diff options
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/GUIX-Reproducible-from-source.org | 6 | ||||
| -rw-r--r-- | doc/README.org | 518 | ||||
| -rw-r--r-- | doc/development.org | 55 | ||||
| -rw-r--r-- | doc/docker-container.org | 89 | ||||
| -rw-r--r-- | doc/testing.org | 66 |
5 files changed, 259 insertions, 475 deletions
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 19e4d14f..fffa9571 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -167,7 +167,7 @@ the Guix suggested environment vars. Check the output of #+begin_src bash guix package --search-paths -export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages" +export PYTHONPATH="/root/.guix-profile/lib/python3.8/site-packages" export R_LIBS_SITE="/root/.guix-profile/site-library/" #+end_src @@ -265,7 +265,7 @@ software. If something is not working, take a hint from the settings file that comes in the Guix installation. It sits in something like -: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py +: cat ~/.guix-profile/lib/python3.8/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py ** Set up nginx port forwarding @@ -380,7 +380,7 @@ After setting the paths for the server #+begin_src bash export PATH=~/.guix-profile/bin:$PATH -export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" +export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages" export R_LIBS_SITE="$HOME/.guix-profile/site-library/" export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0" export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0" diff --git a/doc/README.org b/doc/README.org index c2ef2d57..43c92e3c 100644 --- a/doc/README.org +++ b/doc/README.org @@ -4,9 +4,12 @@ - [[#introduction][Introduction]] - [[#install][Install]] - [[#running-gn2][Running GN2]] + - [[#run-gn-proxy][Run gn-proxy]] + - [[#run-redis][Run Redis]] - [[#run-mariadb-server][Run MariaDB server]] - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]] - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] + - [[#get-genotype-files][Get genotype files]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] - [[#read-more][Read more]] @@ -16,7 +19,6 @@ - [[#cant-run-a-module][Can't run a module]] - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]] - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]] - - [[#irc-session][IRC session]] - [[#notes][NOTES]] - [[#deploying-gn2-official][Deploying GN2 official]] @@ -57,28 +59,39 @@ or you can set environment variables to override individual parameters, e.g. the debug and logging switches can be particularly useful when developing GN2. -* Running Redis +* Run gn-proxy -Install redis. Make sure you add the setting: +GeneNetwork requires a separate gn-proxy server which handles +authorisation and access control. For instructions see the [[https://github.com/genenetwork/gn-proxy][README]]. -: appendonly yes +* Run Redis + +Redis part of GN2 deployment and will be started by the ./bin/genenetwork2 +startup script. * Run MariaDB server ** Install MariaDB with GNU GUIx -/Note: we moved to MariaDB/ - These are the steps you can take to install a fresh installation of mariadb (which comes as part of the GNU Guix genenetwork2 install). -As root configure and run +As root configure the Guix profile + +: . ~/opt/genenetwork2/etc/profile + +and run for example #+BEGIN_SRC bash adduser mariadb && addgroup mariadb -mysqld --datadir=/home/mariadb/database --initialize-insecure -mkdir -p /var/run/mariadbd -chown mariadb.mariadb /var/run/mariadbd -mysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048" +mkdir -p /export2/mariadb/database +chown mariadb.mariadb -R /export2/mariadb/ +mkdir -p /var/run/mysqld +chown mariadb.mariadb /var/run/mysqld +su mariadb +mysql --version + mysql Ver 15.1 Distrib 10.1.45-MariaDB, for Linux (x86_64) using readline 5.1 +mysql_install_db --user=mariadb --datadir=/export2/mariadb/database +mysqld -u mariadb --datadir=/exportdb/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048" #+END_SRC If you want to run as root you may have to set @@ -120,21 +133,22 @@ material. Download one database from -[[http://files.genenetwork.org/raw_database/]] - -[[https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip]] +http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk -Check the md5sum. +After installation unzip the database binary in the MySQL directory -After installation inflate the database binary in the MySQL directory - -: cd ~/mysql -: chown -R mysql:mysql db_webqtl_s/ -: chmod 700 db_webqtl_s/ -: chmod 660 db_webqtl_s/* +#+BEGIN_SRC sh +cd ~/mysql +p7zip -d db_webqtl_s.7z +chown -R mysql:mysql db_webqtl_s/ +chmod 700 db_webqtl_s/ +chmod 660 db_webqtl_s/* +#+END_SRC restart MySQL service (mysqld). Login as root +: mysql_upgrade -u root --force + : myslq -u root and @@ -151,7 +165,7 @@ and Set permissions and match password in your settings file below: -: mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password'; +: mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'webqtl'; You may need to change "localhost" to whatever domain you are connecting from (mysql will give an error). @@ -163,6 +177,17 @@ configuration (see below). Note for the plant database you can rename it to db_webqtl_s, or change the settings in etc/default_settings.py to match your path. +* Get genotype files + +The script looks for genotype files. You can find them in +http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL + +#+BEGIN_SRC sh +mkdir -p $HOME/genotype_files +cd $HOME/genotype_files + +#+END_SRC + * GN2 Dependency Graph Graph of all runtime dependencies as installed by GNU Guix. @@ -193,7 +218,7 @@ information given by guix: On one system: -: export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" +: export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages" : export R_LIBS_SITE="$HOME/.guix-profile/site-library/" : export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0" @@ -249,439 +274,30 @@ if that works run genenetwork after setting SQL_URI to something like : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s - -* IRC session - -Here an IRC session where we installed GN2 from scratch using GNU Guix -and a download of the test database. - -#+begin_src -<pjotrp> time to get binary install sorted :) [07:03] -<pjotrp> Guix is designed for distributed installation servers -<pjotrp> we have one on guix.genenetwork.org -<pjotrp> it contains all the prebuild packages -<pjotrp> for GN -<user01> okay [07:04] -<pjotrp> let's step back however [07:05] -<pjotrp> I presume the environment is set with all guix package --search-paths -<pjotrp> right? -<user01> yep -<user01> set to the ones in ~/.guix-profile/ -<pjotrp> good, and you are in gn-deploy-guix repo [07:06] -<user01> yep [07:07] -<pjotrp> git log shows - -Author: David Thompson <dthompson2@worcester.edu> -Date: Sun Mar 27 21:20:19 2016 -0400 - -<user01> yes -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix - package -A genenetwork2 [07:08] -<pjotrp> shows - -genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2 -genenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4 -genenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4 - -<user01> yeah [07:09] -<pjotrp> OK, we are in sync. This means we should be able to install the exact - same software -<pjotrp> I need to start up my guix daemon - I usually run it in a screen -<pjotrp> screen -S guix-daemon -<user01> hah, I don't have screen installed yet [07:11] -<pjotrp> comes with guix ;) [07:12] -<pjotrp> no worries, you can run it any way you want -<pjotrp> $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild -<user01> then something's weird, because it says I don't have it -<pjotrp> oh, you need to install it first [07:13] -<pjotrp> guix package -A screen -<pjotrp> screen 4.3.1 out gnu/packages/screen.scm:34:2 -<pjotrp> but you can skip this install, for now -<user01> alright [07:14] -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix - package -i genenetwork2 --dry-run -<pjotrp> substitute: updating list of substitutes from - 'https://mirror.hydra.gnu.org'... 79.1% -<pjotrp> you see that? -<pjotrp> followed by [07:15] -substitute: updating list of substitutes from -'https://hydra.gnu.org'... 