Push-Request Etiquette

If you are pushing static docs (path is htdocs), see:http://genomewiki.ucsc.edu/genecats/index.php/Pushing_Static_Docs_(htdocs)

Remember to check your path:

• A bad path will cause issues for cluster-admin
  • do a list "ls /absolute/path/to/requestingPushOf/fileName" before requesting the push
  • But not the path to your source tree Not: /cluster/home/yourLogin/kent/src/hg/htdocs/...
  • Avoid wildcards, they mess up cluster-admins push scripts.
    • Erich writes, avoid ..goldenPath/hg38/vsNeoSch1/*.gz and instead list out all the .gz files individually
    • Or for a directory like axtNet use /usr/local/apache/htdocs-hgdownload/goldenPath/mm10/vsNeoSch1/axtNet but don't say this: /usr/local/apache/htdocs-hgdownload/goldenPath/mm10/vsNeoSch1/axtNet/*

Remember to do your QA on beta

• Beta exists for you to check data before release to the RR
  • This means checking your track and data work properly on beta.
  • This means you'll have to sudo mypush $db $table mysqlbeta
  • This means you'll have to sudo gbdbPush and gbdb data.
  • This means you can't request a push of tables/data from beta unless you've put things on beta.
  • Let people know you are doing a make public on hg19/hg38 mm9/mm10 (most used assemblies)

Remember to check after your push request that your data arrived on the RR (world).

• Don't leave users to check your push, check your push to catch unexpected errors.
  • This is the final QA check, to see your data arrived safely to the RR and works properly
  • Do not just request the push and then forget about it; we need to check the push went through and did not unintentionally break something (or didn't make it).
  • If requesting/pushing hg.conf changes, keep in mind they are instantaneous but can be reversed by asking cluster-admin to undo what you just requested.

Be kind to the cluster-admin

• Make things as easy as possible for cluster-admin
  • Don't expect them to respond immediately to your push-requests
  • Make sure your requests are proper before making them: CORRECT PATH; TABLES EXIST; GBDB EXIST
  • AVOID a late push-request if it can wait until morning (i.e., 5pm Friday push-request, because you'll have to stick around to check it, and they might be heading out the door).
  • Structure push requests so that they are easy to understand and straightforward to execute for cluster-admin:
    • For example, it is better to send several small push requests, than to lump multiple different table/assembly push requests into one email (even if all the pushes are related to the same goal).
    • In essence, if your push request looks very complicated, stop and think about redrafting it.

Example pushes

Go to the PUSH-REQUEST MAILING-LIST TO FIND THE LATEST GOOD EXAMPLES: https://groups.google.com/a/soe.ucsc.edu/g/push-request

Don't trust these below examples (use the above list instead), but here are some examples involving wuhCor1 trackDb/gbdb/table pushes:

• Push trackDb:

2022 UPDATE: Install an alias to run from hgwbeta: alias trackDbPush='ssh qateam@hgwbeta sudo /root/trackDbPush'

Hello Pushers,

Please push trackDb and friends for the following database:

wuhCor1

from hgwbeta-public --> RR/euro/asia

Reason: Staging validated epitopes track on RR refs #26305

Thanks!

• Push gbdb files:

Greetings push masters,

Can you please push the following files:

/gbdb/wuhCor1/bbi/epiValid.bb

from beta ---> RR/euro/asia

Reason: Staging validated epitopes track on RR refs #26305

Thanks!

• Push tables

Hello pushers,

Please push the following table for the wuhCor1 database:

microdel

from hgwbeta --> mysqlrr/genome-euro/genome-asia

Reason: Preparing release of microdeletion track on RR #25609

Thank you,

REMEMBER IT IS BEST TO FIND THE LATEST GOOD EXAMPLES IN THE MAILING-LIST WHERE CLUSTER-ADMIN HAD NO ISSUE WITH THE REQUEST.

Related info and pages

New_track_checklist Pushing_trackDb ThreeStateTrackDb

• In ~/genecats/qa/testTools/pushTools/lsList  you can find Daniel's short push-check script that will check the validity of a whole list of file paths in one step:

lsList 

Paste your list of file paths, ctr-C to exit loop

/gbdb/hg18/geneReviews/geneReviews.bb
/gbdb/hg19/geneReviews/geneReviews.bb
/gbdb/hg38/geneReviews/geneReviews.bb

lrwxrwxrwx 1 chmalee genecats 66 Oct 13 08:02 /gbdb/hg18/geneReviews/geneReviews.bb -> /hive/data/outside/otto/geneReviews/2020-10-13/geneReviews.hg18.bb
lrwxrwxrwx 1 chmalee genecats 66 Oct 13 08:01 /gbdb/hg19/geneReviews/geneReviews.bb -> /hive/data/outside/otto/geneReviews/2020-10-13/geneReviews.hg19.bb
lrwxrwxrwx 1 chmalee genecats 66 Oct 13 08:00 /gbdb/hg38/geneReviews/geneReviews.bb -> /hive/data/outside/otto/geneReviews/2020-10-13/geneReviews.hg38.bb