diff options
Diffstat (limited to 'issues')
24 files changed, 569 insertions, 6 deletions
diff --git a/issues/authorisation.gmi b/issues/authorisation.gmi index 044962d..0adac56 100644 --- a/issues/authorisation.gmi +++ b/issues/authorisation.gmi @@ -2,13 +2,28 @@ 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 + +- [x] Make user able to delete/ add extra value + +- [x] Fetch complete list of samples from database and genotype file + instead of only fetching that list from the database. Look at trait + page for reference. + +- [ ] Extend idea of csv generation to probeset data. Get data from + the genotype file and work out how to update the values from the + database. # Notes @@ -111,4 +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/binderlite/add-configuration-to-set-server-name.gmi b/issues/binderlite/add-configuration-to-set-server-name.gmi new file mode 100644 index 0000000..d54997c --- /dev/null +++ b/issues/binderlite/add-configuration-to-set-server-name.gmi @@ -0,0 +1,11 @@ +# Add configuration to set server name + +* assigned: jgart + +* feature + +Let's use environment variables as configuration + +https://flask.palletsprojects.com/en/2.0.x/cli/?highlight=environment%20variables + +https://docs.python.org/3/library/os.html?highlight=os%20environ#os.environ diff --git a/issues/binderlite/add-spinner-for-submit-form.gmi b/issues/binderlite/add-spinner-for-submit-form.gmi index 0800fa8..de19c55 100644 --- a/issues/binderlite/add-spinner-for-submit-form.gmi +++ b/issues/binderlite/add-spinner-for-submit-form.gmi @@ -13,3 +13,15 @@ a container to be built? A spinning guix gnu logo could be cool. https://www.w3schools.com/howto/howto_css_loader.asp https://spin.js.org/https://spin.js.org/ + + +## Solution + +We're using ansi2html now. + +See the following issue: + +=> ./ansi2html_terminal_user_feedback.gmi + +* closed + diff --git a/issues/binderlite/ansi2html_terminal_user_feedback.gmi b/issues/binderlite/ansi2html_terminal_user_feedback.gmi new file mode 100644 index 0000000..969448a --- /dev/null +++ b/issues/binderlite/ansi2html_terminal_user_feedback.gmi @@ -0,0 +1,36 @@ +# ansi2html terminal user feedback + +* ongoing +* feature-request +* assigned: jgart + +https://builds.sr.ht/~sircmpwn/job/610711 + +https://builds.sr.ht/~sircmpwn/job/611028 + +This issue proposes an alternative way to generate terminal output to the browser +from a process that does not dependent on js libraries but still looks great. + +Drew Devault uses this method in builds.sr.ht, the continuous integration +system/app that is part of the SourceHut suite. + +builds.sr.ht generates terminal output using jinja templates and a relatively +small python library called ansi2html. It is already packaged by guix upstream +as python-ansi2html (It could use an update). + +https://github.com/pycontribs/ansi2html +https://pypi.org/project/ansi2html/ + +Here are two examples of it in action at builds.sr.ht: + +https://builds.sr.ht/~sircmpwn/job/610711 + +https://builds.sr.ht/~sircmpwn/job/611028 + +And, the relevant places in builds.sr.ht code base: + +https://git.sr.ht/~sircmpwn/builds.sr.ht/tree/master/item/buildsrht/templates/job.html#L117 + +https://git.sr.ht/~sircmpwn/builds.sr.ht/tree/master/item/buildsrht/blueprints/jobs.py#L333 + +I've added a diagram showing how it will integrate with binderlite. diff --git a/issues/binderlite/binderlite_ansi2html_terminal_diagram.png b/issues/binderlite/binderlite_ansi2html_terminal_diagram.png Binary files differnew file mode 100644 index 0000000..a4f16b4 --- /dev/null +++ b/issues/binderlite/binderlite_ansi2html_terminal_diagram.png diff --git a/issues/binderlite/error-regarding-static-assets-after-forwarding.gmi b/issues/binderlite/error-regarding-static-assets-after-forwarding.gmi index 27e7bd1..bd39df9 100644 --- a/issues/binderlite/error-regarding-static-assets-after-forwarding.gmi +++ b/issues/binderlite/error-regarding-static-assets-after-forwarding.gmi @@ -50,3 +50,5 @@ http://localhost/49761/?token=f6269bbf48ee5c9887732f5bc76d32f37e1f25483195ae88 The next step is to get jupyter to accept the