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Trac Ticket Queries
Table of Contents
In addition to reports, Trac provides support for custom ticket queries, used to display lists of tickets meeting a specified set of criteria.
To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.
Filters
When you first go to the query page the default filters will display all open tickets, or if you're logged in it will display open tickets assigned to you. Current filters can be removed by clicking the button to the right with the minus sign on the label. New filters are added from the pulldown list in the bottom-right corner of the filters box. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an or of the criteria.
You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.
Once you've edited your filters click the Update button to refresh your results.
Navigating Tickets
Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.
You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.
The query results can be refreshed and cleared of these status indicators by clicking the Update button again.
Saving Queries
While Trac does not yet allow saving a named query and somehow making it available in a navigable list, you can save references to queries in Wiki content, as described below.
Using TracLinks
You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page.
[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]
Which is displayed as:
This uses a very simple query language to specify the criteria (see Query Language).
Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character:
[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]
Which is displayed as:
Using the [[TicketQuery]] Macro
The TicketQuery macro lets you display lists of tickets matching certain criteria anywhere you can use WikiFormatting.
Example:
[[TicketQuery(version=0.6|0.7&resolution=duplicate)]]
This is displayed as:
- #4
- Spike Lowess
- #5
- Center on assay
- #6
- QQPlot
- #7
- Merge on genesymbol
- #8
- COPA
- #9
- Error in ReplicateError
- #10
- ReplicateError
- #11
- Pinbaes normalization
- #16
- BasicReporter and BasicSpot
- #18
- AnnotationFiletr
- #19
- RMA plugin should check that cel files are assigned to correct cdf.
- #20
- extra values pass through
- #92
- Create Illumina SNP raw data type
- #125
- MeV ... files are now supported (by the BASEcore) in the BASE analysis tree
- #192
- MeV unable to launch appplication ... class not found exception
- #245
- net.sf.basedb.illumina: Detection P-value fails if there is no negative controls in bioassayset
- #296
- VirtualArray plug-in can't be installed
- #347
- Exception when trying to register more than one specimen tube for a case
- #393
- Change default value for protocol in "RNA quality control - create aliquots" wizard step 2
- #634
- Retraction wizard
- #866
- Implement the "Start page" extension
Just like the query: wiki links, the parameter of this macro expects a query string formatted according to the rules of the simple ticket query language.
A more compact representation without the ticket summaries is also available:
[[TicketQuery(version=0.6|0.7&resolution=duplicate, compact)]]
This is displayed as:
#4, #5, #6, #7, #8, #9, #10, #11, #16, #18, #19, #20, #92, #125, #192, #245, #296, #347, #393, #634, #866
Finally if you wish to receive only the number of defects that match the query using the count parameter.
[[TicketQuery(version=0.6|0.7&resolution=duplicate, count)]]
This is displayed as:
Customizing the table format
You can also customize the columns displayed in the table format (format=table) by using col=<field> - you can specify multiple fields and what order they are displayed by placing pipes (|) between the columns like below:
[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]
This is displayed as:
Results (1 - 3 of 1547)
Full rows
In table format you can also have full rows by using rows=<field> like below:
[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]
This is displayed as:
Results (1 - 3 of 1547)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #1609 | fixed | Misconfiguration is causing Trimmomatic adapter trimming to be skipped when demuxing RNAseq data | ||
| Description |
In our config file we have the following setting for the adapter trimming step:
The The configuration need to be updated to:
|
|||
| #1608 | fixed | Imputation fails with error: reheader: invalid option -- 'O' | ||
| Description |
java.lang.RuntimeException: reheader: invalid option -- 'O'
About: Modify header of VCF/BCF files, change sample names.
Usage: bcftools reheader [OPTIONS] <in.vcf.gz>
Options:
-f, --fai FILE update sequences and their lengths from the .fai file
-h, --header FILE new header
-o, --output FILE write output to a file [standard output]
-s, --samples FILE new sample names
-T, --temp-prefix PATH template for temporary file name [/tmp/bcftools.XXXXXX]
--threads INT use multithreading with <int> worker threads (BCF only) [0]
Example:
# Write out the header to be modified
bcftools view -h old.bcf > header.txt
# Edit the header using your favorite text editor
vi header.txt
# Reheader the file
bcftools reheader -h header.txt -o new.bcf old.bcf
Failed to read from standard input: unknown file type
srun: error: cnl01: task 0: Exited with exit code 255
at net.sf.basedb.opengrid.service.OpenGridService.updateJobStatusInBase(OpenGridService.java:888)
at net.sf.basedb.opengrid.service.OpenGridService.processAsyncRequests(OpenGridService.java:576)
at net.sf.basedb.opengrid.service.OpenGridService$JobStatusTimerTask.run(OpenGridService.java:933)
at net.sf.basedb.util.timer.ThreadTimerTask$1.run(ThreadTimerTask.java:94)
at java.base/java.lang.Thread.run(Thread.java:833)
The -O (=output format) is typically available on all bcftools command but for some reason not for the 'reheader' command. |
|||
| #1605 | fixed | The JSON importer should ignore text: Fritext (OBS EJ SEMIKOLON) | ||
| Description |
Some fields that are optional to fill used to have the text |
|||
Query Language
query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Basically, the filters are separated by ampersands (&). Each filter then consists of the ticket field name, an operator, and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values.
The available operators are:
= | the field content exactly matches the one of the values |
~= | the field content contains one or more of the values |
^= | the field content starts with one of the values |
$= | the field content ends with one of the values |
All of these operators can also be negated:
!= | the field content matches none of the values |
!~= | the field content does not contain any of the values |
!^= | the field content does not start with any of the values |
!$= | the field content does not end with any of the values |
See also: TracTickets, TracReports, TracGuide
