Re: [galaxy-dev] File Upload doesn't generate any activity
HI Nicola, I did upgrading. It seems that error is gone now but I got these errors. I am not sure if they are critical or due to my settings. galaxy.tools WARNING 2013-02-04 14:04:02,764 A when tag has not been defined for 'master_variable_type (master_variable_type_selector) --> allPairs', assuming empty inputs. galaxy.tools WARNING 2013-02-04 14:04:04,391 A when tag has been defined for 'manipulation (manipulation_selector) --> modify_each_score', but does not appear to be selectable. galaxy.tools.test DEBUG 2013-02-04 14:04:05,164 Error in add_param for report_discordant_pairs: Unable to determine parameter type of test input 'report_discordant_pairs'. Ensure that the parameter exists and that any container groups are defined first. docutils WARNING 2013-02-04 14:04:05,198 :50: (WARNING/2) Literal block expected; none found. galaxy.tools.test DEBUG 2013-02-04 14:04:05,209 Error in add_param for min_coverage_intron: Unable to determine parameter type of test input 'min_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:05,209 Error in add_param for max_coverage_intron: Unable to determine parameter type of test input 'max_coverage_intron'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,487 Error in add_param for force: Unable to determine parameter type of test input 'force'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for input: Unable to determine parameter type of test input 'input'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group1_1: Unable to determine parameter type of test input 'group1_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group1_2: Unable to determine parameter type of test input 'group1_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group1_3: Unable to determine parameter type of test input 'group1_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group2_1: Unable to determine parameter type of test input 'group2_1'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group2_2: Unable to determine parameter type of test input 'group2_2'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2013-02-04 14:04:06,773 Error in add_param for group2_3: Unable to determine parameter type of test input 'group2_3'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools INFO 2013-02-04 14:04:07,068 Parsing the tool configuration ./migrated_tools_conf.xml -Original Message- From: Nicola Soranzo [mailto:sora...@crs4.it] Sent: Monday, February 04, 2013 11:52 AM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] File Upload doesn't generate any activity Il giorno lun, 04/02/2013 alle 17.41 +, Hakeem Almabrazi ha scritto: > Thank you Nicola, > > Should I replace my current galaxy-dist with this version or is there > different way to upgrade? Take a look at this wiki page: http://wiki.galaxyproject.org/Admin/Get% 20Galaxy#Keep_your_code_up_to_date Nicola > -Original Message- > From: Nicola Soranzo [mailto:sora...@crs4.it] > Sent: Monday, February 04, 2013 10:50 AM > To: Hakeem Almabrazi > Cc: Dannon Baker; Galaxy Dev > Subject: Re: [galaxy-dev] File Upload doesn't generate any activity > > Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha > scritto: > > Thank you Dannon. Hopefully things should be moving forward from now on. > > > > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 > > which will be in the next distribution release." > > > > That will be awesome. > > It's already in galaxy-dist since Saturday 2013/02/02, changeset > 8531:3299529e0fe8 . > > Kind Regards, > Nicola > ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Our upload issues seem to have been resolved. Thanks for checking. I added the attached comment to another list-serve message - we did have the referenced error in our startup logs. The attached email mentions I was still having trouble uploading files with the Upload File tool. That is now resolved as well. Steve -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Sunday, February 03, 2013 7:14 PM To: Hakeem Almabrazi Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs Subject: Re: [galaxy-dev] File Upload doesn't generate any activity I just wanted to follow up on this and make sure everything was now working as expected. I've tried to reproduce the original issue and have thus far been unsuccessful in doing so with a fresh instance. Is the configuration of your Galaxy instance special in any way? Did you notice any logged errors (either in the Javascript console or in Galaxy's log)? -Dannon On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi wrote: > Stephen,,, > > Here is your solution: > > In the Tools panel select "Get Data", "Upload File". You can either upload a > file, or enter one or more URLs in the "URL/Text" box. Enter > "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" > > I am not sure what happened there but it seems this triggered some database > updates that was needed. > > It worked J > > > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen > Groenewold > Sent: Friday, February 01, 2013 10:41 