Creating a pushQ Entry: Difference between revisions

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After you have finished creating a track and it is ready for QA, you should add an entry to the qapushq table on hgwbeta.
This page is for documenting the process of pushing a track to the RR.
There is a [http://hgwbeta.cse.ucsc.edu/cgi-bin/qaPushQ CGI] for this.
For the entire hand-off of a Track from Developers to QAers, see the redmine wiki page [http://redmine.soe.ucsc.edu/projects/genomebrowser/wiki/Track here].


'''Add a track to the pushQ only if everything is ready.'''   
There is no pushq CGI anymore. After you have finished creating a track and it is ready for QA, you should update the redmine status to "QA ready" and set the pushq fields in the redmine ticket.
 
'''Set a ticket to pushq-ready only if everything is ready.'''   
This includes:
This includes:


* All tables have been built
* All tables have been built.
* TrackDb has been edited (including track and search lines as appropriate)
* makedoc entry is complete and checked in.
* Make alpha on hgwdev in /trackDb directory
* TrackDb has been edited (including search stanzas). If this is an update to an existing track, you may need to use [http://genomewiki.ucsc.edu/index.php/ThreeStateTrackDb#Updated_trackDb_release_process release tags].
* All underlying files are complete and in the correct location (usually /gbdb/)
* Make alpha on hgwdev in src/hg/makeDb/trackDb directory.
* html text for details page is complete (see also [[Details_pages_--_conventions | description pages]] and [[CBSE_citation_format| citation formats]]) and is in highest logical level for the assembly.
* All underlying files are complete and in the correct location (usually /gbdb/).
* All associated downloads files have been created and are in the correct location (usually /data/apache/htdocs-hgdownload/goldenPath/)
* All associated downloads files have been created and are in the correct location (usually /usr/local/apache/htdocs-hgdownload/goldenPath/), and accompanying README.txt and md5sum.txt files are present.
* All tables have been added to the all.joiner file
* html text for details page (a.k.a. Track Description page) is complete (see also [[Details_pages_--_conventions | description pages]] and [[CBSE_citation_format| citation formats]]) and is in highest logical level for the assembly.  If this is an update to an existing track, you may need to make the updated details page visible on alpha while the original page is visible on beta and public.  This can be achieved with [http://genomewiki.ucsc.edu/index.php/ThreeStateTrackDb#Updated_trackDb_release_process release tags] and an html qualifier in the alpha stanza.
* All tables have been added to the makeDb/schema/all.joiner file.
* Data contributor (if any) has approved of the track display.
* View the track in the browser, check for pile-ups on one whole chromosome.
 
'''Editing the pushQ-like fields in redmine'''
 
Engineers -- When you finish a track or assembly, and it's ready for QA do the following:
* Set status to QA Ready
* Complete Table List & File List
* Put any special instructions in redmine as an update to the ticket
 
QAers -- To see what's ready for QA check the query named "ready for QA": http://redmine.soe.ucsc.edu/projects/genomebrowser/issues?query_id=16
* Claim redmine issue as usual
* Set status to Reviewing
* If you would like for it to have an entry on the Release Log page, complete the Release Log Text and Release Log URL
* When you finish QA and push to the RR: set status to Released and check the "released to RR" checkbox.


'''Editing the pushQ entry:'''
Helpful wiki pages:
* redmine instead of the pushQ:
http://redmine.soe.ucsc.edu/projects/genomebrowser/wiki/PushQ
* process for Tracks in redmine (with no more pushQ):
http://redmine.soe.ucsc.edu/projects/genomebrowser/wiki/Track
 
''NEW TRACK?:''
If this same track exists on this or another assembly, or this is an addition to an existing track, leave this set to N.  If this is a brand new track set this to Y.  If this isn't a track at all, set this to X.
 
''TRACK:''
Put an identifier for the track here.  This is often the shortLabel.


''RELEASE LOG:''
''RELEASE LOG:''
Put the main identifier, usually short label followed by comments in parentheses if any (e.g. Known Gene (data update)).  No need to enter the database name.
Generally you should put the track shortLabel followed by comments in parentheses, if any (e.g. UCSC Genes (data update)).  No need to enter the database name.  This text will appear in the [http://genome.ucsc.edu/goldenPath/releaseLog.html Release Log].


''RELEASE LOG URL''
''RELEASE LOG URL''
If you would like for the [http://genome.ucsc.edu/goldenPath/releaseLog.html Release Log] entry for this track to link to the track description page, then enter a link to it here, e.g.:
If you would like the Release Log entry for this track to link to the track description page, then enter a relative link to it here, e.g.:
  ../../cgi-bin/hgTrackUi?db=hg18&g=wgEncodeBuOrchid
  ../../cgi-bin/hgTrackUi?db=hg18&g=wgEncodeBuOrchid


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''TABLES:''
''TABLES:''
Don't forget to include:
List all tables that should be pushed. Don't forget to include extFile and seq if your track uses them.
* trackDb
* hgFindSpec (if the items in this track are searchable)
* extFile
* seq
 
''CGIs:''
If this track depends on a particular upcoming release of the CGIs, enter the CGI name and the version number here (e.g. hgTracks (v250)).