generated token on the first request without needing to input it manually first. + +* closed diff --git a/issues/binderlite/integrate-styling-with-gn2.gmi b/issues/binderlite/integrate-styling-with-gn2.gmi new file mode 100644 index 0000000..dc158fa --- /dev/null +++ b/issues/binderlite/integrate-styling-with-gn2.gmi @@ -0,0 +1,11 @@ +# Integrate styling of app with GN2 + +* ongoing +* assigned: jgart + +Currently using antiweb for styling with modifications. + +=> https://git.sr.ht/~sircmpwn/antiweb antiweb + +Copying nav bar and fonts from GN2 will make the app look more integrated with +GN2 UI. diff --git a/issues/binderlite/open-files-directly-if-full-path-is-given.gmi b/issues/binderlite/open-files-directly-if-full-path-is-given.gmi new file mode 100644 index 0000000..203e87a --- /dev/null +++ b/issues/binderlite/open-files-directly-if-full-path-is-given.gmi @@ -0,0 +1,18 @@ +# Open notebook directly if full path to notebook file is given + +* feature-request +* assigned: jgart + +We'd like to be able launch a notebook directly if the user gives the fullpath to the notebook file. + +Should we allow urls like this? + +https://github.com/jgarte/guile-notebook-genenetwork-api/blob/master/genenetwork-api.ipynb + +The above is a valid github url that also points to the notebook file. + +Or only this? + +https://github.com/jgarte/guile-notebook-genenetwork-api/genenetwork-api.ipynb + +* closed diff --git a/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi new file mode 100644 index 0000000..49f5d3f --- /dev/null +++ b/issues/binderlite/return-canned-text-if-notebook-description-returns-none.gmi @@ -0,0 +1,25 @@ +# Return canned text if notebook description returns none + +* bug? +* assigned: jgart + +Notebooks that do not have a description will use python's `None` value as the +project's description. + +Should we return some other text instead? + +We could do something like the following idea: + +``` +if notebook.description == None: + return "Project does not have a description." +``` + +Or we could do: + +``` +if notebook.description == None: + return "Could not retrieve description for project." +``` + +WDYT? diff --git a/issues/database-not-responding.gmi b/issues/database-not-responding.gmi index c8e752b..e66c939 100644 --- a/issues/database-not-responding.gmi +++ b/issues/database-not-responding.gmi @@ -1,4 +1,136 @@ -# Mariadb table locked +# Hanging database + +Mariadb occassionally stops responding. + +## Tasks + +* assigned: pjotrp, zsloan +* bug + +# Info + +## Mariadb is 'hanging' + +In the last 12 hours GN2 monitoring shows the website is responding intermittendly. A quick check shows the database is blocking. Rather than simply restarting the database - which is known to sort the issue - the timing is that the US is sleeping so I can do some checking. Let's take a look. + +Mariadb is at 4x CPU + +``` +PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND + 40514 mysql 20 0 37.3g 1.8g 18268 S 394.4 0.7 4855:33 mysqld +``` + +The ps table shows a backup is ongoing + +``` +root 57559 0.0 0.0 2388 756 ? Ss 03:00 0:00 /bin/sh -c /bin/su mysql -c /export/backup/scripts/tux01/backup_mariadb.sh >> ~/cron.log 2>&1 +mysql 57588 0.2 0.0 200112 27292 ? Sl 03:00 0:25 mariabackup --backup --target-dir=/home/backup/tux01_mariadb_new/latest/ --user=webqtlout --password=x xxxxxxx +``` + +Tales in use: + +``` +MariaDB [db_webqtl]> show open tables where in_use > 1; ++-----------+----------------+--------+-------------+ +| Database | Table | In_use | Name_locked | ++-----------+----------------+--------+-------------+ +| db_webqtl | InfoFiles | 5 | 0 | +| db_webqtl | GeneRIF_BASIC | 3 | 0 | +| db_webqtl | ProbeFreeze | 4 | 0 | +| db_webqtl | ProbeSet | 4 | 0 | +| db_webqtl | ProbeSetXRef | 4 | 0 | +| db_webqtl | Species | 4 | 0 | +| db_webqtl | Geno | 4 | 0 | +| db_webqtl | Chr_Length | 2 | 0 | +| db_webqtl | Tissue | 4 | 0 | +| db_webqtl | ProbeSetFreeze | 4 | 0 | +| db_webqtl | InbredSet | 4 | 0 | ++-----------+----------------+--------+-------------+ +11 rows in set (0.001 sec) +``` + +In the error log we seeing a lot of + +``` +2021-12-21 6:17:57 256179 [Warning] Aborted connection 256179 to db: 'db_webqtl' user: 'webqtlout' host: '128.169.5.59' (Got timeout reading communication packets) +``` + +``` +SHOW FULL PROCESSLIST; +458 rows in set (0.003 sec) +``` + +with entries + +``` +| 256363 | webqtlout | 128.169.5.59:59120 | db_webqtl | Query | 15 | Waiting for table flush | SELECT Id, Name, FullName, ShortName, DataScale FROM ProbeSetFreeze WHERE public > 0 AND (Name = "CB_M_0305_R" OR FullName = "CB_M_0305_R" OR ShortName = "CB_M_0305_R") +``` + +waiting for tables to flush! + +at the top of the process list we find + +``` +Id User Host db Command Time State Info Progress 1 system user NULL Daemon NULL InnoDB purge coordinator NULL 0.000 2 system user NULL Daemon NULL InnoDB purge worker NULL 0.000 3 system user NULL Daemon NULL InnoDB purge worker NULL 0.000 4 system user NULL Daemon NULL InnoDB purge worker NULL 0.000 5 system user NULL Daemon NULL InnoDB shutdown handler NULL 0.000 227365 webqtlout 127.0.0.1:33950 db_webqtl Sleep 13015 NULL 0.000 245634 webqtlout 127.0.0.1:38098 db_webqtl Sleep 23180 NULL 0.000 +``` + +This is quite informative: + +=> https://programmer.group/analysis-of-mysql-process-in-waiting-for-table-flush.html + +it suggests that the backup can be the root of the problem. + +And then + +=> https://www.thegeekdiary.com/troubleshooting-mysql-query-hung-waiting-for-table-flush/ + +suggests + +* Wait for the long-running queries which are blocking the FLUSH TABLE to complete; +* Identify the long-running queries and kill them; +* Restart the server + +and that is somewhat amusing. + +Stripping out all reqular queries we get: + +``` +grep localhost test.out |grep -vi probesetfreeze|grep -vi species +255559 webqtlout localhost NULL Query 13092 Waiting for table flush FLUSH NO_WRITE_TO_BINLOG TABLES0.000 +256351 webqtlout localhost db_webqtl Field List 1588 Waiting for table flush NULL 0.000 +256383 webqtlout localhost db_webqtl Query 0 Init SHOW FULL PROCESSLIST 0.000 +``` + +and it appears everyone is waiting for id 255559. Let's kill that. + +``` +kill 255559; +``` + +and inspect + +``` +mysql -u webqtlout -pwebqtlout db_webqtl -A -e "show processlist;"|less +``` + +it started processing again. To speed up recovery back to: + +``` +systemctl restart mysql +``` + +of course that stopped the running backup. But processing is back in business. + +My first conclusion is that this problem was triggered by the backup procedure. Interestingly, it happens irregularly. We also have seen this issue before this backup procedure was instated, so I figure it has to do with Mariadb. + +The version on production is from 2017 - we should update that soon: + +Server version: 10.3.27-MariaDB-0+deb10u1-log Debian 10 + +we have been running a more recent version of mariadb on luna. Still, that is unlikely to fix this issue because I think it really has to do with myisam and locking of large tables. Switching to innodb does away with global locks and is the default on mariadb (there are less and less people using myisam). + + +## Mariadb table locked Arthur reports: MariaDB is not responding Saturday, July 24 2021 at 10:48 pm. I tried to enter data to the table ProbeSetXRef.pValue and when normally takes few seconds, now is more than 10 minutes without completion/responding. diff --git a/issues/deploy.gmi b/issues/deploy.gmi new file mode 100644 index 0000000..94d73ec --- /dev/null +++ b/issues/deploy.gmi @@ -0,0 +1,26 @@ +# Handle Configuration Files + +How we handle our configuration is a mess; and this makes deployment a +hassle. In genenetwork2, our configs live in different places, and it +takes some fiddling tinged with a bit of domain (gn2) knowledge to +work out what setting live where. With the introduction of blueprints +in our code-base, this duplication became a necessary evil because +most of the settings QC checks happen in a "utility/tools.py" which +unfortunately imports the "app" object. This import leads to circular +imports whenever we use blueprints. Unfortunately, a huge chunk of +the code base uses "utility/tools.py" to get