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update cummerbund #110

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martenson opened this issue Apr 18, 2018 · 18 comments · May be fixed by galaxyproject/tools-devteam#506
Open

update cummerbund #110

martenson opened this issue Apr 18, 2018 · 18 comments · May be fixed by galaxyproject/tools-devteam#506
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@natefoo @davebx
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bug fixathon 06/18 Fixathon June 2018 install usegalaxy.org tool install usegalaxy.org requested test/retest-fail failed retest

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@martenson
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last time it failed: galaxyproject/tools-devteam#317
@martenson martenson added the install usegalaxy.org tool install usegalaxy.org requested label Apr 18, 2018
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I tried again, no luck, stuck here:

128.118.201.178 - - [02/May/2018:20:11:39 +0000] "GET /admin/manage_tool_dependencies HTTP/1.0" 200 - "https://main-installer.galaxyproject.org/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.139 Safari/537.36"
galaxy.tools.deps.conda_util DEBUG 2018-05-02 20:12:32,593 Executing command: /cvmfs/main.galaxyproject.org/deps/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name mulled-v1-71206c22effe4f02960f526961e99857b4140cdce3da5f9a9e75417fc1a3e405 r-argparse=1.0.1 bioconductor-cummerbund=2.16.0
Fetching package metadata .................
Solving package specifications: .

@jennaj jennaj added the bug label May 16, 2018
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jennaj commented May 16, 2018

I'll retest and see if fixed

@jennaj jennaj added the test/retest-do active tests label May 16, 2018
@nekrut nekrut added the fixathon 06/18 Fixathon June 2018 label Jun 4, 2018
@martenson martenson assigned davebx and natefoo and unassigned davebx Jun 4, 2018
@natefoo
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natefoo commented Jun 4, 2018

This is due to conda/conda#5536, I've been able to get past the solver hang by temporarily setting the defaults in ~/.condarc to only the main and free channels as described in the issue comments. After successfully solving the packages, I've undone the temporary change and the installation is in progress.

@natefoo
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natefoo commented Jun 4, 2018

I've gotten the dependencies installed, however, uploading the test sqlite database results in a metadata failure:

uploaded sqlite file
WARNING:galaxy.datatypes.binary:<galaxy.datatypes.binary.SQlite object at 0x2b88b4944710>, set_meta Exception: database is locked

@natefoo
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natefoo commented Jun 4, 2018

I've gotten the database to load trying it a second time - it may be some kind of NFS issue. However, you can't run the tool because it seems to fail to read the input dataset. Here's what's logged when you 1. load the tool and 2. click Insert Plots:

galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,859 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,860 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,861 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,862 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.actions INFO 2018-06-04 14:38:15,864 [p:8313,w:5,m:0] [uWSGIWorker5Core1] Added output datasets to history (21.072 ms)
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,864 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,865 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,866 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,867 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,867 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,868 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,869 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,870 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,871 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,872 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,874 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,875 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,876 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,877 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,878 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,878 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,879 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,880 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,882 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,882 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,885 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,886 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,887 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,888 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,889 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,889 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,890 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,891 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,892 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,892 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,894 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,895 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,896 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,897 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,898 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,898 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,900 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,900 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'x' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,901 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,902 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'y' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,903 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,904 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,905 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined
galaxy.tools.parameters.basic DEBUG 2018-06-04 14:38:15,906 [p:8322,w:6,m:0] [uWSGIWorker6Core1] Error determining dynamic options for parameter 'gene_id' in tool 'toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0':
Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
NameError: name 'input_database' is not defined

@jennaj jennaj added test/retest-fail failed retest and removed test/retest-do active tests labels Jun 4, 2018
@jmchilton
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I tried another test on main that doesn't use the dynamic options stuff - and it works fine - so the good news is the dependency issues seem to be resolved! The dynamic options work fine for me locally, so there are problems here - that appear to be differences between how dynamic options are resolved - maybe the difference is the DB, the web server, or the object store.

@natefoo
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natefoo commented Jun 5, 2018

Could you fetch the metadata of your input file from the DB?

@jmchilton
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I'm confused - are you asking if the tool be rewritten to do that or if the dynamic options worked for me on usegalaxy.org? This tool doesn't read options from the metadata - it reads options from the data 😞 - likely this is part of the problem.

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natefoo commented Jun 5, 2018

No I was asking for the HDA metadata from your local instance to compare. Although maybe it's irrelevant, I guess the issue here is that the dynamic option is being called without the dataset being defined in the param dict?

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natefoo commented Jun 5, 2018

Ah. Before those, you get:

Traceback (most recent call last):
  File "lib/galaxy/tools/parameters/basic.py", line 835, in get_options
    return eval(self.dynamic_options, self.tool.code_namespace, call_other_values)
  File "<string>", line 1, in <module>
  File "/galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/78fcfc04fcfe/cummerbund/cummeRbund_options.py", line 10, in get_samples
    samples = conn.execute( 'SELECT sample_name FROM samples ORDER BY sample_name' )
OperationalError: database is locked

@jmchilton
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Well that is illustrative - thanks! Want to just move all the user data on usegalaxy.org to a fast, local SSD and close this out?

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natefoo commented Jun 5, 2018

😒

@jmchilton
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https://docs.python.org/3/library/sqlite3.html

By default, check_same_thread is True and only the creating thread may use the connection. If set False, the returned connection may be shared across multiple threads. When using multiple threads with the same connection writing operations should be serialized by the user to avoid data corruption.

That doesn't seem like the problem but might be worth trying to set that to false when opening sqlite connections - let me see if I can find something more likely to help.

@jmchilton
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Ugh - I'm frustrated I can't find a "just assume I'm the only thread in the world and don't lock anything please" mode for sqlite.

We could try:

# Open database in autocommit mode by setting isolation_level to None.
conn = sqlite3.connect('app.db', isolation_level=None)

# Set journal mode to WAL.
conn.execute('pragma journal_mode=wal')

We could try reading the whole file first before opening the sqlite connection - if it is small keeping it in memory otherwise just hope the read causes everything in NFS to be properly cached ahead of time.

I'm not sure what else... I'm not really sure how to test which of these will work on main in an efficient way.

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natefoo commented Jun 5, 2018

"Testing fixes on Main in an efficient way" is indeed difficult. I do have a TACC instance of my own that I use for testing, so I could run your branch on that, if I can get it to exhibit the same issue as Main does (this could be a multi-VM issue).

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natefoo commented Jun 5, 2018

So, in my TACC instance it doesn't display the locked message, but does have the rest of the dynamic option load failures. So I'm not sure if the locked error happens every time on Main or just happened the one time I saw it.

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natefoo commented Jun 6, 2018

I can't make much sense of the dynamic options code. input_database should be in the locals (call_other_values) passed to eval() but it's not? Except I can't even determine what puts it there. If I knew where that happened I could try to see why it's not happening. Presumably an exception is being silently dropped somewhere? I am not sure how it can be missing when a dataset is selected.

@davebx davebx mentioned this issue Jun 7, 2018
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davebx commented Jun 7, 2018 •
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@natefoo if galaxyproject/galaxy#6302 is merged, I'm going to propose getting the dynamic options from input_dataset.metadata.genes and input_dataset.metadata.samples instead, thus (thankfully, finally) obviating the need for the garbage code file that hasn't worked in years.

@davebx davebx linked a pull request Jun 8, 2018 that will close this issue
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Update cummeRbund to retrieve genes and samples from input metadata. davebx/tools-devteam
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@jmchilton @natefoo @davebx @martenson @nekrut @jennaj