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] File Upload doesn't generate any activity > > We've installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > Any attempt to upload a file using the Browse File box not only fails, it > never even starts. It's as if the Execute button is disabled. > > I've tried changing the ajax-upload parameter to "false" in > tools/data_source/upload.xml (as mentioned in a workaround posted to the list > by Daniel Blankenburg in Aug 2012). I've also tried using different browsers > (including Internet Explorer) and going the route of Adding Data Libraries as > Admin. None of those attempts have worked. > > Am I missing a configuration setup? Could there be permissions issues on the > Galaxy machine? > > Thanks. > > Steve > > ___ > 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: > > http://lists.bx.psu.edu/ --- Begin Message --- We've also seen that same error in our startup log: == Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax === And we are also having trouble uploading files. Originally, even attempts to add files via the Admin Data Libraries process wouldn't work. That seems to have been resolved (coincidentally? or causally?) after another user completed a general upload via a URL. But even now, uploading a specific file with the Get Data -> Upload File process is still non-responsive. Either the Execute button never does anything at all, or the upload process appears in History and turns blue but never completes. -Original Message- From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] Sent: Friday, February 01, 2013 3:14 PM To: Stephen Groenewold Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] File Upload doesn't generate any activity On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold wrote: > We've installed a local instance of Galaxy and are having trouble > with the first step of uploading files. The only thing that will > currently upload is text pasted into the URL/Text box. > > > > Any attempt to upload a file using the Browse File box not only fails, > it never even starts. It's as if the Execute button is disabled. > > > > I've tried changing the ajax-upload parameter to "false" in > tools/data_source/upload.xml (as mentioned in a workaround posted to > the list by
Re: [galaxy-dev] File Upload doesn't generate any activity
Il giorno lun, 04/02/2013 alle 17.41 +, Hakeem Almabrazi ha scritto: > Thank you Nicola, > > Should I replace my current galaxy-dist with this version or is there > different way to upgrade? Take a look at this wiki page: http://wiki.galaxyproject.org/Admin/Get% 20Galaxy#Keep_your_code_up_to_date Nicola > -Original Message- > From: Nicola Soranzo [mailto:sora...@crs4.it] > Sent: Monday, February 04, 2013 10:50 AM > To: Hakeem Almabrazi > Cc: Dannon Baker; Galaxy Dev > Subject: Re: [galaxy-dev] File Upload doesn't generate any activity > > Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha > scritto: > > Thank you Dannon. Hopefully things should be moving forward from now on. > > > > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 > > which will be in the next distribution release." > > > > That will be awesome. > > It's already in galaxy-dist since Saturday 2013/02/02, changeset > 8531:3299529e0fe8 . > > Kind Regards, > Nicola > ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Thanks Nicola for reminding me that we'd already applied that changeset! Hakeem, you should be able to simply 'hg pull -u' from your galaxy-dist directory and then restart galaxy with the changes applied. -Dannon On Feb 4, 2013, at 12:41 PM, Hakeem Almabrazi wrote: > Thank you Nicola, > > Should I replace my current galaxy-dist with this version or is there > different way to upgrade? > > Thank you... > > -Original Message- > From: Nicola Soranzo [mailto:sora...@crs4.it] > Sent: Monday, February 04, 2013 10:50 AM > To: Hakeem Almabrazi > Cc: Dannon Baker; Galaxy Dev > Subject: Re: [galaxy-dev] File Upload doesn't generate any activity > > Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha > scritto: >> Thank you Dannon. Hopefully things should be moving forward from now on. >> >> "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which >> will be in the next distribution release." >> >> That will be awesome. > > It's already in galaxy-dist since Saturday 2013/02/02, changeset > 8531:3299529e0fe8 . > > Kind Regards, > Nicola > > -- > Nicola Soranzo, Ph.D. > CRS4 > Bioinformatics Program > Loc. Piscina Manna > 09010 Pula (CA), Italy > http://www.bioinformatica.crs4.it/ > >> -Original Message- >> From: Dannon Baker [mailto:dannonba...