From 44447ed08940782a4d022cd2dcddbdb2c2813ff4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 14 Nov 2017 15:25:51 -0500 Subject: [PATCH] Use github instead of NCBI for problematic data manager test FASTA. Seems to be failing many of the integration tool runs I've seen today. I've seen a couple different errors: ``` | File "/tmp/tmpVp6xM0/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/b1bc53e9bbc5/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 312, in download_from_ncbi | return get_stream_reader(urlopen(url), tmp_dir) | File "/usr/lib/python2.7/urllib2.py", line 154, in urlopen | return opener.open(url, data, timeout) | File "/usr/lib/python2.7/urllib2.py", line 435, in open | response = meth(req, response) | File "/usr/lib/python2.7/urllib2.py", line 548, in http_response | 'http', request, response, code, msg, hdrs) | File "/usr/lib/python2.7/urllib2.py", line 473, in error | return self._call_chain(*args) | File "/usr/lib/python2.7/urllib2.py", line 407, in _call_chain | result = func(*args) | File "/usr/lib/python2.7/urllib2.py", line 556, in http_error_default | raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) ``` and ``` Timed out after 60.25 seconds waiting on state. -------------------- >> begin captured stdout << --------------------- Problem in history with id adb5f5c93f827949 - summary of datasets below. -------------------------------------- | 1 - Create DBKey and Reference Genome (HID - NAME) | Dataset State: | queued | Dataset Blurb: | queued | Dataset Info: | None | Peek: | None | Dataset Job Standard Output: | None | Dataset Job Standard Error: | None | -------------------------------------- ``` --- test/integration/test_data_manager_table_reload.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/integration/test_data_manager_table_reload.py b/test/integration/test_data_manager_table_reload.py index e2c9cea8fe4..dae7e670ecc 100644 --- a/test/integration/test_data_manager_table_reload.py +++ b/test/integration/test_data_manager_table_reload.py @@ -37,8 +37,8 @@ FETCH_GENOME_DBKEYS_ALL_FASTA_INPUT = {"dbkey_source|dbkey_source_selector": "ne "dbkey_source|dbkey_name": "NC_001617.1", "sequence_name": "NC_001617.1", "sequence_id": "NC_001617.1", - "reference_source|reference_source_selector": "ncbi", - "reference_source|requested_identifier": "NC_001617.1", + "reference_source|reference_source_selector": "url", + "reference_source|user_url": "https://raw.githubusercontent.com/galaxyproject/galaxy-test-data/master/NC_001617.1.fasta", "sorting|sort_selector": "as_is"} SAM_FASTA_ID = "toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2" SAM_FASTA_INPUT = {"all_fasta_source": "NC_001617.1", "sequence_name": "", "sequence_id": ""}