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Update emails for status change #801

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merged 3 commits into from
Jan 18, 2024
Merged

Update emails for status change #801

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71bc5ae
update signature and iRODS documentation link
jmtcsngr Jan 17, 2024
ae982c2
use https for tracking urls in emails
jmtcsngr Jan 18, 2024
8b955db
remove illumina lane qc link from emails
jmtcsngr Jan 17, 2024
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4 changes: 4 additions & 0 deletions Changes
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,10 @@ LIST OF CHANGES
- Extended the code for the samplesheet daemon to generate samplesheets for
NovaSeqX instruments.
- Removed remaining unused test data from the era of xml st::api::lims driver.
- Updated signature and iRODS documentation link in template for emails
- Updated NPG tracking url to https protocol and port for links in emails
- Removed link to illumina/runs qc page in emails reporting status change event
to subscribers

release 98.1.0
- Added a new method, latest_revision_for_modification, to
Expand Down
3 changes: 1 addition & 2 deletions data/npg_tracking_email/templates/run_status2followers.tt2
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Expand Up @@ -11,13 +11,12 @@ Study '[% lanes.0.study_name %]' has samples in the following lanes of this run:
Sequencing and default analysis for this run completed. Run is now pending manual QC review. Meanwhile, we will be loading analysis results into iRODS.
[%- END %]
[%- IF status_description == 'qc complete' -%]
The manual QC review is complete and your data should now be available from iRODS (see http://scratchy.internal.sanger.ac.uk/wiki/index.php/IRODS_for_Sequencing_Users ).
The manual QC review is complete and your data should now be available from iRODS (see https://ssg-confluence.internal.sanger.ac.uk/display/FARM/iRODS ).
[%- END %]

NPG page for the run:
[% PROCESS urls.tt2 %][% npg_tracking_url %]/run/[% id_run %]

Analysis and QC information for this run will be/is available:
[% seqqc_url %]/illumina/runs/[% id_run %]
[% seqqc_url %]/checks/runs/[% id_run %]
[% END %]
2 changes: 1 addition & 1 deletion data/npg_tracking_email/templates/urls.tt2
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@@ -1,4 +1,4 @@
[%
seqqc_url = 'http://sfweb.internal.sanger.ac.uk:1959';
npg_tracking_url = 'http://sfweb.internal.sanger.ac.uk:9000/perl/npg';
npg_tracking_url = 'https://sfweb.internal.sanger.ac.uk:12443/perl/npg';
%]
2 changes: 1 addition & 1 deletion data/npg_tracking_email/templates/wrapper.tt2
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@@ -1,2 +1,2 @@
[% content %]
NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
28 changes: 14 additions & 14 deletions t/80-npg_tracking-report-event2subscribers.t
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Expand Up @@ -154,9 +154,9 @@ Run 21915 was assigned status "run pending" on 2017-02-08 11:49:39 by joe_events


NPG page for this run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT
is ($e->report_full(), $report, 'full report text');

Expand All @@ -171,9 +171,9 @@ Run 21915 was assigned status "run pending" on 2017-02-08 11:49:39 by joe_events

$lims_summary
NPG page for this run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT1
is ($e->report_full($e->lims()), $report, 'full report text with LIMs data');

Expand Down Expand Up @@ -215,9 +215,9 @@ subtest 'instrument status event' => sub {
Instrument HS8 status changed to "wash performed" on $date_as_string by joe_approver

NPG page for this instrument:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT2
is ($e->report_full($e->lims()), $report, 'full report text');

Expand All @@ -229,9 +229,9 @@ REPORT2
Instrument HS8 status changed to "wash performed" on $date_as_string by joe_approver. Comment: my comment

NPG page for this instrument:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT3
is ($e->report_full($e->lims()), $report, 'full report text with a comment');
is (scalar @{$e->reports}, 1, 'One report generated');
Expand Down Expand Up @@ -270,9 +270,9 @@ Run 21915 annotated by joe_loader on $date_as_string - New run annotation

$lims_summary
NPG page for this run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT4
is ($e->report_full($e->lims()), $report, 'full report text with LIMs data');
};
Expand Down Expand Up @@ -323,9 +323,9 @@ Lane 2: Samples


NPG page for this run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT5
is ($e->report_full($e->lims()), $report, 'full report text with LIMs data');
};
Expand Down Expand Up @@ -360,9 +360,9 @@ subtest 'instrument annotation event' => sub {
Instrument HS8 annotated by joe_loader on $date_as_string - New instrument annotation

NPG page for this instrument:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/instrument/HS8

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP
REPORT6
is ($e->report_full($e->lims()), $report, 'full report text');
};
Expand Down
5 changes: 2 additions & 3 deletions t/data/report/report_text_1
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Expand Up @@ -31,11 +31,10 @@ Lane 3: Samples
Sequencing and default analysis for this run completed. Run is now pending manual QC review. Meanwhile, we will be loading analysis results into iRODS.

NPG page for the run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

Analysis and QC information for this run will be/is available:
http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915
http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP

7 changes: 3 additions & 4 deletions t/data/report/report_text_5
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Expand Up @@ -36,14 +36,13 @@ Lane 7: Samples
... 6 samples in total


The manual QC review is complete and your data should now be available from iRODS (see http://scratchy.internal.sanger.ac.uk/wiki/index.php/IRODS_for_Sequencing_Users ).
The manual QC review is complete and your data should now be available from iRODS (see https://ssg-confluence.internal.sanger.ac.uk/display/FARM/iRODS ).

NPG page for the run:
http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915
https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915

Analysis and QC information for this run will be/is available:
http://sfweb.internal.sanger.ac.uk:1959/illumina/runs/21915
http://sfweb.internal.sanger.ac.uk:1959/checks/runs/21915

NPG, DNA Pipelines Informatics
NPG on behalf of DNA Pipelines and GSLP