@me.com] >> Sent: Monday, February 04, 2013 9:40 AM >> To: Hakeem Almabrazi >> Cc: Galaxy Dev >> Subject: Re: [galaxy-dev] File Upload doesn't generate any activity >> >> On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote: >>> No there was nothing special about this installation. I installed it on >>> CentOS and I tried to follow instructions in installing and configuring >>> tools and data. The only thing that I did not was to test this feature >>> before I integrate it with postgres, nginx, tools such as bwa, samtools, >>> bowtie etc. I might have done something not right while doing so. But >>> once I was done with all the configuration steps, I tried to load files via >>> "Get Data" or "Data Library". It kept spinning and nothing is actually >>> being written to the system. I tailed the logs and it was writing some >>> logs every seconds but no errors or warnings. >>> >>> The issue was resolved when I used "URL/Text" to go to this link as another >>> trail test. After that everything works just fine. Now we can load files >>> via either way. >> >> Very strange, but I'm glad it's working for you now. If this does crop up >> again, let me know and we can try to reproduce what's happening and fix it. >> >>> The only error I keep seeing in the log is when we restart the server and >>> from what I read, this is a bug... >>> >>> Traceback (most recent call last): >>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", >>> line 447, in _load_plugin >>> module = __import__( module_name ) >>> File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", >>> line 232 >>> worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), >>> target=self.run_next ) >>>^ >>> SyntaxError: invalid syntax >>> >>> >>> >>> Please let me know if you want me to do anything else that might help >>> debugging this issue. > > ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Thank you Nicola, Should I replace my current galaxy-dist with this version or is there different way to upgrade? Thank you... -Original Message- From: Nicola Soranzo [mailto:sora...@crs4.it] Sent: Monday, February 04, 2013 10:50 AM To: Hakeem Almabrazi Cc: Dannon Baker; Galaxy Dev Subject: Re: [galaxy-dev] File Upload doesn't generate any activity Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha scritto: > Thank you Dannon. Hopefully things should be moving forward from now on. > > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which > will be in the next distribution release." > > That will be awesome. It's already in galaxy-dist since Saturday 2013/02/02, changeset 8531:3299529e0fe8 . Kind Regards, Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ > -Original Message- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: Monday, February 04, 2013 9:40 AM > To: Hakeem Almabrazi > Cc: Galaxy Dev > Subject: Re: [galaxy-dev] File Upload doesn't generate any activity > > On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote: > > No there was nothing special about this installation. I installed it on > > CentOS and I tried to follow instructions in installing and configuring > > tools and data. The only thing that I did not was to test this feature > > before I integrate it with postgres, nginx, tools such as bwa, samtools, > > bowtie etc. I might have done something not right while doing so. But > > once I was done with all the configuration steps, I tried to load files via > > "Get Data" or "Data Library". It kept spinning and nothing is actually > > being written to the system. I tailed the logs and it was writing some > > logs every seconds but no errors or warnings. > > > > The issue was resolved when I used "URL/Text" to go to this link as another > > trail test. After that everything works just fine. Now we can load files > > via either way. > > Very strange, but I'm glad it's working for you now. If this does crop up > again, let me know and we can try to reproduce what's happening and fix it. > > > The only error I keep seeing in the log is when we restart the server and > > from what I read, this is a bug... > > > > Traceback (most recent call last): > > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", > > line 447, in _load_plugin > >module = __import__( module_name ) > > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", > > line 232 > >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), > > target=self.run_next ) > > ^ > > SyntaxError: invalid syntax > > > > > > > > Please let me know if you want me to do anything else that might help > > debugging this issue. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Il giorno lun, 04/02/2013 alle 16.33 +, Hakeem Almabrazi ha scritto: > Thank you Dannon. Hopefully things should be moving forward from now on. > > "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which > will be in the next distribution release." > > That will be awesome. It's already in galaxy-dist since Saturday 2013/02/02, changeset 8531:3299529e0fe8 . Kind Regards, Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/ > -Original Message- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: Monday, February 04, 2013 9:40 AM > To: Hakeem Almabrazi > Cc: Galaxy Dev > Subject: Re: [galaxy-dev] File Upload doesn't generate any activity > > On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote: > > No there was nothing special about this installation. I installed it on > > CentOS and I tried to follow instructions in installing and configuring > > tools and data. The only thing that I did not was