zombie undeletable files in toolshed, and versioning question
Hi, I have a tool on the main galaxy toolshed called fastq_groomer_parallel. During an update, with a new tar.gz upload I accidentally included in an unrelated big folder of stuff under the folder build/ The upload failed (with no helpful error message, only to turn on debug mode) I went and browsed the files via the web interface and the folder is there, but when I tried to delete it it says "No changes to repository. " Everything is normal, ie I can install this from a galaxy instance and the build/ folder is not there. when I hg pull and push etc the folder is not there. I have another question with versioning. So far with my experimentation on the testtoolshed, The version is only bumped when I upload via an archive not when I push to the repo. Is this meant to be the case? Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to work, I basically have to install a new instance again, is this normal? Regards, Kevin.
Hello Kevin, On Sep 14, 2012, at 3:48 AM, kevyin wrote:
Hi, I have a tool on the main galaxy toolshed called fastq_groomer_parallel. During an update, with a new tar.gz upload I accidentally included in an unrelated big folder of stuff under the folder build/
The upload failed (with no helpful error message, only to turn on debug mode) I went and browsed the files via the web interface and the folder is there, but when I tried to delete it it says "No changes to repository. " Everything is normal, ie I can install this from a galaxy instance and the build/ folder is not there. when I hg pull and push etc the folder is not there.
I'm not sure how you were seeing anything related to a large folder named "build". Looking at you change log, I see the following changeset revisions, none of which include this folder. Description: First upload 0.3.0 Commit: 0:18a08d476d5e added: README fastq_groomer_parallel.py fastq_groomer_parallel.xml Description: Deleted selected files Commit: 1:2f394cd7db91 removed: README fastq_groomer_parallel.py fastq_groomer_parallel.xml Description: Uploaded Commit: 2:cac848910bd8 added: README fastq_groomer_parallel.py fastq_groomer_parallel.xml
I have another question with versioning. So far with my experimentation on the testtoolshed, The version is only bumped when I upload via an archive not when I push to the repo. Is this meant to be the case?
This is probably not the case. A new change set is created every time you make a change to the repository, either by uploading something new or by deleting one or more files. Whenever a new change set is produced, it is associated with a revision number and string. The following sections of the tool shed wiki may provide more clarification. http://wiki.g2.bx.psu.edu/Tool%20Shed#The_mercurial_repository_change_log http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_uploading_a_new_... http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_valid_tool_versi...
Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to work, I basically have to install a new instance again, is this normal?
It depends - the following section of the tool shed wiki should clarify this: http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_reposito... Greg Von Kuster
Regards, Kevin.
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Hi Greg, Thanks for the toolshed links I'll make sure to go over them. I think when the upload failed, mercurial didn't get to the point of tracking the build folder.
From a mercurial point of view there seems to be no issue, pulling/cloning or even installing is fine because it's not tracked.
But the folder seems to be there when I go to "Browse or delete repository tip files" via the web interface.
From a user and our point of view this is isn't causing any usability issues at the moment, though it is weird.
Hope this clarifies things and thanks for the help! Kevin. On Wed, Sep 19, 2012 at 4:41 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hello Kevin,
On Sep 14, 2012, at 3:48 AM, kevyin wrote:
Hi, I have a tool on the main galaxy toolshed called fastq_groomer_parallel. During an update, with a new tar.gz upload I accidentally included in an unrelated big folder of stuff under the folder build/
The upload failed (with no helpful error message, only to turn on debug mode) I went and browsed the files via the web interface and the folder is there, but when I tried to delete it it says "No changes to repository. " Everything is normal, ie I can install this from a galaxy instance and the build/ folder is not there. when I hg pull and push etc the folder is not there.
I'm not sure how you were seeing anything related to a large folder named "build". Looking at you change log, I see the following changeset revisions, none of which include this folder.
Description: First upload 0.3.0<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=18a08d476d5e&id=d0d30f5138c21420> Commit: 0:18a08d476d5e<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=18a08d476d5e&id=d0d30f5138c21420> *added:* README<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=18a08d476d5e&id=d0d30f5138c21420#README> fastq_groomer_parallel.py<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=18a08d476d5e&id=d0d30f5138c21420#fastq_groomer_parallel.py> fastq_groomer_parallel.xml<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=18a08d476d5e&id=d0d30f5138c21420#fastq_groomer_parallel.xml>
Description: Deleted selected files<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=2f394cd7db91&id=d0d30f5138c21420> Commit: 1:2f394cd7db91<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=2f394cd7db91&id=d0d30f5138c21420> *removed:* README<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=2f394cd7db91&id=d0d30f5138c21420#README> fastq_groomer_parallel.py<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=2f394cd7db91&id=d0d30f5138c21420#fastq_groomer_parallel.py> fastq_groomer_parallel.xml<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=2f394cd7db91&id=d0d30f5138c21420#fastq_groomer_parallel.xml>
Description: Uploaded<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=cac848910bd8&id=d0d30f5138c21420> Commit: 2:cac848910bd8<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=cac848910bd8&id=d0d30f5138c21420> *added:* README<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=cac848910bd8&id=d0d30f5138c21420#README> fastq_groomer_parallel.py<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=cac848910bd8&id=d0d30f5138c21420#fastq_groomer_parallel.py> fastq_groomer_parallel.xml<http://toolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=cac848910bd8&id=d0d30f5138c21420#fastq_groomer_parallel.xml>
I have another question with versioning. So far with my experimentation on the testtoolshed, The version is only bumped when I upload via an archive not when I push to the repo. Is this meant to be the case?
