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kbaseattic / assembly

An extensible framework for genome assembly.
MIT License
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fix binary blob in automated test #197

Closed sebhtml closed 10 years ago

sebhtml commented 10 years ago

The binary blob is generated by arast.t, not by the wrapper.

[boisvert@kbase-test-june-2014 test]$ ./arast.t &> my-log [boisvert@kbase-test-june-2014 test]$ less my-log

ok 90 - main::test_json_input > cat job.12 | ar-get -w -p > contigs.12 1..90 ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@

levinas commented 10 years ago

Will look into this later today.

On Jul 26, 2014, at 11:17 AM, Sébastien Boisvert notifications@github.com wrote:

The binary blob is generated by arast.t, not by the wrapper.

[boisvert@kbase-test-june-2014 test]$ ./arast.t &> my-log [boisvert@kbase-test-june-2014 test]$ less my-log

ok 90 - main::test_json_input > cat job.12 | ar-get -w -p > contigs.12 1..90 ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ^@^@^@^@^@^@^@

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sebhtml commented 10 years ago

This is fine, no blob:

[boisvert@kbase-test-june-2014 test]$ ./arast.t &> my-log2

The problem is that my-log is already open by previous hanged tests (dev):

[boisvert@kbase-test-june-2014 test]$ lsof|grep my-log test_SRS2 1827 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log test_SRS2 1827 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 5869 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 5869 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 5869 boisvert 6w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 5869 boisvert 7w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sh 6021 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sh 6021 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log ar-get 6023 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 6025 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log arast 6042 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log python 6043 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 8491 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 8491 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 8491 boisvert 6w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 8491 boisvert 7w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sh 8644 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sh 8644 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log ar-get 8646 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log perl 8648 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log arast 8657 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log python 8658 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sleep 15517 boisvert 1w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log sleep 15517 boisvert 2w REG 252,17 397025 6817179 /mnt/stuff/boisvert/assembly/test/my-log

Solution:

Use mktemp to generate file name:

[boisvert@kbase-test-june-2014 test]$ mktemp /tmp/tmp.IMIQ0sarhh

sebhtml commented 10 years ago

I am testing a fix right now and will push in 30 minutes.

levinas commented 10 years ago

I updated the dev branch too. We can close this issue if the tests tonight pass.

sebhtml commented 10 years ago

OK.

I think we can close it since Amazon AWS sent us a notification that was correct.

Let me know if you agree (I am the assignee).

levinas commented 10 years ago

Yes let's close it.

Sent from my iPhone

On Jul 26, 2014, at 6:27 PM, Sébastien Boisvert notifications@github.com wrote:

OK.

I think we can close it since Amazon AWS sent us a notification that was correct.

Let me know if you agree (I am the assignee).

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