configuration +settings; and removing this would make gn2 as is disfunctional. + +# Tags + +* assigned: bonfacem + +# Notes + +Here's an example of how to use json as our settings: + +=> https://stackoverflow.com/questions/15122312/how-to-import-from-config-file-in-flask + +Here's Flask's official documentation on handling configuration: + +=> https://flask.palletsprojects.com/en/1.1.x/config/ diff --git a/issues/fix-broken-builds-in-gn2-and-gn3.gmi b/issues/fix-broken-builds-in-gn2-and-gn3.gmi index cf9506f..3c0e6aa 100644 --- a/issues/fix-broken-builds-in-gn2-and-gn3.gmi +++ b/issues/fix-broken-builds-in-gn2-and-gn3.gmi @@ -5,7 +5,55 @@ gn3 and gn2. ## Tasks -* assigned: bonfacekilz +* assigned: bonfacekilz, efraim -* [ ] Fix pylint/ mypy issues in gn3 -* [ ] Update docker image in gn2 +### Notes + +At the moment, we are getting the following build failures in gn2, + +``` +Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wqflask/wgcna/wgcna_analysis.py'... +Compiling '/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/wsgi.py'... +error: in phase 'install': uncaught exception: +%exception #<&invoke-error program: "python" arguments: ("-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9") exit-status: 1 term-signal: #f stop-signal: #f> +phase `install' failed after 0.9 seconds +command "python" "-m" "compileall" "--invalidation-mode=unchecked-hash" "/gnu/store/bm0909ha5nv5chgp3bk5fw0my6mrsabr-genenetwork2-3.11-guix-fe345c9" failed with status 1 +note: keeping build directory `/tmp/guix-build-genenetwork2-3.11-guix-fe345c9.drv-0' +builder for `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed with exit code 1 +build of /gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv failed +View build log at '/var/log/guix/drvs/l5/hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv.bz2'. +guix build: error: build of `/gnu/store/l5hb8bfz3di3zga93963arlka03lijn8-genenetwork2-3.11-guix-fe345c9.drv' failed + +``` + +Some missing bits from the build log: + +``` +Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/redis_tools.py'... +Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/startup_config.py'... +Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py'... +*** File "/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/svg.py", line 113 + True = 1 + ^ + SyntaxError: cannot assign to True + +Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/temp_data.py'... +Compiling '/gnu/store/n2w3bdka4zfl3jw0iqk49km1hgl8i7g5-genenetwork2-3.11-guix-fe345c9/lib/python3.9/site-packages/wqflask/utility/tools.py'... + +``` + +This starts happening (not yet comfirmed) when python is bumped up +from 3.8 to 3.9 + +In addition, there are some dependencies of genenetwork2 which FTBFS, due to incorrect versions of inputs. + +``` + starting phase `sanity-check'¬ + validating 'pingouin' /gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages¬ + ...checking requirements: ERROR: pingouin==0.5.0 (statsmodels 0.11.1 (/gnu/store/ab8k9bwmaml2bplq4bd9xkg08z7bn8fr-python-statsmodels-0.11.1/lib/python3.9/site-packages), Requirement.parse('statsmodels>=0.12.0'), {'pingouin'})¬ + error: in phase 'sanity-check': uncaught exception:¬ + %exception #<&invoke-error program: "python" arguments: ("/gnu/store/nwwr89v2vyg1hs48i49m083vhczsgh3m-sanity-check.py" "/gnu/store/dpy5ln4zjgv53l8jpm1qalwn45cagxfm-python-pingouin-0.5.0/lib/python3.9/site-packages") exit-status: 1 term-signal: #f stop-signal: #f>▸¬ + phase `sanity-check' failed after 0.1 seconds¬ +``` + +This was fixed by reverting the update to python-pingouin, dropping it back to 0.3.12. diff --git a/issues/gemma/gemma-wrapper-has-incomplete-files.gmi b/issues/gemma/gemma-wrapper-has-incomplete-files.gmi new file mode 100644 index 0000000..d530fb4 --- /dev/null +++ b/issues/gemma/gemma-wrapper-has-incomplete-files.gmi @@ -0,0 +1,42 @@ +# gemma-wrapper has incomplete files + +Gemma wrapper caches files - but it can happen a cached file is incomplete and never updated again. The problem appears when GNU parallel is invoked and hits an error. The task here is to make gemma-wrapper