to test this feature > > before I integrate it with postgres, nginx, tools such as bwa, samtools, > > bowtie etc. I might have done something not right while doing so. But > > once I was done with all the configuration steps, I tried to load files via > > "Get Data" or "Data Library". It kept spinning and nothing is actually > > being written to the system. I tailed the logs and it was writing some > > logs every seconds but no errors or warnings. > > > > The issue was resolved when I used "URL/Text" to go to this link as another > > trail test. After that everything works just fine. Now we can load files > > via either way. > > Very strange, but I'm glad it's working for you now. If this does crop up > again, let me know and we can try to reproduce what's happening and fix it. > > > The only error I keep seeing in the log is when we restart the server and > > from what I read, this is a bug... > > > > Traceback (most recent call last): > > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", > > line 447, in _load_plugin > >module = __import__( module_name ) > > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", > > line 232 > >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), > > target=self.run_next ) > > ^ > > SyntaxError: invalid syntax > > > > > > > > Please let me know if you want me to do anything else that might help > > debugging this issue. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Thank you Dannon. Hopefully things should be moving forward from now on. "This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which will be in the next distribution release." That will be awesome. Regards, -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Monday, February 04, 2013 9:40 AM To: Hakeem Almabrazi Cc: Galaxy Dev Subject: Re: [galaxy-dev] File Upload doesn't generate any activity On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote: > No there was nothing special about this installation. I installed it on > CentOS and I tried to follow instructions in installing and configuring tools > and data. The only thing that I did not was to test this feature before I > integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc. > I might have done something not right while doing so. But once I was done > with all the configuration steps, I tried to load files via "Get Data" or > "Data Library". It kept spinning and nothing is actually being written to > the system. I tailed the logs and it was writing some logs every seconds but > no errors or warnings. > > The issue was resolved when I used "URL/Text" to go to this link as another > trail test. After that everything works just fine. Now we can load files > via either way. Very strange, but I'm glad it's working for you now. If this does crop up again, let me know and we can try to reproduce what's happening and fix it. > The only error I keep seeing in the log is when we restart the server and > from what I read, this is a bug... > > Traceback (most recent call last): > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", > line 447, in _load_plugin >module = __import__( module_name ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", > line 232 >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), > target=self.run_next ) > ^ > SyntaxError: invalid syntax > > > > Please let me know if you want me to do anything else that might help > debugging this issue. This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which will be in the next distribution release. -Dannon ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote: > No there was nothing special about this installation. I installed it on > CentOS and I tried to follow instructions in installing and configuring tools > and data. The only thing that I did not was to test this feature before I > integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc. > I might have done something not right while doing so. But once I was done > with all the configuration steps, I tried to load files via "Get Data" or > "Data Library". It kept spinning and nothing is actually being written to > the system. I tailed the logs and it was writing some logs every seconds but > no errors or warnings. > > The issue was resolved when I used "URL/Text" to go to this link as another > trail test. After that everything works just fine. Now we can load files > via either way. Very strange, but I'm glad it's working for you now. If this does crop up again, let me know and we can try to reproduce what's happening and fix it. > The only error I keep seeing in the log is when we restart the server and > from what I read, this is a bug... > > Traceback (most recent call last): > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", > line 447, in _load_plugin >module = __import__( module_name ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", > line 232 >worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), > target=self.run_next ) > ^ > SyntaxError: invalid syntax > > > > Please let me know if you want me to do anything else that might help > debugging this issue. This issue with the LWR has been fixed in changeset 8731:3299529e0fe8 which will be in the next distribution release. -Dannon ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Thank you Dannon for looking into this. No there was nothing special about this installation. I installed it on CentOS and I tried to follow instructions in installing and configuring tools and data. The only thing that I did not was to test this feature before I integrate it with postgres, nginx, tools such as bwa, samtools, bowtie etc. I might have done something not right while doing so. But once I was done with all the configuration steps, I tried to load files via "Get Data" or "Data Library". It kept spinning and nothing is actually being written to the system. I tailed the logs and it was writing some logs every seconds but no errors or warnings. The issue was resolved when I used "URL/Text" to go to this link as another trail test. After that everything works just fine. Now we can load files via either way. The only error I keep seeing in the log is when we restart the server and from what I read, this is a bug... Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax Please let me know if you want me to do anything else that might help debugging this issue. Regards, -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Sunday, February 03, 2013 7:14 PM To: Hakeem Almabrazi Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs Subject: Re: [galaxy-dev] File Upload doesn't generate any activity I just wanted to follow up on this and make sure everything was now working as expected. I've tried to reproduce the original issue and have thus far been unsuccessful in doing so with a fresh instance. Is the configuration of your Galaxy instance special in any way? Did you notice any logged errors (either in the Javascript console or in Galaxy's log)? -Dannon On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi wrote: > Stephen,,, > > Here is your solution: > > In the Tools panel select "Get Data", "Upload File". You can either upload a > file, or enter one or more URLs in the "URL/Text" box. Enter > "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" > > I am not sure what happened there but it seems this triggered some database > updates that was needed. > > It worked J > > > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen Groenewold > Sent: Friday, February 01, 2013 10:41 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] File Upload doesn't generate any activity > > We've installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > Any attempt to upload a file using the Browse File box not only fails, it > never even starts. It's as if the Execute button is disabled. > > I've tried changing the ajax-upload parameter to "false" in > tools/data_source/upload.xml (as mentioned in a workaround posted to the list > by Daniel Blankenburg in Aug 2012). I've also tried using different browsers > (including Internet Explorer) and going the route of Adding Data Libraries as > Admin. None of those attempts have worked. > > Am I missing a configuration setup? Could there be permissions issues on the > Galaxy machine? > > Thanks. > > Steve > > ___ > 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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
I just wanted to follow up on this and make sure everything was now working as expected. I've tried to reproduce the original issue and have thus far been unsuccessful in doing so with a fresh instance. Is the configuration of your Galaxy instance special in any way? Did you notice any logged errors (either in the Javascript console or in Galaxy's log)? -Dannon On Feb 1, 2013, at 3:37 PM, Hakeem Almabrazi wrote: > Stephen,,, > > Here is your solution: > > In the Tools panel select "Get Data", "Upload File". You can either upload a > file, or enter one or more URLs in the "URL/Text" box. Enter > "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" > > I am not sure what happened there but it seems this triggered some database > updates that was needed. > > It worked J…. > > > From: galaxy-dev-boun...@lists.bx.psu.edu > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen Groenewold > Sent: Friday, February 01, 2013 10:41 AM > To: galaxy-dev@lists.bx.psu.edu > Subject: [galaxy-dev] File Upload doesn't generate any activity > > We’ve installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > Any attempt to upload a file using the Browse File box not only fails, it > never even starts. It’s as if the Execute button is disabled. > > I’ve tried changing the ajax-upload parameter to “false” in > tools/data_source/upload.xml (as mentioned in a workaround posted to the list > by Daniel Blankenburg in Aug 2012). I’ve also tried using different browsers > (including Internet Explorer) and going the route of Adding Data Libraries as > Admin. None of those attempts have worked. > > Am I missing a configuration setup? Could there be permissions issues on the > Galaxy machine? > > Thanks. > > Steve > > ___ > 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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
