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mvdbeek / usegalaxy-tests

Run tests against usegalaxy.org
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Test gops_coverage_1 1.0.0 #24

Closed jennaj closed 2 years ago

jennaj commented 2 years ago

All GOPS tools except for "Join" are failing with a metadata error at org. With both bed and interval input/outputs.

toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

Ref: https://help.galaxyproject.org/t/error-galaxy-set-metadata-command-not-found/7551

Test history: https://usegalaxy.org/u/jen/h/test-gops

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 3
Error 0
Failure 0
Skipped 0
Passed s *
✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /corral4/main/jobs/041/228/41228210/galaxy_41228210.sh: line 123: galaxy-set-metadata: command not found ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "bed" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #2)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /corral4/main/jobs/041/228/41228196/galaxy_41228196.sh: line 123: galaxy-set-metadata: command not found ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "bed" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console /corral4/main/jobs/041/228/41228201/galaxy_41228201.sh: line 123: galaxy-set-metadata: command not found ``` **Standard Output:** * ```console Skipped 1 invalid lines of 1st dataset, 1st line #9: "chrM 4294967295 4294967322 EAS38_1_45_638_677 2 + ", problem: 4294967295 is larger than the size of this BitSet (536870912). ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "bed" ` |

jennaj commented 2 years ago

Technically "successful" with that same metadata error. Same as in the test history and reports from user's examined.

We should fix this before the Smorg if possible

confirmed by @mvdbeek -- needs "set-metadata script reinstalled"

jennaj commented 2 years ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0

mvdbeek commented 2 years ago

Results (powered by Planemo)

Summary

State Count
Total 3
Passed 2
Error 1
Failure 0
Skipped 0
Errored s *
❌ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #2)
**Execution Problem:** * ``` The attributes of this dataset are not properly set. Click the pencil icon in the history item to set the chrom, start, end and strand columns. ```

Passed s *
✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #1)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "bed" ` |
  • ✅ toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1 (Test #3)
    **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Skipped 1 invalid lines of 1st dataset, 1st line #9: "chrM 4294967295 4294967322 EAS38_1_45_638_677 2 + ", problem: 4294967295 is larger than the size of this BitSet (536870912). ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "bed" ` |

jennaj commented 2 years ago

Hum, this doesn't show up at org. Just a green dataset, no warnings.

The attributes of this dataset are not properly set. Click the pencil icon in the history item to set the chrom, start, end and strand columns.

Under attributes, score is set for c4 instead of c5. I don't think that is new for this output -- it is making an interval dataset that we label as bed. c4 is a number instead of a dot or word (doesn't fit strict bed). Think that is Ok.