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Added Nextflow run URL column to experiments table for Today and Mage…
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@sandeepreddy792
sandeepreddy792 committed Nov 13, 2024
1 parent fa0f17d commit 817e8a1
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Showing 3 changed files with 17 additions and 6 deletions.
14 changes: 9 additions & 5 deletions sbRestApiServer.js
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ app.use(express.static('ui'));
// Global variables
// Column headings in TSV output - corresponding to experimentsDBQuery
var experimentTSVFields =
['accession','user','directory','name','checker_score','atlas_status','in_curation','status','software','date_submitted','date_last_processed', 'version', 'curator','comment', 'file_validation_status'];
['accession','user','directory','name','checker_score','atlas_status','in_curation','status','software','date_submitted','date_last_processed', 'version', 'curator','comment', 'file_validation_status', 'nextflow_run_id'];

var protocolsTSVFields =
['experiment_accession','protocol_accession','date_last_processed','type','user_accession','name','description','hardware','software'];

var todayTSVFields =
['accession', 'directory', 'name', 'checker_score', 'atlas_fail_score', 'in_curation', 'status', 'date_submitted', 'date_last_processed', 'curator', 'comment', 'file_validation_status'];
['accession', 'directory', 'name', 'checker_score', 'atlas_fail_score', 'in_curation', 'status', 'date_submitted', 'date_last_processed', 'curator', 'comment', 'file_validation_status', 'nextflow_run_id'];

var fastqValidationTSVFields =
['annotare_submission_id', 'date_last_processed', 'library_layout','annotare_file1_id', 'file1_name', 'annotare_file2_id','file2_name','status','comment'];
Expand All @@ -36,7 +36,7 @@ var experimentsDBQuery=
"IF(e.in_curation=1,'yes','no') in_curation, e.status, e.software, " +
"DATE_FORMAT(e.date_submitted, '%Y-%m-%d %H:%i') date_submitted, DATE_FORMAT(e.date_last_processed, '%Y-%m-%d %H:%i GMT') date_last_processed, " +
"e.num_submissions version, " +
"e.curator, REPLACE(e.comment,'\n','') comment, e.file_validation_status " +
"e.curator, REPLACE(e.comment,'\n','') comment, e.file_validation_status, nextflow_run_id " +
"FROM experiments e " +
"join users u on (e.user_id = u.id) " +
"WHERE (e.is_deleted=0 and experiment_type='MAGE-TAB') " +
Expand Down Expand Up @@ -66,7 +66,7 @@ var todayDBQuery =
"SELECT accession, concat('MAGE-TAB_', id) directory, name, checker_score, atlas_fail_score, " +
"IF(in_curation=1,'yes','no') in_curation, status," +
"DATE_FORMAT(date_submitted, '%Y-%m-%d %H:%i') date_submitted, DATE_FORMAT(date_last_processed, '%Y-%m-%d %H:%i GMT') date_last_processed, " +
"curator, comment, file_validation_status " +
"curator, comment, file_validation_status, nextflow_run_id " +
"FROM experiments " +
"WHERE experiment_type='MAGE-TAB' AND date_last_processed >= NOW() - INTERVAL 1 DAY " +
"ORDER BY date_last_processed desc";
Expand Down Expand Up @@ -129,7 +129,11 @@ function returnResults(res, err, results, format, tsvFields) {
// Note that dates in DB are always GMT - hence are incorrect during BST period - hence the adjustment below
var dateTimeInCurrentTimeZone = dateFormat(new Date(result[entry]),'yyyy-mm-dd HH:MM');
row.push(dateTimeInCurrentTimeZone);
} else {
} else if (entry === "nextflow_run_id" && result[entry] != null && result[entry] != undefined) {
var nextFlowRunURL = "https://cloud.seqera.io/orgs/aexpress/workspaces/aexpress_workspace/watch/" + result[entry];
var URLHTMLElelment = "<a href='" + nextFlowRunURL + "' target=\"_blank\">" + result[entry] + "</a>";
row.push(URLHTMLElelment);
} else {
row.push(val);
}
});
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3 changes: 3 additions & 0 deletions ui/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ <h1 class="page_title"><font color="ENV_COLOUR">ENVIRONMENT Submissions Tracking
rowspan="1" colspan="1" aria-label="Comment: activate to sort column ascending" style="width: 250px;">Comment</th>
<th class="sorting" tabindex="0" aria-controls="example"
rowspan="1" colspan="1" aria-label="File validation: activate to sort column ascending" style="width: 70px;">File validation</th>
<th class="sorting" tabindex="0" aria-controls="example"
rowspan="1" colspan="1" aria-label="Nextflow run id: activate to sort column ascending" style="width: 70px;">Nextflow run id</th>
</tr>
</thead>
<tfoot>
Expand All @@ -87,6 +89,7 @@ <h1 class="page_title"><font color="ENV_COLOUR">ENVIRONMENT Submissions Tracking
<th rowspan="1" colspan="1">Curator</th>
<th rowspan="1" colspan="1">Comment</th>
<th rowspan="1" colspan="1">File validation</th>
<th rowspan="1" colspan="1">Nextflow run id</th>
</tr>
</tfoot>
</table>
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6 changes: 5 additions & 1 deletion ui/today.html
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,10 @@ <h1 class="page_title"><font color="ENV_COLOUR">ENVIRONMENT Submissions Tracking
rowspan="1" colspan="1" aria-label="Curator: activate to sort column ascending" style="width: 50px;">Curator</th>
<th class="sorting" tabindex="0" aria-controls="example"
rowspan="1" colspan="1" aria-label="Comment: activate to sort column ascending" style="width: 250px;">Comment</th>
<th class="sorting" tabindex="0" aria-controls="example" rowspan="1" colspan="1" aria-label="File validation: activate to sort column ascending" style="width: 70px;">File validation</th>
<th class="sorting" tabindex="0" aria-controls="example"
rowspan="1" colspan="1" aria-label="File validation: activate to sort column ascending" style="width: 70px;">File validation</th>
<th class="sorting" tabindex="0" aria-controls="example"
rowspan="1" colspan="1" aria-label="Nextflow run id: activate to sort column ascending" style="width: 70px;">Nextflow run id</th>
</tr>
</thead>
<tfoot>
Expand All @@ -79,6 +82,7 @@ <h1 class="page_title"><font color="ENV_COLOUR">ENVIRONMENT Submissions Tracking
<th rowspan="1" colspan="1">Curator</th>
<th rowspan="1" colspan="1">Comment</th>
<th rowspan="1" colspan="1">File validation</th>
<th rowspan="1" colspan="1">Nextflow run id</th>
</tr>
</tfoot>
</table>
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