanes: {
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+ preSelect: [ { rows: ['default'], column: 0 } ],
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+ },
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+ // options to match default jobs table
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+ pageLength: 25,
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+ layout: {
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+ topStart: null,
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+ topEnd: null,
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+ bottomStart: null,
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+ bottomEnd: null,
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+ top1Start: "searchPanes",
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+ top: [
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+ 'pageLength',
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+ 'info',
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+ { paging: { numbers: false } }
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+ ],
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+ },
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+ language: {
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+ info: "_START_ to _END_ of _TOTAL_",
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+ infoEmpty: "0 to 0 of 0",
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+ entries: { _: "parameters", 1: "parameter" },
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+ paginate: {
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+ first: '&laquo; First',
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+ previous: '&lsaquo; Prev',
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+ next: 'Next &rsaquo;',
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+ last: 'Last &raquo;'
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+ },
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+ },
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+ });
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+ }
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+ function renderDatetime(data, type, row) {
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+ return (type === 'display') ? moment.utc(data).local().format('YYYY-MM-DD h:mm:ss a') : data;
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+ }
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+ function renderParameterButton(data, type, row) {
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+ if (type == 'display') {
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+ return (
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+ `<button type="button" class="btn btn-link btn-sm"
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+ data-bs-toggle="modal"
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+ data-bs-target="#param-modal"
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+ data-bs-param-name=${data}
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+ data-bs-job-type=${row.job_type}
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+ data-bs-task-id=${row.task_id}
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+ data-bs-modality=${row.modality}
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+ >${data}
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+ </button>`
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+ );
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+ }
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+ return data;
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+ }
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+ </script>
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+ </body>
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+ </html>