transactional. + +## Tags + +* assigned: pjotrp, zachs + +## Tasks + +* [X] parse parallel job log for failed tasks and remove the output files. +* [X] create a (global) lock file for gemma-wrapper + +## Info + +GNU parallel can fail, but does not tell how individual processes did. Need to check if it can return a thread (number). If not we have the option of checking the GEMMA status file and/or see if the output file is complete (by counting number of lines). + +The 'obvious' fix would be to create an error handler in GEMMA itself that would clean up output files on error exit. E.g. using + +=> https://www.cplusplus.com/reference/exception/set_terminate/ + +The problem is that it is NOT a catch all. If there is a hardware fault or a problem in a library, such as openblas, there is no guarantee that the terminate handler will be called. Another complication is that a terminate handler needs to be aware of the files being output - i.e., we need to carry the state down somehow. I think we can probably address these issues as much is handled in the GEMMA PARAM class, but it is not worth the effort (I'll take care of it in a GEMMA rewrite). + +It turns out that GNU parallel can keep track of jobs in a job log - and even rerun the ones missing using the `--joblog` and `--resume` switches. The last we don't need because we are using a cache. But we can use the log file to remove any incomplete output files! To me this is the obvious solution because 'parallel' is monitoring outside the GEMMA process and is a hardened piece of software. On failure it simply designates runs that way and we can clean up any (partly) produced files followed by a safe rerun. The lock routine below ascertains no processes are creating the same output at the same time. + +## Delete files on failure + +Implemented in + +=> https://github.com/genetics-statistics/gemma-wrapper/commit/624ed0d805f29ab682cffbe46bc104dffd0d713c + +## Dealing with locks + +There is another parallel issue (pun intended) where gemma-wrapper is invoked twice for the same job. This is quite possible when people get impatient waiting for a first job to finish. + +One solution is to write a lock file using the inputs as a hash. The lock file can contain a PID and we can check if that is still alive. I should do the same for sheepdog locks(!) + +=> https://github.com/genetics-statistics/gemma-wrapper/commit/e7e516ec5a6ffc5b398302fa204685a40e76e171 Added locking support + +I added the same code to replace sheepdog locks. Sheepdog is running every minute on our machines so it is a great test case. + +=> https://github.com/pjotrp/deploy/commit/4790b81ee897c8244280169edb3cac751eb0a9b3 sheepdog locking 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/issues/genenetwork/http-https.gmi b/issues/genenetwork/http-https.gmi new file mode 100644 index 0000000..80306bf --- /dev/null +++ b/issues/genenetwork/http-https.gmi @@ -0,0 +1,15 @@ +# Arthur mentioned last meet that GeneNetwork2 does not redirect http urls to https. + +He'd like http to redirect to https. + +http://genenetwork.org/ -> https://genenetwork.org/ + +# nginx snippet + +``` +if ($scheme = http) { + return 301 https://$server_name$request_uri; +} +``` + +* assigned: pjotr, arthur, jgart 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/issues/gnbug/add-convenience-templates.gmi b/issues/gnbug/add-convenience-templates.gmi new file mode 100644 index 0000000..41eb975 --- /dev/null +++ b/issues/gnbug/add-convenience-templates.gmi @@ -0,0 +1,29 @@ +# Add convenienve templates + +* feature-request + +WDYT of adding a subcommand called `report` to generate a template for a bug report? + +I was thinking of an interface like the following: + +``` +gnbug report feature-request "New feature: IPFS Downloads" +``` + +Or expressed as generic command parameters: + +``` +command subcommand tag(s) title +``` + +Which creates a file in issues/binderlite directory with a template like the +following: + + +``` +# New feature: IPFS Downloads + +* feature-request +``` + +Might be bloat but might be nice and convenient also. WDYT? diff --git a/issues/gnbug/add-linter.gmi