Open hexylena opened 8 years ago
jjkoehorst
commented
8 years ago Great to see the progress made! About SPARQL endpoints, would this also include plain text rdf files in the galaxy history? Which can perhaps be loaded into a temporarily RDF endpoint or through HDT files?
hexylena
commented
8 years ago @jjkoehorst meant to get sparql done earlier, but GCC snuck up on me.
I imagine that this would be possible. A plain text RDF would just be a read-only data store? Hmm. I think I can give you a better answer once I've gotten the SPARQL portion done. Hopefully soon... I demoed a heavily dockerized, heavily interconnected GMOD stack today and would love to add sparql export to a lot of places.
jjkoehorst
commented
8 years ago @erasche no worries, glad it is still on the map! A plain text RDF (Turtle/N3/RDFXML, etc) could be a read only store but requires loading into a memory or disk store (jena/sparqlwrapper/blazegraph). However if jbrowse would support update queries, if that is what you mean, that would be even more amazing but probably a bridge to far?...
HDT is a binary disk image. I have been looking into JENA but this creates multiple index files which is not suitable for galaxy history (I think) and currently using blaze graph which creates a single index file.
Most importantly at least from my point of view would be the ability to create predefined (and modify) SPARQL queries for jbrowse views. As yes there are some kind of ontologies for storing locations but not everything is suitable at all times.
bernt-matthias
commented
4 years ago Seems that the issue can be closed since now 1.16.5 is already wrapped
hexylena
commented
4 years ago Hey @bernt-matthias, this is just a roadmap issue, not tied to a specific release. I've been leaving it open so we can track requests we get for galaxy-jbrowse features without filling new issues / making noise every time. If the IUC has a better way to do that, I'm happy to move it there. Currently there are still a number of open TODOs on this one that I'd like to keep track of.
hexylena
commented
4 years ago bug: can't use the same bigwig twice due to symlink behaviour. replace with cp?
ln: failed to create symbolic link ‘data/raw/5302296cad2d7c9d5f1a73751b42aa68_0.bw’: File exists
jennaj
commented
4 years ago Hi @hexylena
If you want this in a distinct ticket, lmk, will move it.
We (@dannon & @mvdbeek) were wondering if there was a way to adjust Jbrowse to be able run in anonymous (not logged in) sessions. Currently, there is a dependency requiring the "user email" to access a genome input from history. If not logged in, this fails the tool, immediately.
Or, maybe login should be required (and if not logged in, report that back to the user in the read error dataset, maybe in job info & stderr? so shows up in dataset itself and bug reporting preview). "You must be logged in to use this tool" or similar.
This may be complicated to do -- options like "JBrowse-in-Galaxy Action" > "Update existing ..." might be bothersome. Unless prior sessions all linked back that same anon history's datasets Ok.
The test example comes from this GTN tutorial: https://training.galaxyproject.org/training-material/topics/visualisation/tutorials/jbrowse/tutorial.html
Tested it as not logged in originally vs logged in from start, just to compare (at .org). Just did the not-logged-in-first at .eu. Same result -- only not being logged in during actual tool execution triggers the failure:
Clicking not on the "eye" icon (logged in, successful run, give an additional pop-up warning at .eu (don't show up at .org). It doesn't seem to impact the viz through. Or, I'm not sure what to look for.
The message displayed in the red error dataset is a bit different between the two servers as well. Eu is more informative.
org: cannot find 'email'
eu: cannot find 'email' while searching for 'reference_genome.genome.history.user.email'
This shows up at both servers, in the bug report. Is a bug have seen in a few other tool, not sure where it is coming from exactly. The inputs are not duplicated :)
Detected Common Potential Problems
The tool was executed with one or more duplicate input datasets. This frequently results in tool errors due to problematic input choices.Full traceback from org (bug report sent into myself :). The job details > stderr & stdout reports at both servers are empty. (Expected, given bug report contents).
tool id: toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy0
tool version: 1.16.8+galaxy0
job pid or drm id: None
job tool version: None
-----------------------------------------------------------------------------
job command line:
None
-----------------------------------------------------------------------------
job stderr:
-----------------------------------------------------------------------------
job stdout:
-----------------------------------------------------------------------------
job info:
cannot find 'email'
-----------------------------------------------------------------------------
job traceback:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 231, in _valueForName
nextObj = getattr(obj, key)
AttributeError: 'NoneType' object has no attribute 'email'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 1049, in unicodify
value = text_type(value)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1587388900_1572237_44025.py", line 133, in respond
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 292, in valueFromSearchList
executeCallables=executeCallables)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 233, in _valueForName
_raiseNotFoundException(key, obj)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 178, in _raiseNotFoundException
raise NotFound(excString)
Cheetah.NameMapper.NotFound: cannot find 'email'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 231, in _valueForName
nextObj = getattr(obj, key)
AttributeError: 'NoneType' object has no attribute 'email'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 1051, in unicodify
value = str(value)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1587388900_1572237_44025.py", line 133, in respond
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 292, in valueFromSearchList
executeCallables=executeCallables)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 233, in _valueForName
_raiseNotFoundException(key, obj)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 178, in _raiseNotFoundException
raise NotFound(excString)
Cheetah.NameMapper.NotFound: cannot find 'email'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 231, in _valueForName
nextObj = getattr(obj, key)
AttributeError: 'NoneType' object has no attribute 'email'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/__init__.py", line 236, in prepare_job
job_wrapper.prepare()
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 1085, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 462, in build
raise e
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 458, in build
self.__build_config_files()
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 533, in __build_config_files
self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/tools/evaluation.py", line 616, in __write_workdir_file
value = fill_template(content, context=context, python_template_version=self.tool.python_template_version)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/template.py", line 94, in fill_template
raise first_exception or e
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/template.py", line 67, in fill_template
return unicodify(t)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/util/__init__.py", line 1057, in unicodify
msg = "Value '%s' could not be coerced to Unicode" % value
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/Template.py", line 1053, in __unicode__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1587388900_1572237_44025.py", line 133, in respond
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 292, in valueFromSearchList
executeCallables=executeCallables)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 233, in _valueForName
_raiseNotFoundException(key, obj)
File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/Cheetah/NameMapper.py", line 178, in _raiseNotFoundException
raise NotFound(excString)
Cheetah.NameMapper.NotFound: cannot find 'email'Hi @jennaj sure, we can fix that. It was never to intentionally exclude anonymous users, I just totally forgot they exist :joy:, easy fix though.
"Error reading from name store" - know bug, never figured out how to solve it unfortunately.
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