100.0% -The following derivations would be built: - /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv - -/gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv - /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv - /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv - -<pjotrp> which should have the same HASH values /gnu/store/7b0qjybvf... etc. - [07:16] -<user01> profile has a different hash -<pjotrp> but the next ones? -<user01> they're the same -<pjotrp> not sure why profile differs. Do you see the contact with - mirror.hydra.org? [07:17] -<user01> yeah -<pjotrp> OK, that means you set the key correctly for that one :) -<pjotrp> alright we are at the same state now. You can see most packages need - to be rebuild because they are no longer cached as binaries on hydra - [07:18] -<pjotrp> things move fast... -<user01> hehe -<pjotrp> let me also do the same on my laptop - which I have staged before - [07:19] -<pjotrp> btw, to set the path I often do [07:20] -<pjotrp> export - PATH="/home/wrk/.guix-profile/bin:/home/wrk/.guix-profile/sbin":$PATH -<pjotrp> to keep things like 'screen' from Debian -<pjotrp> Once past building guix itself that is normally OK [07:21] -<user01> ah, okay -<user01> will do that -<pjotrp> the guix build requires certain versions of tools, so you don't want - to mix foreign tools in [07:23] -<user01> makes sense [07:24] -<pjotrp> On my laptop I am trying the main updating list of substitutes from - 'http://hydra.gnu.org'... 10.5% [07:27] -<pjotrp> it is a bit slow, but let's see if there is a difference with the - mirror -<pjotrp> you can see there are two servers here. Actually with recent daemons, - if the mirror fails it will try the main server [07:28] -<pjotrp> I documented the use of a caching server here [07:29] -<pjotrp> https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org -<pjotrp> this is exactly what we are doing now -<user01> alrighty [07:35] -<pjotrp> To see if a remote server has a guix server running it should respond - [07:36] -<pjotrp> lynx http://guix.genenetwork.org:8080 --dump -<pjotrp> Resource not found: / -<pjotrp> -<pjotrp> you see that? -<user01> yes [07:37] -<pjotrp> good. The main hydra server is too slow. So on my laptop I forced - using the mirror with [07:38] -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix - package -i genenetwork2 --dry-run - --substitute-urls="http://mirror.hydra.gnu.org" -<pjotrp> -<pjotrp> the list looks the same to me [07:40] -<user01> me too -<pjotrp> note that some packages will be built and some downloaded, right? - [07:41] -<user01> yes -<pjotrp> atlas is actually a binary on my system [07:43] -<pjotrp> I mean in that list -<pjotrp> so, it should not build. Same as yours? -<user01> yeah, atlas and r-gtable are the ones to be downloaded -<pjotrp> You should not have seen that error ;) -<pjotrp> we should try and install it this way, try [07:44] -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix - package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46] -<pjotrp> set CPUs and max-jobs to something sensible -<pjotrp> Does your VM have multiple cores? -<pjotrp> note you can always press Ctrl-C during install -<user01> it doesn't, I'll reboot it and give it another core [07:47] -<user02> Hey [07:48] -<user02> I'm here -<user02> Will be stepping away for some breakfast -<pjotrp> Can you do the same as us -<pjotrp> Can you see the irc log -<user02> Alright -<user02> Yes, I can -<user02> Please email me a copy in five minutes -<pjotrp> user01: so when I use the GN server [07:56] -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix - package -i genenetwork2 --dry-run - --substitute-urls=http://guix.genenetwork.org:8080 -<pjotrp> I don't need to build anything [07:57] -<pjotrp> (this won't work for you, yet) -<pjotrp> to get it to work you need to 'trust' it [07:58] -<pjotrp> but, first get the build going -<pjotrp> I'll have a coffee while you and get building -<user01> yeah it's doing its thing now [08:01] -<pjotrp> cool [08:02] -<pjotrp> in a separate terminal you can try and install with the gn mirror - [08:05] -<pjotrp> I'll send you the public key and you