''FILES:''
''FILES:''
Don't forget to include:
List all files that should be pushed.  Don't forget to include:
* gbdb files
* download files
* download files
''CURRENT LOCATION:''
Set to hgwdev.


''SIZE:''
''SIZE:''
Press the Show Sizes button.
Press the Show Sizes button.  All tables and files should be found without errors (if they are not, you probably have entered a path incorrectly or have a typo in the lists).  Scroll to the bottom of the page and click the "Set Size as ..." link.


''MAKEDOC VERIFIED:''
''MAKEDOC VERIFIED:''
Line 54: Line 73:
Leave this set to N.
Leave this set to N.


''EXTERNAL SOURCE:''  
''REVIEWER:''
Enter the name and email address of the collaborator.  Or enter the name of the website or lab where the data came from.
Leave blank.
 
''NOTES:''
Add notes to the QA team in this section.  Be as specific as possible -- the more you enter here, the less QA will have to ask you for.  Also, if this track has been requested by a user, enter the user's email address here.  QA will send an email to that user after the track has been pushed to the RR.  If this track is replacing an existing track, be sure to list the tables/files to drop. Please include the redmine issue number here (for cross-reference).
 
<hr>
After the track has been QAd and pushed to the public website, you can edit the original tables and files genome-test as you like.  This new data will not be QAd and pushed until you add another pushQ entry.
 
<hr>
If this is the release of an entire assembly, use Angie's [[makePushQSql.pl]] script.


[[Category:Browser QA]]
[[Category:Browser QA]]
[[Category:Browser QA dev handoff]]
[[Category:Browser QA dev handoff]]

Latest revision as of 16:55, 29 August 2018

This page is for documenting the process of pushing a track to the RR. For the entire hand-off of a Track from Developers to QAers, see the redmine wiki page here.

There is no pushq CGI anymore. After you have finished creating a track and it is ready for QA, you should update the redmine status to "QA ready" and set the pushq fields in the redmine ticket.

Set a ticket to pushq-ready only if everything is ready. This includes:

  • All tables have been built.
  • makedoc entry is complete and checked in.
  • TrackDb has been edited (including search stanzas). If this is an update to an existing track, you may need to use release tags.
  • Make alpha on hgwdev in src/hg/makeDb/trackDb directory.
  • All underlying files are complete and in the correct location (usually /gbdb/).
  • All associated downloads files have been created and are in the correct location (usually /usr/local/apache/htdocs-hgdownload/goldenPath/), and accompanying README.txt and md5sum.txt files are present.
  • html text for details page (a.k.a. Track Description page) is complete (see also description pages and citation formats) and is in highest logical level for the assembly. If this is an update to an existing track, you may need to make the updated details page visible on alpha while the original page is visible on beta and public. This can be achieved with release tags and an html qualifier in the alpha stanza.
  • All tables have been added to the makeDb/schema/all.joiner file.
  • Data contributor (if any) has approved of the track display.
  • View the track in the browser, check for pile-ups on one whole chromosome.

Editing the pushQ-like fields in redmine

Engineers -- When you finish a track or assembly, and it's ready for QA do the following:

  • Set status to QA Ready
  • Complete Table List & File List
  • Put any special instructions in redmine as an update to the ticket

QAers -- To see what's ready for QA check the query named "ready for QA": http://redmine.soe.ucsc.edu/projects/genomebrowser/issues?query_id=16

  • Claim redmine issue as usual
  • Set status to Reviewing
  • If you would like for it to have an entry on the Release Log page, complete the Release Log Text and Release Log URL
  • When you finish QA and push to the RR: set status to Released and check the "released to RR" checkbox.

Helpful wiki pages:

  • redmine instead of the pushQ:

http://redmine.soe.ucsc.edu/projects/genomebrowser/wiki/PushQ

  • process for Tracks in redmine (with no more pushQ):

http://redmine.soe.ucsc.edu/projects/genomebrowser/wiki/Track

NEW TRACK?: If this same track exists on this or another assembly, or this is an addition to an existing track, leave this set to N. If this is a brand new track set this to Y. If this isn't a track at all, set this to X.

TRACK: Put an identifier for the track here. This is often the shortLabel.

RELEASE LOG: Generally you should put the track shortLabel followed by comments in parentheses, if any (e.g. UCSC Genes (data update)). No need to enter the database name. This text will appear in the Release Log.

RELEASE LOG URL If you would like the Release Log entry for this track to link to the track description page, then enter a relative link to it here, e.g.: 

../../cgi-bin/hgTrackUi?db=hg18&g=wgEncodeBuOrchid

DATABASES: List the database(s) where your table(s) are located (e.g. hg19, hgFixed).

TABLES: List all tables that should be pushed. Don't forget to include extFile and seq if your track uses them.

FILES: List all files that should be pushed. Don't forget to include:

  • gbdb files
  • download files

SIZE: Press the Show Sizes button. All tables and files should be found without errors (if they are not, you probably have entered a path incorrectly or have a typo in the lists). Scroll to the bottom of the page and click the "Set Size as ..." link.

MAKEDOC VERIFIED: Leave this set to N.

INDEX VERIFIED: Leave this set to N.

ALL.JOINER VERIFIED: Leave this set to N.

REVIEWER: Leave blank.

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