Re: [galaxy-dev] Error when trying to download workflow
Hi Sarah, I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look. Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev. Thanks, J. On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 file:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error - <type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
Hi Jeremy, I just updated to the newest galaxy-dist and the export of the workflow still does not work. The error is the same. Best regards, Sarah On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev.
Thanks, J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 fil e:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
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Sarah, Can you make your server available to me and I'll take a look? If not, you'll have to do some debugging yourself. Here are some things you might try: *on your local instance, try exporting simpler workflows and seeing if there's a tool or configuration that does or does work. *on our public instance, try creating a workflow identical to the one that's failing for you and seeing if you can export it. If we can figure out how to reproduce the problem on a Galaxy instance that I have access to, I can probably fix it. Thanks, J. On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the workflow still does not work. The error is the same.
Best regards, Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev.
Thanks, J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 fil e:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Jeremy, I could narrow the problem down to the histogram tool. I attached a screenshot of a really simple workflow whose download fails. I recreated the workflow at the public instance at http://main.g2.bx.psu.edu and shared it with you. There the download also fails for me. Best regards, Sarah On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not, you'll have to do some debugging yourself. Here are some things you might try:
*on your local instance, try exporting simpler workflows and seeing if there's a tool or configuration that does or does work. *on our public instance, try creating a workflow identical to the one that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance that I have access to, I can probably fix it.
Thanks, J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the workflow still does not work. The error is the same.
Best regards, Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev.
Thanks, J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 fil e:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I could narrow it down even further. As soon as I set anything to "To be set at runtime" the download fails. On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a screenshot of a really simple workflow whose download fails. I recreated the workflow at the public instance at http://main.g2.bx.psu.edu and shared it with you. There the download also fails for me.
Best regards, Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not, you'll have to do some debugging yourself. Here are some things you might try:
*on your local instance, try exporting simpler workflows and seeing if there's a tool or configuration that does or does work. *on our public instance, try creating a workflow identical to the one that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance that I have access to, I can probably fix it.
Thanks, J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the workflow still does not work. The error is the same.
Best regards, Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev.
Thanks, J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 fil e:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Thanks Sarah. I was having trouble reproducing because I hadn't set a runtime parameter. I've fixed the bug in galaxy-central changeset 5387:835656900dd0 ; after making this change, I was able to successfully export and import workflows with runtime parameters. Best, J. On Apr 14, 2011, at 10:01 AM, Sarah Diehl wrote:
I could narrow it down even further. As soon as I set anything to "To be set at runtime" the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a screenshot of a really simple workflow whose download fails. I recreated the workflow at the public instance at http://main.g2.bx.psu.edu and shared it with you. There the download also fails for me.
Best regards, Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not, you'll have to do some debugging yourself. Here are some things you might try:
*on your local instance, try exporting simpler workflows and seeing if there's a tool or configuration that does or does work. *on our public instance, try creating a workflow identical to the one that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance that I have access to, I can probably fix it.
Thanks, J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the workflow still does not work. The error is the same.
Best regards, Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev.
Thanks, J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging.
Best regards, Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 fil e:///home/diehl/Pictures/Screenshot.png Fedora/3.6.16-1.fc14 Firefox/3.6.16" Error -<type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file stored_dict = self._workflow_to_dict( trans, stored ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) TypeError: 'WorkflowStep' object is unsubscriptable <Screenshot.png>
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Jeremy Goecks -
Sarah Diehl