can paste it as said - https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org - [08:06] -<user01> alright -<pjotrp> should be in the E-mail [08:09] -<pjotrp> getting it working it kinda nasty since the server gives no feedback -<pjotrp> it works when you see no more in the build list ;) [08:11] -<pjotrp> btw, you can install software in parallel. Guix does that. -<pjotrp> even the same packages -<pjotrp> so keep building ;) -<pjotrp> try and do this with Debian... -<pjotrp> coffee for me [08:12] -<user01> the first build failed [08:15] -<pjotrp> OK, Dennis fixed that one yesterday [08:27] -<pjotrp> the problem is that sometime source tarballs disappear [08:28] -<pjotrp> R is notorious for that -<user01> haha, that's inconvenient.. -<pjotrp> well, it is good that Guix catches them -<pjotrp> but we do not cache sources -<pjotrp> binaries are cached - to some degree - so we don't have to rebuild - those [08:29] -<pjotrp> time to use the guix cache at guix.genenetwork.org -<pjotrp> try and install the key (it is in the E-mail) -<pjotrp> and see what this lists [08:31] -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix - package -i genenetwork2 - --substitute-urls=http://guix.genenetwork.org --dry-run -<pjotrp> should be all binary installs -<user01> it's not.. [08:32] -<user01> if I remove --substitute-urls, the list changes, does that mean I - have the key set up correctly at least? [08:33] -<pjotrp> dunno [08:35] -<pjotrp> how many packages does it want to build? -<pjotrp> should be zero -<user01> four -<pjotrp> Ah, that is OK - those are default profile things -<user01> genenetwork2 is among the ones to be downloaded so [08:36] -<pjotrp> remove --dry-run -<pjotrp> yeah, good sign :) -<pjotrp> we'll still hit a snag, but run it -<pjotrp> should be fast -<user01> doing it [08:37] -<user01> it worked! [08:38] -<user01> I think [08:39] -<pjotrp> heh [08:40] -<pjotrp> you mean it is finished? -<user01> yep -<pjotrp> type genenetwork2 -<user01> complains about not being able to connect to the database [08:41] -<pjotrp> last snag :) -<pjotrp> no database -<pjotrp> well, we succeeded in installing a same-byte install of a very - complex system :) [08:42] -<pjotrp> (always take time to congratulate yourself) -<pjotrp> now we need to install mysql -<user01> hehe :) -<pjotrp> this can be done throug guix or through debian [08:43] -<pjotrp> the latter is a bit easier here, so let's do that -<pjotrp> fun note: you can mix debian and guix -<pjotrp> Follow instructions on [08:44] -<pjotrp> - https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server -<pjotrp> apt-get install mysql-common [08:45] -<pjotrp> may do it -<pjotrp> You can also install with guix, but I need to document that -<pjotrp> btw your internet must be fast :) [08:46] -<user01> hehe it is ;) -<pjotrp> when the database is installed [08:48] -<pjotrp> be sure to set the password as instructed [08:50] -<pjotrp> when mysql is set the genenetwork2 command should fire up the web - server on localhost:5003 [08:58] -<pjotrp> btw my internet is way slower :) [09:00] -<user02> I'm back [09:04] -<user02> fixed router firmware upgrade problem -<user02> unbricking -<pjotrp> tssk [09:07] -<user02> I'll never leave routers to update themselves again [09:08] -<user02> self-brick highway -<user02> Resuming [09:09] -<pjotrp> auto-updates are evil -<pjotrp> always switch them off -<pjotrp> user02: can you install genenetwork like user has done? [09:10] -<pjotrp> pretty well documented here now :) -<user02> Yes I can [09:11] -<user02> Already installed key -<pjotrp> user02: you are getting binary packages only now? [09:13] -<user02> That's the sanest way to go now -<user02> seriously -<pjotrp> everything should be pre-built from guix.genenetwork.org -<pjotrp> you are downloading? -<user02> yes [09:15] -<pjotrp> cool. Maybe an idea to set up a server -<pjotrp> for your own use -<user02> Stuck at downloading preprocesscore -<pjotrp> should not [09:24] -<pjotrp> what does env GUIX_PACKAGE_PATH=../guix-bioinformatics/ - ./pre-inst-env guix package -i genenetwork2 - --substitute-urls="http://guix.genenetwork.org" --dry-run - [09:25] -<pjotrp> say for r-prepocesscore -<pjotrp> download or build? -<pjotrp> mine says download [09:26] -<user02> it only lists the derivatives to be built -<user02> nothing else happens [09:27] -<pjotrp> OK, so there is a problem -<pjotrp> your key may not be working -<pjotrp> everything should be listed as 'to be download' [09:28] -<user02> Hmm -<user02> Ah -<user02> I know where I messed up -<pjotrp> where? -<user02> I did add the key -<user02> However -<pjotrp> (I am documenting) -<user02> I did not tell guix to trust it -<pjotrp> yes -<pjotrp> and there is another potential problem -<user02> Remember the documentation on installing guix? -<user02> You have to tell guix to trust the default key [09:29] -<user02> Right? -<user02> So in this case -<pjotrp> read the IRC log -<user02> That step is mandatory -<pjotrp> user01: how are you doing? -<pjotrp> user02: - https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive - [09:30] -<user01> a little bit left on the db download -<pjotrp> user02: you should see no more building -<pjotrp> user02: another issue may be that you updated r-preprocesscore - package in guix-buinformatics [09:32] -<pjotrp> all downstream packages will want to rebuild -<user02> no, not really -<user02> It's not even installed -<pjotrp> checkout a branch of the the old version - make sure we are in synch -<pjotrp> should be at - /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0 - [09:33] -<pjotrp> -<user03> pjotrp: Possibly we should use the archive utility of Guix to do - deployment to avoid such out-of-sync differences :) [09:34] -<pjotrp> maybe. I did not get archive to update profiles properly [09:37] -<pjotrp> Also it is good that they get to understand guix - this way -<pjotrp> carved in stone, eh [09:38] -<user02> Yeah, all good [09:39] -<user02> My mistake was skipping the guix archive part -<user02> Can we begin with the install? -<user02> It's telling me of derivatives that will be downloaded [09:40] -<user02> So we're good -<user02> Here goes -<pjotrp> yeeha [09:42] -<user02> pjotrp, where is this guix.genenetwork.org located at? -<pjotrp> Tennessee -<user02> It's...it's....sloooooooowwwwwwwwwwwwww -<pjotrp> not from Europe -<pjotrp> is it downloading at all? -<user02> It should be extended -<user02> Yes...like at 100KB/s [09:43] -<user02> tear-jerker -<user02> Verizon problems -<user02> who's the host? -<pjotrp> I am getting 500Kb/s -<pjotrp> UT -<user02> Guix's servers can run off more than one server, right? -<user02> I'd like to host that particular server here -<user02> For speed -<pjotrp> yes -<user02> Sooner or later -<user02> It will be a necessity [09:45] -<pjotrp> exactly what I am doing - this is our server -<pjotrp> guix.genenetwork.org:8080 -<user02> All done installing [09:46] -<pjotrp> what? -<user02> Now the databases -<pjotrp> what do you mean by slow exactly? -<user02> Yes, it's installed -<pjotrp> can you run genenetwork2 -<user02> setting variables -<user02> If I try running it now, it will fail as I don't have the DBs [09:47] -<pjotrp> cool - you had a lot of prebuilt packages already -<pjotrp> OK, follow the instructions I wrote above -<user01> now everything seems to be working for me :) -<user02> OK -<pjotrp> user01: excellent! -<pjotrp> you see a webserver? -<user01> yep, can connect to localhost:5003 [09:48] -<pjotrp> So now you are running a guix copy of GN2 -<pjotrp> you can see where it lives with `which genenetwork2` or ls -l - ~/.guix-profile/bin/genenetwork2 [09:49] -<pjotrp> - /gnu/store/1kma5xszvzsvmbb4k699h7gvdncw901i-genenetwork2-2.0-a8fcff4/bin/genenetwork2 -<pjotrp> it is a script -<pjotrp> written by guix, open it [09:50] -<pjotrp> inside it points to paths and our script at -<pjotrp> - /gnu/store/1kma5xszvzsvmbb4k699h7gvdncw901i-genenetwork2-2.0-a8fcff4/bin/.genenetwork2-real -<pjotrp> if you open that you can see how the webserver is started [09:51] -<pjotrp> next step is to run a recent version of GN2 -<user01> okay [09:52] -<pjotrp> See - https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-your-own-copy-of-gn2 -<pjotrp> but do not