From bfaf199cf3a7ec29aeaaf9ec4e387ea8bc5f16db Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 6 Nov 2021 11:56:49 +0100 Subject: Progress in machine room --- tasks/dana.gmi | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) (limited to 'tasks') diff --git a/tasks/dana.gmi b/tasks/dana.gmi index af053b7..51f33b6 100644 --- a/tasks/dana.gmi +++ b/tasks/dana.gmi @@ -6,9 +6,16 @@ ## Tasks -* [X] Tux02 https firewalling * [ ] Octopus 10Gbs switch + cables -* [ ] Mount 4TB SSDs for Tux01 and Tux02 + - a test shows Octopus08 is at 10Gbs on the second interface + - need to hook up new cables +* [ ] Add gateway on 10Gbs switch => ../topics/systems/decommission-machines.gmi +Completed: + +* [X] Tux02 https firewalling +* [X] Mount 4TB SSDs for Tux01 and Tux02 + + ## Info -- cgit v1.2.3 From 50797e6b3edadf2ba2c93c635ca67fc589b7622b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 16 Nov 2021 06:22:13 -0600 Subject: genewiki and global search --- issues/genenetwork/genewiki.gmi | 24 ++++++++++++++++++++++++ issues/genenetwork/global-search.gmi | 12 ++++++++++++ tasks/zsloan.gmi | 12 ++++++++++++ topics/documentation/gn-documentation.gmi | 4 ++++ 4 files changed, 52 insertions(+) create mode 100644 issues/genenetwork/genewiki.gmi create mode 100644 issues/genenetwork/global-search.gmi create mode 100644 tasks/zsloan.gmi (limited to 'tasks') diff --git a/issues/genenetwork/genewiki.gmi b/issues/genenetwork/genewiki.gmi new file mode 100644 index 0000000..e7096dc --- /dev/null +++ b/issues/genenetwork/genewiki.gmi @@ -0,0 +1,24 @@ +# Genewiki conversion + +GeneNetwork1 contains a genewiki: + +=> http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol=BRCA2 + +We want to migrate it to markdown documents that can be fetched from + +=> https://github.com/genenetwork/gn-docs/genes + +So the steps are to (1) migrate the existing genewiki data in the database to named markdown documents in that repository and (2) create a rendered page that is found through + +=> https://genenetwork.org/doc/genes/BRCA2 + +with an edit button, similar to + +=> http://genenetwork.org/facilities/ + +## Tags + +* assigned: pjotrp, zsloan +* enhancement + +## Tasks diff --git a/issues/genenetwork/global-search.gmi b/issues/genenetwork/global-search.gmi new file mode 100644 index 0000000..01d9c0f --- /dev/null +++ b/issues/genenetwork/global-search.gmi @@ -0,0 +1,12 @@ +# Global search problems + +Global search is the top bar of GN2 + +## Tags + +* assigned: pjotrp, zsloan + +## Tasks + +* [ ] BRCA2 does not render results in table +* [ ] 'Brca2' with quotes gives a SQL error diff --git a/tasks/zsloan.gmi b/tasks/zsloan.gmi new file mode 100644 index 0000000..7e60240 --- /dev/null +++ b/tasks/zsloan.gmi @@ -0,0 +1,12 @@ +# Tasks for Zach + +## Tags + +* assigned: zsloan + +## Tasks + +* [ ] Fix global search +=> ../issues/genenetwork/global-search.gmi fix global search +* [ ] GN1 migrate genewiki pages +=> ../issues/genenetwork/genewiki.gmi diff --git a/topics/documentation/gn-documentation.gmi b/topics/documentation/gn-documentation.gmi index 617c8d2..653a1a4 100644 --- a/topics/documentation/gn-documentation.gmi +++ b/topics/documentation/gn-documentation.gmi @@ -14,4 +14,8 @@ the markdown is rendered on github, which makes it easy to edit for most users, * assigned: pjotrp +## Tasks + +=> storyboards + ## Info -- cgit v1.2.3 From deca20da6e0a7b17b7222bb031a7da5fb43ede27 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 23 Nov 2021 10:36:38 +0100 Subject: GN1 and machine room --- issues/authorisation.gmi | 7 +++++-- issues/genenetwork1/gn1-symbols.gmi | 23 +++++++++++++++++++++++ tasks/pjotrp.gmi | 3 ++- topics/systems/machine-room.gmi | 7 ++++--- 4 files changed, 34 insertions(+), 6 deletions(-) create mode 100644 issues/genenetwork1/gn1-symbols.gmi (limited to 'tasks') diff --git a/issues/authorisation.gmi b/issues/authorisation.gmi index c98509b..751ec86 100644 --- a/issues/authorisation.gmi +++ b/issues/authorisation.gmi @@ -2,13 +2,16 @@ Look at Chris' authorisation code: -=> https://github.com/chfi/gn-proxy +=> https://github.com/genenetwork/gn-proxy Atm genenetwork2's handling of authorisation is a bit clunky; Since @Bonface is working on the data data up-loader, and it requires authorisation, this is a good time to clean up authorisation. +# Tags + +* assigned: bonfacem, pjotrp, zachs # TODO @@ -123,4 +126,4 @@ On the UI(quote from Zach): to the show trait page. Key point is that I changed the URLs and moved them to their own module. Particularly for published datasets. -- New PR: https://github.com/genenetwork/genenetwork2/pull/614 \ No newline at end of file +- New PR: https://github.com/genenetwork/genenetwork2/pull/614 diff --git a/issues/genenetwork1/gn1-symbols.gmi b/issues/genenetwork1/gn1-symbols.gmi new file mode 100644 index 0000000..ac4cf71 --- /dev/null +++ b/issues/genenetwork1/gn1-symbols.gmi @@ -0,0 +1,23 @@ +# GN1 symbols + +# Tags + +* assigned: pjotrp, arthurc + +# Tasks + +* [ ] fix font issue +* [ ] fix linked webqtl images + +# Info + +The fonts differ on + +=> http://gn1-lily.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=2 +=> http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=2 + +There is a deeper problem. When you click on one of the symbols it wants to show, for example: + +=> http://www.webqtl.org/array_images/S092UM-1F2.png + +This fails both for GN1 and Lily. Do we still want to show those images, or simply disable? If we want to show them, where are they? diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index 5b5178e..f6554fd 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -7,7 +7,8 @@ ## Tasks * [ ] Rabbit https and GN2 https -* [X] Allow @bonfacem to run redis on P2 +* [ ] fix GN1 images linking to http://www.webqtl.org/array_images/S238-1F1-U74Av2.png +=> http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=2 => ../topics/systems/tux02-production.gmi Set up stable GN service * [ ] Pluto tool with Zach => ../issues/genenetwork1/gn1-production-system-issues.gmi diff --git a/topics/systems/machine-room.gmi b/topics/systems/machine-room.gmi index bece333..d75883a 100644 --- a/topics/systems/machine-room.gmi +++ b/topics/systems/machine-room.gmi @@ -6,9 +6,10 @@ ## Tasks -* [ ] Make tux02e visible from outside -* [ ] Network switch 10Gbs -* [ ] Add disks to tux01 - Sep 28 To Brock +* [X] Make tux02e visible from outside +* [ ] Network switch 10Gbs - add hosts +* [ ] Add disks to tux01 and tux02 - need to reboot +* [ ] Set up E-mail relay for tux01 and tux02 smtp.uthsc.edu, port 25 => tux02-production.gmi setup new production machine => decommission-machines.gmi Decommission machines -- cgit v1.2.3