GN1

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
+```