checkout that genetwork2_diet -<pjotrp> we reverted to the main tree -<pjotrp> clone git@github.com:genenetwork/genenetwork2.git [09:53] -<pjotrp> instead and checkout the staging branch -<pjotrp> that is effectively my branch [09:54] -<pjotrp> when that is done you should be able to fire up the webserver from - there [09:55] -<pjotrp> using ./bin/genenetwork2 -<user02> now installing DBs -<user02> Downloading -<pjotrp> annoyingly the source tree is ~700Mb [09:56] -<user02> Can it also be done by installing the guix package - genenetwork2-database-small? -<pjotrp> I changed it in the diet version to 8Mb, but I had to revert -<user01> I need to make my VM bigger... -<pjotrp> user02: not ready [09:57] -<user02> ok -<pjotrp> user01: sorry -<pjotrp> user01: you could mount a local dir inside the VM for development -<pjotrp> that would allow you to use MAC tools for editing -<pjotrp> just an idea -<user01> yeah, I figure I'll do something like that -<pjotrp> do you use emacs? [09:58] -<user01> yep -<pjotrp> that can also run on remote files over ssh -<pjotrp> that's an alternative -<pjotrp> kudos for using emacs :), wdyt user03 -<user02> 79 minutes to go downloading the db -<pjotrp> user02: sorry about that [09:59] -<pjotrp> it is 2GB -<user02> user, you can also mount the directory via sshfs -<user02> Mac OSX runs OpenSSH -<pjotrp> user02: sopa -<user02> You can therefore mount a directory outside the VM to the VM via - sshfs [10:00] -<pjotrp> yes, 3 options now -<user02> That way, you can set up a VM only for it's logic -<user02> Apps + the OS it runs [10:01] -<user02> For data, let it reside on physical host accessible via sshfs -<user02> Use this Arch wiki reference: - https://wiki.archlinux.org/index.php/SSHFS -<user02> I edited that last somewhere in 2015, may have been updated since - then -<user01> alright, cool! [10:04] -<pjotrp> user01: you are almost done [10:06] -<pjotrp> I wrote an elixir package for guix :) -<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix - package -A elixir - --substitute-urls="http://guix.genenetwork.org" [10:08] -<pjotrp> elixir 1.2.3 out - ../guix-bioinformatics/gn/packages/elixir.scm:31:2 -<pjotrp> -<pjotrp> I am building it on guix.genenetwork.org right now [10:09] -<user01> nice [10:10] -#+end_src - * NOTES ** Deploying GN2 official Let's see how fast we can deploy a second copy of GN2. -- [-] Base install - + [X] First install a Debian server with GNU Guix on board - + [X] Get Guix build going - - [X] Build the correct version of Guix - - [X] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics - - [X] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable - + [X] Create a gn2 user and home with space - + [X] Install redis (currently debian) - - [X] add to systemd - - [X] update redis.cnf - - [X] update database - + [X] Install mariadb (currently debian mariadb-server) - - [X] add to systemd - - [X] system stop mysql - - [X] update mysql.cnf - - [X] update database (see gn-services/services/mariadb.md) - - [X] check tables - + [ ] run gn2 (rust-qtlreaper not working) - + [X] update nginx +- [ ] Base install + + [ ] First install a Debian server with GNU Guix on board + + [ ] Get Guix build going + - [ ] Build the correct version of Guix + - [ ] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics + - [ ] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable + + [ ] Create a gn2 user and home with space + + [ ] Install redis + - [ ] add to systemd + - [ ] update redis.cnf + - [ ] update database + + [ ] Install mariadb (currently debian mariadb-server) + - [ ] add to systemd + - [ ] system stop mysql + - [ ] update mysql.cnf + - [ ] update database (see gn-services/services/mariadb.md) + - [ ] check tables + + [ ] run gn2 + + [ ] update nginx + [ ] install genenetwork3 - [ ] add to systemd diff --git a/doc/development.org b/doc/development.org index 5e6e318b..cd3beea3 100644 --- a/doc/development.org +++ b/doc/development.org @@ -41,3 +41,58 @@ JS_GN_PATH (3) is for development purposes. By default is is set to $HOME/genenetwork/javascript. Say you are working on an updated version of a JS module