diff options
| -rw-r--r-- | issues/genenetwork1/gn1-annotation-page-is-broken.gmi | 4 | ||||
| -rw-r--r-- | issues/genenetwork1/gn1-github-problem.gmi | 53 | ||||
| -rw-r--r-- | issues/genenetwork1/gn1-mapping-broken.gmi | 7 | ||||
| -rw-r--r-- | issues/genenetwork1/gn1-pairscan.gmi | 4 | ||||
| -rw-r--r-- | topics/starting_gn1.gmi | 30 |
5 files changed, 95 insertions, 3 deletions
diff --git a/issues/genenetwork1/gn1-annotation-page-is-broken.gmi b/issues/genenetwork1/gn1-annotation-page-is-broken.gmi index 64d9201..a03b195 100644 --- a/issues/genenetwork1/gn1-annotation-page-is-broken.gmi +++ b/issues/genenetwork1/gn1-annotation-page-is-broken.gmi @@ -196,3 +196,7 @@ Uncaught ReferenceError: CKEDITOR is not defined Turns out that lily URLs were hard-coded in the source. So, that was an easy fix. There are still some complaints about CSS links missing in the browser console, but until someone sees a difference I does not need fixing. Changing the status to testing now. + +## Updating production + +The source code is now in sync on 'master' branch. Now I need to update guix-bioinformatics package to set up the container correctly with Apache httpd.conf. diff --git a/issues/genenetwork1/gn1-github-problem.gmi b/issues/genenetwork1/gn1-github-problem.gmi new file mode 100644 index 0000000..113d75d --- /dev/null +++ b/issues/genenetwork1/gn1-github-problem.gmi @@ -0,0 +1,53 @@ +# GN1 github problem + +When trying to push to github, a commit from 2018 is blocking: + +``` +tux01:~/genenetwork1$ git push +Enumerating objects: 41, done. +Counting objects: 100% (41/41), done. +Delta compression using up to 128 threads +Compressing objects: 100% (21/21), done. +Writing objects: 100% (23/23), 118.03 MiB | 23.15 MiB/s, done. +Total 23 (delta 20), reused 3 (delta 2) +remote: Resolving deltas: 100% (20/20), completed with 18 local objects. +remote: error: File web/images/upload/MouseTissuesRWWMay08.xls is 262.53 MB; this exceeds GitHub's file size limit of 100.00 MB +remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com. +To github.com:genenetwork/genenetwork1.git + ! [remote rejected] lily -> lily (pre-receive hook declined) +error: failed to push some refs to 'git@github.com:genenetwork/genenetwork1.git' +``` + +This is because of a resync of lily. I should not do that again. + + +# Tags + +* assigned: pjotrp +* status: in progress +* priority: medium +* type: system administration +* keywords: systems, tux02, production, gn1 + +# Info + +To solve this I have to remove the large file(s). Fortunately not many people are using genenetwork1 code base, so I can rewrite the git store. + +``` +find . -size +20M -exec ls -lh \{\} \; +-rwxr-xr-x 1 wrk wrk 263M Dec 15 15:38 ./web/images/upload/MouseTissuesRWWMay08.xls +``` + +Make a backup(!) + +Remove a file (dir with rm -rf). Make sure you do it for open branches too + +``` +rm ./web/images/upload/MouseTissuesRWWMay08.xls +git filter-branch --tree-filter 'rm -f web/images/upload/MouseTissuesRWWMay08.xls' HEAD +git filter-branch --force --index-filter 'git rm --cached --ignore-unmatch \ + MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all +git reflog expire --expire=now --all && git gc --prune=now --aggressive +``` + +Note this rewrites git history. It is a dangerous command. Also, make sure all others do a fresh checkout of the repo. diff --git a/issues/genenetwork1/gn1-mapping-broken.gmi b/issues/genenetwork1/gn1-mapping-broken.gmi index dd6785b..1b97a26 100644 --- a/issues/genenetwork1/gn1-mapping-broken.gmi +++ b/issues/genenetwork1/gn1-mapping-broken.gmi @@ -18,6 +18,9 @@ AttributeError: 'genotype' object has no attribute 'regression' * assigned: zachs, pjotrp * type: bug * priority: high -* status: unclear +* status: closed * keywords: marker,GN1 -* status: unclear + +## Info + +Works on production now. diff --git a/issues/genenetwork1/gn1-pairscan.gmi b/issues/genenetwork1/gn1-pairscan.gmi index a2be87f..b944a13 100644 --- a/issues/genenetwork1/gn1-pairscan.gmi +++ b/issues/genenetwork1/gn1-pairscan.gmi @@ -20,7 +20,7 @@ ImportError: No module named direct * priority: critical * keywords: missing dependency, binary blob, GN1 * assigned: pjotrp -* status: testing +* status: closed # Notes @@ -108,3 +108,5 @@ genenetwork1 container so Pjotr said he'd test it out. The direct.so binary is now on files.genenetwork.org. => https://files.genenetwork.org/software/ + +and part of deployment in guix-bioinformatics. Works on production. diff --git a/topics/starting_gn1.gmi b/topics/starting_gn1.gmi index 455e832..a5788ab 100644 --- a/topics/starting_gn1.gmi +++ b/topics/starting_gn1.gmi @@ -1,5 +1,17 @@ # Starting GN1 +The GN1 repos are at + +=> https://github.com/genenetwork/genenetwork1 + +Branches are: + +* master: my main branch - used in pjotr-test +* lily: running but almost discontinued +* production: on tux01 + +Note that there are some hard coded paths/IPs - so simply merging is not a great idea. + On tux01 GN1 is running inside a Guix container. Start a screen and run the guix deploy script. See the README file in @@ -62,3 +74,21 @@ SQL may also need to be updated here: => /gnshare/gn/web/webqtl/base/webqtlConfigLocal.py => /gnshare/gn/web/infoshare/includes/config.html => /gnshare/gn/web/infoshare/includes/db.inc + +## Updating from lily + +Git sync + +``` +gn1@tux01:~/production/gnshare/gn-pjotr-test$ +git checkout lily +git pull pjotr@lily.genenetwork.org:/gnshare/gn/ +``` + +Menu sync + +``` +gn1@tux01:~/production/gnshare/gn-pjotr-test$ +scp pjotr@lily.genenetwork.org:/gnshare/gn/web/javascript/*.js web/javascript/ +git status +``` |