Hi, just wondering if anyone has any insight into this issue, as it is driving me crazy, especially given that the correct list control element is selected (hg19).<br><br><div class="gmail_quote">On Sat, Jul 14, 2012 at 8:54 PM, christopher fletez-brant <span dir="ltr">&lt;<a href="mailto:cafletezbrant@gmail.com" target="_blank">cafletezbrant@gmail.com</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Nate,<div><br></div><div>Thanks for the reply.  Error messages are output at the bottom of the message.  Setup is that the tool has a number of inputs, one of which is actually a directory containing reference files.  We pass the directory by allowing users to select from a menu the genome whose information is held in that directory; this is done by means of a *.loc file, whose value in the tool config is &#39;indices_path&#39; below.  Run from the Galaxy server, this tool works perfectly.  However, I think that perhaps it cannot find the directory for some reason?  I just note that diff reports the values listed as missing, but no &#39;+&#39; values indicating what is in their place.  Any advice would be appreciated.</div>

<div><br></div><div>Thank you,</div><div>Kipper</div><div><br></div><div><div><div>alaxy.tools.actions.upload_common INFO 2012-07-14 20:39:41,302 tool upload1 created job id 1</div><div>galaxy.jobs.manager DEBUG 2012-07-14 20:39:47,663 (1) Job assigned to handler &#39;main&#39;</div>

<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2012-07-14 20:39:52,828 (1) Working directory for job is: /home/fake/galaxy-dist/database/job_working_directory/000/1</div><div>galaxy.jobs.handler DEBUG 2012-07-14 20:39:52,829 dispatching job 1 to local runner</div>

<div>galaxy.jobs.handler INFO 2012-07-14 20:39:53,008 (1) Job dispatched</div><div>galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:53,255 executing: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL         1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat</div>

<div>galaxy.jobs.runners.local DEBUG 2012-07-14 20:39:54,480 execution finished: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL         1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat</div>

<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a> DEBUG 2012-07-14 20:39:54,759 job 1 ended</div><div>base.twilltestcase INFO 2012-07-14 20:39:55,782 ## files diff on /home/fake/galaxy-dist/test-data/nullseq_output.bed and /tmp/tmpeEp5KR/database/tmp/tmpuT588_nullseq_output.bed lines_diff=0, found diff = 200</div>

<div>---------------------- &gt;&gt; begin tool stdout &lt;&lt; -----------------------</div><div><br></div><div>----------------------- &gt;&gt; end tool stdout &lt;&lt; ------------------------</div><div><br></div><div>

---------------------- &gt;&gt; begin tool stderr &lt;&lt; -----------------------</div><div><br></div><div>----------------------- &gt;&gt; end tool stderr &lt;&lt; ------------------------</div><div><br></div><div>FAIL</div>

<div><br></div><div>======================================================================</div><div>FAIL: test_tool_000000 (functional.test_toolbox.TestForTool_kmersvm_nullseq)</div><div>Generate Null Sequence ( kmersvm_nullseq ) &gt; Test-1</div>

<div>----------------------------------------------------------------------</div><div class="im"><div>Traceback (most recent call last):</div></div><div><div class="h5"><div>  File &quot;/home/fake/galaxy-dist/test/functional/test_toolbox.py&quot;, line 171, in test_tool</div>

<div>    self.do_it( td, shed_tool_id=shed_tool_id )</div><div>  File &quot;/home/fake/galaxy-dist/test/functional/test_toolbox.py&quot;, line 102, in do_it</div><div>    self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id )</div>

<div>  File &quot;/home/fake/galaxy-dist/test/base/twilltestcase.py&quot;, line 733, in verify_dataset_correctness</div><div>    raise AssertionError( errmsg )</div><div>AssertionError: History item 1 different than expected, difference (using diff):</div>