We've also seen that same error in our startup log: == Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/handler.py", line 447, in _load_plugin module = __import__( module_name ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 232 worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), target=self.run_next ) ^ SyntaxError: invalid syntax === And we are also having trouble uploading files. Originally, even attempts to add files via the Admin Data Libraries process wouldn't work. That seems to have been resolved (coincidentally? or causally?) after another user completed a general upload via a URL. But even now, uploading a specific file with the Get Data -> Upload File process is still non-responsive. Either the Execute button never does anything at all, or the upload process appears in History and turns blue but never completes. -Original Message- From: Dan Tenenbaum [mailto:dtene...@fhcrc.org] Sent: Friday, February 01, 2013 3:14 PM To: Stephen Groenewold Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] File Upload doesn't generate any activity On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold wrote: > We've installed a local instance of Galaxy and are having trouble > with the first step of uploading files. The only thing that will > currently upload is text pasted into the URL/Text box. > > > > Any attempt to upload a file using the Browse File box not only fails, > it never even starts. It's as if the Execute button is disabled. > > > > I've tried changing the ajax-upload parameter to "false" in > tools/data_source/upload.xml (as mentioned in a workaround posted to > the list by Daniel Blankenburg in Aug 2012). I've also tried using > different browsers (including Internet Explorer) and going the route > of Adding Data Libraries as Admin. None of those attempts have worked. > > > > Am I missing a configuration setup? Could there be permissions issues > on the Galaxy machine? > > This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960 Dan > > Thanks. > > > > Steve > > > > > ___ > 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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold wrote: > We’ve installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > > > Any attempt to upload a file using the Browse File box not only fails, it > never even starts. It’s as if the Execute button is disabled. > > > > I’ve tried changing the ajax-upload parameter to “false” in > tools/data_source/upload.xml (as mentioned in a workaround posted to the > list by Daniel Blankenburg in Aug 2012). I’ve also tried using different > browsers (including Internet Explorer) and going the route of Adding Data > Libraries as Admin. None of those attempts have worked. > > > > Am I missing a configuration setup? Could there be permissions issues on the > Galaxy machine? > > This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installation-this-request-returned-None-from-get-history-td4657958.html#a4657960 Dan > > Thanks. > > > > Steve > > > > > ___ > 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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] File Upload doesn't generate any activity
Stephen,,, Here is your solution: In the Tools panel select "Get Data", "Upload File". You can either upload a file, or enter one or more URLs in the "URL/Text" box. Enter "http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute" I am not sure what happened there but it seems this triggered some database updates that was needed. It worked :) From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stephen Groenewold Sent: Friday, February 01, 2013 10:41 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] File Upload doesn't generate any activity We've installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It's as if the Execute button is disabled. I've tried changing the ajax-upload parameter to "false" in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I've also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? Thanks. Steve ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] File Upload doesn't generate any activity
We've installed a local instance of Galaxy and are having trouble with the first step of uploading files. The only thing that will currently upload is text pasted into the URL/Text box. Any attempt to upload a file using the Browse File box not only fails, it never even starts. It's as if the Execute button is disabled. I've tried changing the ajax-upload parameter to "false" in tools/data_source/upload.xml (as mentioned in a workaround posted to the list by Daniel Blankenburg in Aug 2012). I've also tried using different browsers (including Internet Explorer) and going the route of Adding Data Libraries as Admin. None of those attempts have worked. Am I missing a configuration setup? Could there be permissions issues on the Galaxy machine? Thanks. Steve ___ 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: http://lists.bx.psu.edu/
