aind-data-transfer-service 1.16.0__py3-none-any.whl → 1.17.2__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- aind_data_transfer_service/__init__.py +1 -1
- aind_data_transfer_service/hpc/client.py +28 -25
- aind_data_transfer_service/models/internal.py +35 -10
- aind_data_transfer_service/server.py +188 -64
- {aind_data_transfer_service-1.16.0.dist-info → aind_data_transfer_service-1.17.2.dist-info}/METADATA +2 -2
- aind_data_transfer_service-1.17.2.dist-info/RECORD +18 -0
- aind_data_transfer_service/templates/admin.html +0 -36
- aind_data_transfer_service/templates/index.html +0 -258
- aind_data_transfer_service/templates/job_params.html +0 -195
- aind_data_transfer_service/templates/job_status.html +0 -324
- aind_data_transfer_service/templates/job_tasks_table.html +0 -146
- aind_data_transfer_service/templates/task_logs.html +0 -31
- aind_data_transfer_service-1.16.0.dist-info/RECORD +0 -24
- {aind_data_transfer_service-1.16.0.dist-info → aind_data_transfer_service-1.17.2.dist-info}/WHEEL +0 -0
- {aind_data_transfer_service-1.16.0.dist-info → aind_data_transfer_service-1.17.2.dist-info}/licenses/LICENSE +0 -0
- {aind_data_transfer_service-1.16.0.dist-info → aind_data_transfer_service-1.17.2.dist-info}/top_level.txt +0 -0
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aind_data_transfer_service/__init__.py,sha256=cCMYl-lxHhXlEMAHdJ7INgHPd0O6ETEp9wsqf6DT8TQ,272
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aind_data_transfer_service/log_handler.py,sha256=c7a-gLmZeRpeCUBwCz6XsTszWXQeQdR7eKZtas4llXM,1700
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aind_data_transfer_service/server.py,sha256=CQdOkX86qn8RQm36NqS5b0aUyNCjvaEbTIObaza6RY0,48910
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aind_data_transfer_service/configs/__init__.py,sha256=9W5GTuso9Is1B9X16RXcdb_GxasZvj6qDzOBDv0AbTc,36
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aind_data_transfer_service/configs/csv_handler.py,sha256=hCdfAYZW_49-l1rbua5On2Tw2ks674Z-MgB_NJlIkU4,5746
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aind_data_transfer_service/configs/job_configs.py,sha256=T-h5N6lyY9xTZ_xg_5FxkyYuMdagApbE6xalxFQ-bqA,18848
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aind_data_transfer_service/configs/job_upload_template.py,sha256=aC5m1uD_YcpbggFQ-yZ7ZJSUUGX1yQqQLF3SwmljrLk,5127
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aind_data_transfer_service/hpc/__init__.py,sha256=YNc68YNlmXwKIPFMIViz_K4XzVVHkLPEBOFyO5DKMKI,53
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aind_data_transfer_service/hpc/client.py,sha256=-WwNjpV2FAJMiXT3Y_JCllSbXPyvqrkPxpNWE0BAWzY,5084
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aind_data_transfer_service/hpc/models.py,sha256=-7HhV16s_MUyKPy0x0FGIbnq8DPL2qJAzJO5G7003AE,16184
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aind_data_transfer_service/models/__init__.py,sha256=Meym73bEZ9nQr4QoeyhQmV3nRTYtd_4kWKPNygsBfJg,25
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aind_data_transfer_service/models/core.py,sha256=uXtPUqjxKalg-sE8MxaJr11w_T_KKBRBSJuUgwoMZlQ,10135
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aind_data_transfer_service/models/internal.py,sha256=tWO1yRMu9hHLv0mt7QhOwTPWGbKApWmCf1wwajx5qjI,10681
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aind_data_transfer_service-1.17.2.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
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aind_data_transfer_service-1.17.2.dist-info/METADATA,sha256=DotVNzRhHX0woD5qMefPipnYAja4EbXje8luub37g9I,2478
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aind_data_transfer_service-1.17.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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aind_data_transfer_service-1.17.2.dist-info/top_level.txt,sha256=XmxH0q27Jholj2-VYh-6WMrh9Lw6kkuCX_fdsj3SaFE,27
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aind_data_transfer_service-1.17.2.dist-info/RECORD,,
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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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<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js"></script>
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<title>{% block title %} {% endblock %} AIND Data Transfer Service Admin</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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</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"
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target="_blank">Help</a> |
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<a href="/admin">Admin</a> |
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<a href="/logout">Log out</a>
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</nav>
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<div>
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<h3>Admin</h3>
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<div>Hello {{user_name}}, welcome to the admin page</div>
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<div>Email: {{user_email}}</div>
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</div>
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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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<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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<a href="/admin">Admin</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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<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="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": "Validating...",
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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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}
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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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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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$.ajax({
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type: "POST",
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data: formData,
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cache: false,
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contentType: false,
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processData: false,
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beforeSend: function() {
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setMessage(msgTypes.validatePending);
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$("#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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[ "job_type", "project_name", "s3_bucket", "platform", "subject_id", "acq_datetime", "metadata_dir", "modality", "modality.input_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.tasks?.modality_transformation_settings;
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if (modalities) {
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modalities = Object.entries(modalities).map(([key, value]) => ({
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abbreviation: key,
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input_source: value.job_settings?.input_source
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}))
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}
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let metadata_dir = job.tasks?.gather_preliminary_metadata?.job_settings?.metadata_dir
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addTableRow(
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[
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{ value: job.job_type, rowspan: modalitiesLength },
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{ value: job.project_name, 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: metadata_dir ?? "", rowspan: modalitiesLength },
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modalities ? modalities[0].abbreviation : "",
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modalities ? modalities[0].input_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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addTableRow(
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[ modality.abbreviation, modality.input_source ],
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);
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}
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},
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error: function(data) {
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jobs = []
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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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if (mail_user !== "" && mail_user !== undefined) {
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<html>
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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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}
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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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}
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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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<a href="/admin">Admin</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-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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},
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});
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// Event listener for version dropdown
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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: '« First',
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previous: '‹ Prev',
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next: 'Next ›',
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last: 'Last »'
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|
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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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}
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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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|
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`<button type="button" class="btn btn-link btn-sm"
|
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|
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data-bs-toggle="modal"
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|
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data-bs-target="#param-modal"
|
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|
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data-bs-param-name=${data}
|
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|
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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=${row.modality}
|
|
187
|
-
>${data}
|
|
188
|
-
</button>`
|
|
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|
-
);
|
|
190
|
-
}
|
|
191
|
-
return data;
|
|
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|
-
}
|
|
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|
-
</script>
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|
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|
-
</body>
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|
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|
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</html>
|