<div>--- local_file</div><div>+++ history_data</div><div>@@ -1,100 +1,100 @@</div><div>-chr10<span style="white-space:pre-wrap">	</span>4522044<span style="white-space:pre-wrap">	</span>4522438</div>
<div>-chr10<span style="white-space:pre-wrap">	</span>5650896<span style="white-space:pre-wrap">	</span>5651310</div><div>-chr10<span style="white-space:pre-wrap">	</span>5772258<span style="white-space:pre-wrap">	</span>5772663</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>9135867<span style="white-space:pre-wrap">	</span>9136467</div><div>-chr10<span style="white-space:pre-wrap">	</span>9946900<span style="white-space:pre-wrap">	</span>9947273</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>10793689<span style="white-space:pre-wrap">	</span>10794313</div><div>-chr10<span style="white-space:pre-wrap">	</span>15790023<span style="white-space:pre-wrap">	</span>15790478</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>16048435<span style="white-space:pre-wrap">	</span>16049028</div><div>-chr10<span style="white-space:pre-wrap">	</span>17620155<span style="white-space:pre-wrap">	</span>17620367</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>21718404<span style="white-space:pre-wrap">	</span>21719020</div><div>-chr10<span style="white-space:pre-wrap">	</span>22967169<span style="white-space:pre-wrap">	</span>22967533</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>22999383<span style="white-space:pre-wrap">	</span>22999802</div><div>-chr10<span style="white-space:pre-wrap">	</span>24511845<span style="white-space:pre-wrap">	</span>24512748</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>24773636<span style="white-space:pre-wrap">	</span>24774006</div><div>-chr10<span style="white-space:pre-wrap">	</span>25975943<span style="white-space:pre-wrap">	</span>25976389</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>26620032<span style="white-space:pre-wrap">	</span>26620396</div><div>-chr10<span style="white-space:pre-wrap">	</span>26907992<span style="white-space:pre-wrap">	</span>26908408</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>28309833<span style="white-space:pre-wrap">	</span>28310034</div><div>-chr10<span style="white-space:pre-wrap">	</span>30908407<span style="white-space:pre-wrap">	</span>30909220</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>31184776<span style="white-space:pre-wrap">	</span>31185151</div><div>-chr10<span style="white-space:pre-wrap">	</span>31191717<span style="white-space:pre-wrap">	</span>31192170</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>31651098<span style="white-space:pre-wrap">	</span>31651551</div><div>-chr10<span style="white-space:pre-wrap">	</span>32422502<span style="white-space:pre-wrap">	</span>32422880</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>33316453<span style="white-space:pre-wrap">	</span>33316817</div><div>-chr10<span style="white-space:pre-wrap">	</span>34353700<span style="white-space:pre-wrap">	</span>34354168</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>34570612<span style="white-space:pre-wrap">	</span>34571026</div><div>-chr10<span style="white-space:pre-wrap">	</span>34853178<span style="white-space:pre-wrap">	</span>34853542</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>34857471<span style="white-space:pre-wrap">	</span>34857818</div><div>-chr10<span style="white-space:pre-wrap">	</span>34994111<span style="white-space:pre-wrap">	</span>34994269</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>38557788<span style="white-space:pre-wrap">	</span>38558691</div><div>-chr10<span style="white-space:pre-wrap">	</span>43296854<span style="white-space:pre-wrap">	</span>43297454</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>44159102<span style="white-space:pre-wrap">	</span>44159480</div><div>-chr10<span style="white-space:pre-wrap">	</span>45208753<span style="white-space:pre-wrap">	</span>45209123</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>45246414<span style="white-space:pre-wrap">	</span>45246794</div><div>-chr10<span style="white-space:pre-wrap">	</span>46861707<span style="white-space:pre-wrap">	</span>46862080</div>

<div>-chr10<span style="white-space:pre-wrap">	</span>47021051<span style="white-space:pre-wrap">	</span>47021457</div><div>-chr10<span style="white-space:pre-wrap">	</span>47716908<span style="white-space:pre-wrap">	</span>47717259</div>

<div><br></div><div>-------------------- &gt;&gt; begin captured stdout &lt;&lt; ---------------------</div><div><br></div></div></div><div>Uploaded file:  nullseq_test.bed , ftype:  bed , extra:  {&#39;ftype&#39;: &#39;bed&#39;, &#39;value&#39;: &#39;nullseq_test.bed&#39;, &#39;children&#39;: []}</div>
<div class="im">
<div>excluded not declared in tool test, will not change default value.</div><div><br></div><div>form &#39;tool_form&#39; contains the following controls ( note the values )</div><div>control 0: &lt;HiddenControl(tool_id=kmersvm_nullseq) (readonly)&gt;</div>

<div>control 1: &lt;HiddenControl(tool_state=80025461010000396439396665663230383837313531356332333061366366376365626135376535623937323433343a37623232356635663730363136373635356635663232336132303330326332303232373237303734356636353732373232323361323032323563323233303265333033323563323232323263323032323732373336353635363432323361323032323563323233313563323232323263323032323636366636633634323233613230323235633232333135633232323232633230323236393665363436393633363537333566373036313734363832323361323032323563323236643664333935633232323232633230323236353738363336633735363436353634323233613230323236653735366336633232326332303232363736333566363537323732323233613230323235633232333032653330333235633232323232633230323236393665373037353734323233613230323233313232376471002e) (readonly)&gt;</div>

<div>control 2: &lt;TextControl(fold=1)&gt;</div><div>control 3: &lt;TextControl(gc_err=0.02)&gt;</div><div>control 4: &lt;TextControl(rpt_err=0.02)&gt;</div><div>control 5: &lt;TextControl(rseed=1)&gt;</div><div>control 6: &lt;SelectControl(input=[*1])&gt;</div>