not yet in (1) you can simply check out that module in that path and it should show up. + +* Python modules + +Python modules are automatically found in the Guix profile. + +For development purposes it may be useful to try some Python package. +Obviously this is only a temporary measure and when you decide to +include the package it should be packaged in [[http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][our GNU Guix software +stack]]! + +To add packages you need to make sure the correct Python is used (currently +Python 2.7) to install a package. E.g.. + +#+BEGIN_SRC sh +python --version + Python 2.7.16 +pip --version + pip 18.1 from /usr/lib/python2.7/dist-packages/pip (python 2.7) +#+END_SRC + +You can install a Python package locally with pip, e.g. + +#+BEGIN_SRC sh +pip install hjson +#+END_SRC + +This installed in ~$HOME/.local/lib/python3.8/site-packages~. To add +the search path for GeneNetwork use the environment variable + +#+BEGIN_SRC sh +export PYTHON_GN_PATH=$HOME/.local/lib/python3.8/site-packages +#+END_SRC + +Now you should be able to do + +#+BEGIN_SRC python +import hjson +#+END_SRC + +In fact you can kick off a Python shell with something like + +#+BEGIN_SRC python +env SERVER_PORT=5013 WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \ + SQL_URI=mysql://gn2:webqtl@localhost/db_webqtl_s \ + GN2_PROFILE=~/opt/genenetwork2 \ + ./bin/genenetwork2 ./etc/default_settings.py -c +Python 2.7.17 (default, Jan 1 1970, 00:00:01) +[GCC 7.5.0] on linux2 +Type "help", "copyright", "credits" or "license" for more information. +>>> import hjson +#+END_SRC + +It should now also work in GN2. + +* TODO External tools diff --git a/doc/docker-container.org b/doc/docker-container.org new file mode 100644 index 00000000..ec91824a --- /dev/null +++ b/doc/docker-container.org @@ -0,0 +1,89 @@ +#+TITLE: Genenetwork2 Dockerized + +* Table of Contents :TOC: +- [[#introduction][Introduction]] +- [[#creating-the-docker-images][Creating the Docker Images]] +- [[#pushing-to-dockerhub][Pushing to DockerHub]] + +* Introduction + +The CI(Continuous Integration) system for Genenetwork2 uses [[https://github.com/features/actions][Github +Actions]]. As such, it's important to have a way to run tests using +facilities provided by GUIX in a reproducible way. This project +leverages GUIX to generate a docker container from which the unittests +are ran from. + +Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This +document will not get into that. It's assumed that you have a working +docker setup. + +The rest of this document outlines how the docker container used in +the CI builds was created. + +* Creating the Docker Images + +The general idea is that GUIX is used to generate a set of binaries, +which will be added to a base mariaDB image. + +First create the gn2 tar archive by running: + +#+begin_src sh +# For the Python 2 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack --no-grafts\ + -S /gn2-profile=/ \ + screen genenetwork2 + +# For the Python 3 version: +env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \ + ./pre-inst-env guix pack --no-grafts\ + -S /gn2-profile=/ \ + screen python3-genenetwork2 + #+end_src + +The output will look something similar to: + +: /gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz + +Now create a folder from which will host the following dockerfile. You +can name this file Dockerfile. Note that mariadb is the base image +since it already has mariadb installed for us. + +#+begin_src conf :mkdirp yes :tangle ~/docker/Dockerfile +FROM mariadb:latest + +COPY ./gn2.tar.gz /tmp/gn2.tar.gz +RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \ + mkdir -p /usr/local/mysql /genotype_files/genotype/json +#+end_src + +Build the image(Note the fullstop at the end): + +: sudo docker build -t python2-genenetwork2:latest -f Dockerfile . + +To load the image interactively you've just created: + +: docker run -ti "python2-genenetwork2:latest" bash + +Assuming you have a docker instance running, you could always run +commands in it e.g: + +: docker run "python2-genenetwork2:latest" python --version + +* Pushing to