diff --git a/Changes b/Changes index 7ad9e0d3..43e91f1a 100644 --- a/Changes +++ b/Changes @@ -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 diff --git a/data/npg_tracking_email/templates/run_status2followers.tt2 b/data/npg_tracking_email/templates/run_status2followers.tt2 index 8289a6f1..d77bb51d 100644 --- a/data/npg_tracking_email/templates/run_status2followers.tt2 +++ b/data/npg_tracking_email/templates/run_status2followers.tt2 @@ -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 %] diff --git a/data/npg_tracking_email/templates/urls.tt2 b/data/npg_tracking_email/templates/urls.tt2 index dcca50be..c0e48511 100644 --- a/data/npg_tracking_email/templates/urls.tt2 +++ b/data/npg_tracking_email/templates/urls.tt2 @@ -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'; %] \ No newline at end of file diff --git a/data/npg_tracking_email/templates/wrapper.tt2 b/data/npg_tracking_email/templates/wrapper.tt2 index ddc9998b..a125e281 100644 --- a/data/npg_tracking_email/templates/wrapper.tt2 +++ b/data/npg_tracking_email/templates/wrapper.tt2 @@ -1,2 +1,2 @@ [% content %] -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP diff --git a/t/80-npg_tracking-report-event2subscribers.t b/t/80-npg_tracking-report-event2subscribers.t index 0aeb8372..39264a9f 100644 --- a/t/80-npg_tracking-report-event2subscribers.t +++ b/t/80-npg_tracking-report-event2subscribers.t @@ -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'); @@ -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'); @@ -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'); @@ -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'); @@ -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()), $report, 'full report text with LIMs data'); }; @@ -323,9 +323,9 @@ Lane 2: Samples NPG page for this run: -http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 +https://sfweb.internal.sanger.ac.uk:12443/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT5 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); }; @@ -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'); }; diff --git a/t/data/report/report_text_1 b/t/data/report/report_text_1 index cc591d00..b19b4651 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -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 diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index 46ad211f..ca961e6d 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -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