From 71bc5ae8d57b346c28d6ea7cf700617148388d65 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 17 Jan 2024 16:30:17 +0000 Subject: [PATCH 1/3] update signature and iRODS documentation link --- Changes | 1 + .../templates/run_status2followers.tt2 | 2 +- data/npg_tracking_email/templates/wrapper.tt2 | 2 +- t/80-npg_tracking-report-event2subscribers.t | 14 +++++++------- t/data/report/report_text_1 | 2 +- t/data/report/report_text_5 | 4 ++-- 6 files changed, 13 insertions(+), 12 deletions(-) diff --git a/Changes b/Changes index 7ad9e0d3..ec59ecb1 100644 --- a/Changes +++ b/Changes @@ -14,6 +14,7 @@ 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 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..38c6fd5a 100644 --- a/data/npg_tracking_email/templates/run_status2followers.tt2 +++ b/data/npg_tracking_email/templates/run_status2followers.tt2 @@ -11,7 +11,7 @@ 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: 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..2d7347c2 100644 --- a/t/80-npg_tracking-report-event2subscribers.t +++ b/t/80-npg_tracking-report-event2subscribers.t @@ -156,7 +156,7 @@ 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 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT is ($e->report_full(), $report, 'full report text'); @@ -173,7 +173,7 @@ $lims_summary NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT1 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); @@ -217,7 +217,7 @@ Instrument HS8 status changed to "wash performed" on $date_as_string by joe_appr NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT2 is ($e->report_full($e->lims()), $report, 'full report text'); @@ -231,7 +231,7 @@ Instrument HS8 status changed to "wash performed" on $date_as_string by joe_appr NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT3 is ($e->report_full($e->lims()), $report, 'full report text with a comment'); is (scalar @{$e->reports}, 1, 'One report generated'); @@ -272,7 +272,7 @@ $lims_summary NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT4 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); }; @@ -325,7 +325,7 @@ Lane 2: Samples NPG page for this run: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/run/21915 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT5 is ($e->report_full($e->lims()), $report, 'full report text with LIMs data'); }; @@ -362,7 +362,7 @@ Instrument HS8 annotated by joe_loader on $date_as_string - New instrument annot NPG page for this instrument: http://sfweb.internal.sanger.ac.uk:9000/perl/npg/instrument/HS8 -NPG, DNA Pipelines Informatics +NPG on behalf of DNA Pipelines and GSLP REPORT6 is ($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..58a0bf08 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -37,5 +37,5 @@ 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..ef72e655 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -36,7 +36,7 @@ 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 @@ -45,5 +45,5 @@ 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 From ae982c23621da58234053373811d044e64d5c92b Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 18 Jan 2024 14:27:14 +0000 Subject: [PATCH 2/3] use https for tracking urls in emails --- Changes | 1 + data/npg_tracking_email/templates/urls.tt2 | 2 +- t/80-npg_tracking-report-event2subscribers.t | 14 +++++++------- t/data/report/report_text_1 | 2 +- t/data/report/report_text_5 | 2 +- 5 files changed, 11 insertions(+), 10 deletions(-) diff --git a/Changes b/Changes index ec59ecb1..bbd4f89b 100644 --- a/Changes +++ b/Changes @@ -15,6 +15,7 @@ LIST OF CHANGES 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 release 98.1.0 - Added a new method, latest_revision_for_modification, to 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/t/80-npg_tracking-report-event2subscribers.t b/t/80-npg_tracking-report-event2subscribers.t index 2d7347c2..39264a9f 100644 --- a/t/80-npg_tracking-report-event2subscribers.t +++ b/t/80-npg_tracking-report-event2subscribers.t @@ -154,7 +154,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT @@ -171,7 +171,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT1 @@ -215,7 +215,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT2 @@ -229,7 +229,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT3 @@ -270,7 +270,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT4 @@ -323,7 +323,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT5 @@ -360,7 +360,7 @@ 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 on behalf of DNA Pipelines and GSLP REPORT6 diff --git a/t/data/report/report_text_1 b/t/data/report/report_text_1 index 58a0bf08..25c4b581 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -31,7 +31,7 @@ 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 diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index ef72e655..667b55b3 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -39,7 +39,7 @@ Lane 7: Samples 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 From 8b955db08e5e1ab7d84715b4cadfa0fccc522d03 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Wed, 17 Jan 2024 17:01:10 +0000 Subject: [PATCH 3/3] remove illumina lane qc link from emails --- Changes | 2 ++ data/npg_tracking_email/templates/run_status2followers.tt2 | 1 - t/data/report/report_text_1 | 1 - t/data/report/report_text_5 | 1 - 4 files changed, 2 insertions(+), 3 deletions(-) diff --git a/Changes b/Changes index bbd4f89b..43e91f1a 100644 --- a/Changes +++ b/Changes @@ -16,6 +16,8 @@ LIST OF CHANGES - 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 38c6fd5a..d77bb51d 100644 --- a/data/npg_tracking_email/templates/run_status2followers.tt2 +++ b/data/npg_tracking_email/templates/run_status2followers.tt2 @@ -18,6 +18,5 @@ 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/t/data/report/report_text_1 b/t/data/report/report_text_1 index 25c4b581..b19b4651 100644 --- a/t/data/report/report_text_1 +++ b/t/data/report/report_text_1 @@ -34,7 +34,6 @@ NPG page for the run: 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 on behalf of DNA Pipelines and GSLP diff --git a/t/data/report/report_text_5 b/t/data/report/report_text_5 index 667b55b3..ca961e6d 100644 --- a/t/data/report/report_text_5 +++ b/t/data/report/report_text_5 @@ -42,7 +42,6 @@ NPG page for the run: 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 on behalf of DNA Pipelines and GSLP