DockerHub + +We use DockerHub to store the docker images from which we use on our +CI environment using Github Actions. + +To push to dockerhub, first get the image name by running =docker +images=. Push to dockerhub using a command similar to: + +: docker push bonfacekilz/python2-genenetwork2:latest + +Right now, we have 2 images on DockerHub: + +- https://hub.docker.com/repository/docker/bonfacekilz/python2-genenetwork2: + Contains the python2 version of gn2. Don't use this. Please use the + python3 image! +- https://hub.docker.com/repository/docker/bonfacekilz/python3-genenetwork2: + Contains the python3 version of gn2. diff --git a/doc/testing.org b/doc/testing.org index 1d5cc8b8..d5ab117d 100644 --- a/doc/testing.org +++ b/doc/testing.org @@ -1,43 +1,67 @@ #+TITLE: Testing GN2 * Table of Contents :TOC: - - [[#introduction][Introduction]] - - [[#run-tests][Run tests]] - - [[#setup][Setup]] - - [[#running][Running]] +- [[#introduction][Introduction]] +- [[#run-tests][Run tests]] + - [[#setup][Setup]] + - [[#running][Running]] * Introduction -For integration testing we currently use the brilliant Ruby Mechanize -gem against the small database; a setup we call mechanical Rob because -it emulates someone clicking through the website and checking results. +For integration testing, we currently use [[https://github.com/genenetwork/genenetwork2/tree/testing/test/requests][Mechanica Rob]] against the +small [[https://github.com/genenetwork/genenetwork2/blob/testing/doc/database.org][database]]; a setup we call Mechanical Rob because it emulates +someone clicking through the website and checking results. -These scripts invoke calls to a running webserver and test the -response. If a page changes or is broken tests will break and we are -informed. In principle, Mechanical Rob is run before code merges are -committed to the main server. +These scripts invoke calls to a running webserver and test the response. +If a page changes or breaks, tests will fail. In principle, Mechanical +Rob runs before code merges get committed to the main server. -In the future we may move to Python mechanize - it'll be easy to mix -the Ruby and Python versions. +For unit tests, we use python's =unittest= framework. Coverage reports +get generated using [[https://coverage.readthedocs.io/en/coverage-5.2.1/][coverage.py]] which you could also use to run +unit tests. When adding new functionality, it is advisable to add +unit tests. * Run tests ** Setup -Mechanize is not yet included in Guix deployment. +Everything required for testing is already package with guix: +: ./pre-ins-env guix package -i genenetwork2 -p ~/opt/genenetwork2 ** Running -Run the tests from the root of the genenetwork2 source tree as, for -example, +Run the tests from the root of the genenetwork2 source tree as. Ensure +that Redis and Mariadb are running. -: ./bin/test-website http://localhost:5003/ (default) +To run Mechanical Rob: +: time env GN2_PROFILE=~/opt/genenetwork2 TMPDIR=~/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -c ~/projects/genenetwork2/test/requests/test-website.py -a http://localhost:5004 -If you are using the small deployment database you can use +Use these aliases for the following examples. -: ./bin/test-website --skip -n +#+begin_src sh +alias runpython="env GN2_PROFILE=~/opt/gn-latest TMPDIR=/tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 -To run individual tests on localhost you can do +alias runcmd="time env GN2_PROFILE=~/opt/gn-latest TMPDIR=//tmp SERVER_PORT=5004 GENENETWORK_FILES=/gnu/data/gn2_data/ ./bin/genenetwork2 ./etc/default_settings.py -cli" +#+end_src -: ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/" +You could use them in your =.bashrc= or =.zshrc= file. + +To run unit tests: + +: runpython -m unittest discover -v + +Or alternatively using the coverage tool: + +: runcmd coverage run -m unittest discover -v + +To generate a html coverage report in =wqflask/coverage_html_report/= + +: runcmd coverage html + +To output the report to =STDOUT=: + +: runcmd coverage report + +All the configs for running the coverage tool are in +=wqflask/.coveragerc= |