b/issues/gnbug/add-linter.gmi index 7992753..1a8a301 100644 --- a/issues/gnbug/add-linter.gmi +++ b/issues/gnbug/add-linter.gmi @@ -14,3 +14,11 @@ support. I am not sure. Pjotr is of the philosophy that we should keep the text as unstructured and unrestrictive as possible, and I agree with this philosophy. Linters are likely to annoy users more than help them. They might discourage casual use of the issue tracker. Especially with tags, we don't really want to restrict the user from coming up with new tags. WDYT? Am I missing some scenario where the linter could be essential? + +Nope, it was just something I thought could be convenient if we wanted to restrict +the format for tags, etc... + +If we'd like to "keep the text as unstructured and unrestrictive as possible" I'm +fine with that too. + +I was just worried about using "invalid" tags. Now, I know it's ok :) diff --git a/issues/per-service-profile-for-shepherd-services.gmi b/issues/per-service-profile-for-shepherd-services.gmi new file mode 100644 index 0000000..b22448b --- /dev/null +++ b/issues/per-service-profile-for-shepherd-services.gmi @@ -0,0 +1,33 @@ +# Each shepherd service needs its own guix profile. + +Currently there are a bunch of shepherd services (on Penguin2, as user shepherd) who are using the global shepherd guix profile and loading guix-bioinformatics at service start time to start their services. This is bad because: + +* we aren't using per-service guix-bioinformatics worktrees, so the branch changes between service refreshes +* service start times are high because we have to rebuild the service (due to above) +* services which are restarted are in an "untested" state until they work + +## Services which need to be migrated: + +* covid19-pubseq (uses shared (broken!) guix profile, uses shared config directory)(currently running by hand by Pjotr) +* hrdp-project (uses shared (broken!) guix profile) (upstream source is gone) +* ratspub (uses own guix profile, uses shared guix-bioinformatics)(deprecated(?)) +* pluto (uses own guix profile, uses shared config directory)(currently disabled) + +## Services which need to be monitored: + +* genenetwork1 (uses own guix profile, uses shared config directory) +* genome_browser (uses own guix profile, uses shared config directory) +* mcron (uses shared guix profile, probably OK) +* virtuoso (uses shared guix profile, probably OK) + +## Services which already have their own profile: + +* bnw +* cronjob-gitea +* cronjob-pubmed (genecup) +* genecup +* gitea +* ipfs +* power +* rn6app +* singlecell diff --git a/issues/quality-control/enumerate-all-qc-checks.gmi b/issues/quality-control/enumerate-all-qc-checks.gmi new file mode 100644 index 0000000..2f72f24 --- /dev/null +++ b/issues/quality-control/enumerate-all-qc-checks.gmi @@ -0,0 +1,7 @@ +# Enumerating all QC checks + +We need to enumerate all QC checks and platforms that we want to test against. + +* assigned: jgart, arthur + +* in progress diff --git a/issues/quality-control/gene-symbols.gmi b/issues/quality-control/gene-symbols.gmi new file mode 100644 index 0000000..63265ea --- /dev/null +++ b/issues/quality-control/gene-symbols.gmi @@ -0,0 +1,13 @@ +# Gene Symbol Mappings + +How can/should I lookup *all* the known mappings between different representations of symbol names? + +For example, B6 maps to C57BL/6J and D2 maps to DBA/2J. + +I'll need that mapping information for every strain, symbol etc... that has an alias in order to make the conversions. + +Ideally, I can have those mappings in some machine-readable format like csv, json, etc... + +* assigned: jgart, arthur + +* in progress diff --git a/issues/redis-data.gmi b/issues/redis-data.gmi new file mode 100644 index 0000000..2246c96 --- /dev/null +++ b/issues/redis-data.gmi @@ -0,0 +1,6 @@ +# Document redis data + +ATM how we store data in redis is undocumented. Without this, it's +hard for contributors to work out how to modify some things. For +example, PJ would want to add himself to the editors group. Doing +this was non-trivial for him.
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