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HumanCellAtlas / data-consumer-vignettes

Simple walk-throughs of interacting with the DCP as a downstream data consumer.
MIT License
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Notebook tests are hanging #91

Open chmreid opened 4 years ago

chmreid commented 4 years ago

The treon notebook test suite, which we fixed up yesterday, is now hanging, causing all Travis tests to fail.

This issue was not seen with the PRs yesterday that fixed the treon test harness, but those PRs did not have any failing notebooks either, so it may be that the tests only hang when the tests fail.

Relevant Travis build log: https://travis-ci.com/HumanCellAtlas/data-consumer-vignettes/jobs/268705001

$ eval "treon $(awk '{printf " --exclude " $0}' test/ignore)"
Executing treon version 0.1.3
Recursively scanning /home/travis/build/HumanCellAtlas/data-consumer-vignettes for notebooks...
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/login/login.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/explore-hca-dataset-scanpy-may-2019/notebooks_hca_demo_scanpy.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-smartseq2-matrix-scanpy/download-smartseq2-matrix-scanpy.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/install-hca/install-hca.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/explore-hca-dataset-scanpy-nov-2018/hca_demo_scanpy.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/find-cell-type-count/find-cell-type-count.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-any-bam-file/download-any-bam-file.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-10x-seq-tcell/download-10x-seq-tcell.ipynb
Triggered test for /home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-all-fastq-files/download-all-fastq-files.ipynb
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-all-fastq-files/download-all-fastq-files.ipynb     -- PASSED 
ERROR in testing /home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-10x-seq-tcell/download-10x-seq-tcell.ipynb
An error occurred while executing the following cell:
------------------
import hca.dss, json
client = hca.dss.DSSClient()
# Print the first bundle we get from this query
search_results = client.post_search(es_query=query, replica='aws', output_format='raw')
print(json.dumps(search_results['results'][0], indent=4, sort_keys=True))
------------------
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-2-23f77063d8e8> in <module>
      5 
      6 search_results = client.post_search(es_query=query, replica='aws', output_format='raw')
----> 7 print(json.dumps(search_results['results'][0], indent=4, sort_keys=True))
IndexError: list index out of range
IndexError: list index out of range
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/install-hca/install-hca.ipynb     -- PASSED 
ERROR in testing /home/travis/build/HumanCellAtlas/data-consumer-vignettes/find-cell-type-count/find-cell-type-count.ipynb
An error occurred while executing the following cell:
------------------
client.post_search(es_query={}, replica='aws', output_format='raw')['results'][20]
------------------
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-4-092746661615> in <module>
----> 1 client.post_search(es_query={}, replica='aws', output_format='raw')['results'][20]
IndexError: list index out of range
IndexError: list index out of range
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-any-bam-file/download-any-bam-file.ipynb     -- PASSED 
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/download-smartseq2-matrix-scanpy/download-smartseq2-matrix-scanpy.ipynb     -- PASSED 
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/explore-hca-dataset-scanpy-may-2019/notebooks_hca_demo_scanpy.ipynb     -- PASSED 
/home/travis/build/HumanCellAtlas/data-consumer-vignettes/explore-hca-dataset-scanpy-nov-2018/hca_demo_scanpy.ipynb     -- PASSED 
No output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.
Check the details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received
The build has been terminated
chmreid commented 4 years ago

The first error is due to a cell containing code that will always fail, I don't know how that passed Travis tests for Natan's test harness PR.

The second error is due to the fact that I can't reproduce the results of the queries that are described in the notebook. We need to figure that out.