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Fix 2230 #2372

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Merged
merged 9 commits into from
Oct 23, 2017
+26 −17
Merged

Fix 2230 #2372

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cc97e89
fix calls to system_call and ebi submissions
antgonza Oct 12, 2017
292e193
fixing errors
antgonza Oct 12, 2017
6a553f6
fix if state == submitting:
antgonza Oct 12, 2017
f27c230
just raise error
antgonza Oct 12, 2017
d721f85
EBISubmissionError -> ComputeError
antgonza Oct 12, 2017
9e10d9c
Merge pull request #2345 from biocore/fix-ebi-1012
josenavas Oct 14, 2017
d5636ae
Fix #2230 solved using modal in order to prevent large file download
Oct 21, 2017
29da4e4
fix conflicts
danteese Oct 21, 2017
7ef56fa
Function moved into in order to keep order. Some details fixed.
danteese Oct 23, 2017
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fixing errors
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@antgonza
antgonza committed Oct 12, 2017
commit 292e193416c0b46a0c3a23645027f1eb811610f9
12 changes: 6 additions & 6 deletions qiita_pet/support_files/doc/source/tutorials/prepare-information-files.rst
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Expand Up @@ -177,13 +177,13 @@ Without this columns you will not be able to submit to EBI. These are the column

Valid values for instrument_model per platform, taken from ftp://ftp.sra.ebi.ac.uk/meta/xsd/sra_1_5/SRA.common.xsd

+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+==============+==================================================================================================================================================================================================================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, or ``unspecified`` |
+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+--------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+==============+===================================================================================================================================================================================================================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, or ``unspecified`` |
+--------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| ``Illumina`` | ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, ``Illumina Genome Analyzer IIx``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 2000``, ``Illumina HiSeq 1500``, ``Illumina HiSeq 1000``, ``Illumina MiSeq``, ``Illumina HiScanSQ``, ``HiSeq X Ten``, ``NextSeq 500``, ``unspecified`` |
+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+--------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

.. _required-fields-for-preprocessing-target-gene-data:

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4 changes: 2 additions & 2 deletions qiita_pet/test/test_download.py
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Expand Up @@ -140,7 +140,7 @@ def test_download_study(self):
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'- 36615 /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'- 39752 /protected/BIOM/{0}/otu_table.biom '
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
Expand All @@ -161,7 +161,7 @@ def test_download_study(self):
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- 39752 /protected/BIOM/{0}/otu_table.biom '
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
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