<div>control 7: &lt;SelectControl(excluded=[1, *None])&gt;</div><div>control 8: &lt;SelectControl(indices_path=[*mm9, mm8, hg18, hg19])&gt;</div><div>control 9: &lt;SubmitControl(runtool_btn=Execute) (readonly)&gt;</div>
<div>
page_inputs (0) {&#39;rpt_err&#39;: [&quot;0&#39;02&quot;], &#39;rseed&#39;: [&#39;1&#39;], &#39;fold&#39;: [&#39;1&#39;], &#39;indices_path&#39;: [&#39;hg19&#39;], &#39;gc_err&#39;: [&#39;0.02&#39;], &#39;input&#39;: [&#39;nullseq_test.bed&#39;]}</div>

<div><br></div><div>--------------------- &gt;&gt; end captured stdout &lt;&lt; ----------------------</div><div>-------------------- &gt;&gt; begin captured logging &lt;&lt; --------------------</div></div><div>galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): <a href="http://localhost:8368/" target="_blank">http://localhost:8368/</a></div>

<div>galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): <a href="http://localhost:8368/" target="_blank">http://localhost:8368/</a></div><div>galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): <a href="http://localhost:8368/user/logout" target="_blank">http://localhost:8368/user/logout</a></div>

<div>galaxy.web.framework: DEBUG: Error: this request returned None from get_history(): <a href="http://localhost:8368/" target="_blank">http://localhost:8368/</a></div><div class="im"><div>galaxy.tools.actions.upload_common: INFO: tool upload1 created job id 1</div>

<div>galaxy.jobs.manager: DEBUG: (1) Job assigned to handler &#39;main&#39;</div><div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a>: DEBUG: (1) Working directory for job is: /home/fake/galaxy-dist/database/job_working_directory/000/1</div>

<div>galaxy.jobs.handler: DEBUG: dispatching job 1 to local runner</div><div>galaxy.jobs.handler: INFO: (1) Job dispatched</div></div><div>galaxy.jobs.runners.local: DEBUG: executing: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL         1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat</div>

<div>galaxy.jobs.runners.local: DEBUG: execution finished: python /home/fake/galaxy-dist/tools/data_source/upload.py /home/fake/galaxy-dist /tmp/tmpeEp5KR/database/tmp/tmpfYngg0 /tmp/tmpeEp5KR/database/tmp/tmpMKsPIL         1:/home/fake/galaxy-dist/database/job_working_directory/000/1/dataset_1_files:/tmp/tmpeEp5KR/database/files/000/dataset_1.dat</div>
<div class="im">
<div><a href="http://galaxy.jobs" target="_blank">galaxy.jobs</a>: DEBUG: job 1 ended</div></div><div>base.twilltestcase: INFO: ## files diff on /home/fake/galaxy-dist/test-data/nullseq_output.bed and /tmp/tmpeEp5KR/database/tmp/tmpuT588_nullseq_output.bed lines_diff=0, found diff = 200</div>
<div class="im">
<div>--------------------- &gt;&gt; end captured logging &lt;&lt; ---------------------</div><div><br></div></div><div>----------------------------------------------------------------------</div><div>Ran 1 test in 16.540s</div>

<div><br></div><div>FAILED (failures=1)</div></div><div><div class="h5"><div><br></div><br><div class="gmail_quote">On Thu, Jul 12, 2012 at 4:20 PM, Nate Coraor <span dir="ltr">&lt;<a href="mailto:nate@bx.psu.edu" target="_blank">nate@bx.psu.edu</a>&gt;</span> wrote:<br>


<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On Jul 5, 2012, at 8:20 PM, christopher fletez-brant wrote:<br>
<br>
&gt; Dear Dev List,<br>
&gt;<br>
&gt; I am currently writing tests for a tool I am developing and am coming up short in understanding why it&#39;s failing.  Using the test data, I can generate output identical to the output provided for testing every time I run the tool from my local Galaxy server.  However, when I run the tool test through run_functional_tests.sh, it always fails, and apparently fails on every line.<br>



&gt;<br>
&gt; Because I consistently see the same output from the Galaxy server-based tool, I&#39;m sure I&#39;m missing something simple and want to look at the test-generated output.  Is there a way I can set run_functional_tests to print the generated tool output file in its entirety?<br>



<br>
</div>Hi Kipper,<br>
<br>
It&#39;d be helpful if you could provide the output of run_functional_tests.sh so we could see exactly what was failing.<br>
<br>
Thanks,<br>
--nate<br>
<br>
&gt;<br>
&gt; Thank you,<br>
&gt; Kipper Fletez-Brant<br>
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</blockquote></div><br></div></div></div>
</blockquote></div><br>