This is probably not the case. A new change set is created every time you make a change to the repository, either by uploading something new or by deleting one or more files. Whenever a new change set is produced, it is associated with a revision number and string. The following sections of the tool shed wiki may provide more clarification.
http://wiki.g2.bx.psu.edu/Tool%20Shed#The_mercurial_repository_change_log
http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_uploading_a_new_...
http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_valid_tool_versi...
Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to work, I basically have to install a new instance again, is this normal?
It depends - the following section of the tool shed wiki should clarify this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_reposito...
Greg Von Kuster
Regards, Kevin.
___________________________________________________________ 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:
Hello Kevyin, As you stated, the build directory was not being tracked in your fastq_groomer_parallel repository in the tool shed - running hg status on your repository produced this: %hg status ? build/README ? build/fastq_groomer_parallel.py ? build/fastq_groomer_parallel.xml ? build/ipython/IPython/__init__.py ? build/ipython/IPython/config/__init__.py ? build/ipython/IPython/config/application.py ? build/ipython/IPython/config/configurable.py ... Since it was not tracked, I just deleted the directory and it's contents from disk, so your repository contents now look like this. I hope this is what you intended, but if not, let me know and I'll help with what's needed. Contents: fastq_groomer_parallel README fastq_groomer_parallel.py fastq_groomer_parallel.xml Thanks, Greg Von Kuster On Sep 18, 2012, at 7:44 PM, kevyin wrote:
Hi Greg, Thanks for the toolshed links I'll make sure to go over them.
I think when the upload failed, mercurial didn't get to the point of tracking the build folder. From a mercurial point of view there seems to be no issue, pulling/cloning or even installing is fine because it's not tracked.
But the folder seems to be there when I go to "Browse or delete repository tip files" via the web interface.
From a user and our point of view this is isn't causing any usability issues at the moment, though it is weird.
Hope this clarifies things and thanks for the help! Kevin.
On Wed, Sep 19, 2012 at 4:41 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hello Kevin,
On Sep 14, 2012, at 3:48 AM, kevyin wrote:
Hi, I have a tool on the main galaxy toolshed called fastq_groomer_parallel. During an update, with a new tar.gz upload I accidentally included in an unrelated big folder of stuff under the folder build/
The upload failed (with no helpful error message, only to turn on debug mode) I went and browsed the files via the web interface and the folder is there, but when I tried to delete it it says "No changes to repository. " Everything is normal, ie I can install this from a galaxy instance and the build/ folder is not there. when I hg pull and push etc the folder is not there.
I'm not sure how you were seeing anything related to a large folder named "build". Looking at you change log, I see the following changeset revisions, none of which include this folder.
Description: First upload 0.3.0 Commit: 0:18a08d476d5e added: README fastq_groomer_parallel.py fastq_groomer_parallel.xml
Description: Deleted selected files Commit: 1:2f394cd7db91 removed: README fastq_groomer_parallel.py fastq_groomer_parallel.xml
Description: Uploaded Commit: 2:cac848910bd8 added: README fastq_groomer_parallel.py fastq_groomer_parallel.xml
I have another question with versioning. So far with my experimentation on the testtoolshed, The version is only bumped when I upload via an archive not when I push to the repo. Is this meant to be the case?
This is probably not the case. A new change set is created every time you make a change to the repository, either by uploading something new or by deleting one or more files. Whenever a new change set is produced, it is associated with a revision number and string. The following sections of the tool shed wiki may provide more clarification.
http://wiki.g2.bx.psu.edu/Tool%20Shed#The_mercurial_repository_change_log http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_uploading_a_new_... http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_valid_tool_versi...
Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to work, I basically have to install a new instance again, is this normal?
It depends - the following section of the tool shed wiki should clarify this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_reposito...
Greg Von Kuster
Regards, Kevin.
___________________________________________________________ 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:
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