Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
Morning Greg, seems to be also fixed in latest release. Will reopen the thread if I encounter it again. Thanks a lot, Bjoern > Hello Peter and Bjoern, > > > I believe this issue was handled in the August Galaxy release, but the > main tool shed had not yet been upgraded to that release when you were > seeing this behavior. Unless I misunderstand the steps necessary to > reproduce the behavior, I am not able to do so. > > > Here is what I've tried in my local tool shed: > > > 1) Create a repopsitory named package_atlas_3_10 owned by username > "test" with repository type "tool_dependency_definition". > > > 2 Populate the package_atlas_3_10 repository with a > tool_dependencies.xml file that looks like this: > > > > > > > > type="download_by_url">file:///var/chemicaltoolbox/atlas.tar > > > . > > $INSTALL_DIR > > > > action="set_to">$INSTALL_DIR/lib > action="set_to">$INSTALL_DIR/include > > > > ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR will be set (including > libatlas.a). > During ATLAS library compilation, ATLAS performs code efficiency > checks. These checks can only provide optimal results, if "frequency scaling" > is disabled on the CPU, and no other load-intense processes are running. > Ideally, you should compile on an empty cluster node with CPU > frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set"). > > > > > > 3) Create a repository named package_confab_1_0_1owned by "test" with > repository type "tool_dependency_definition". > > > 4) Attempt to upload a tool_dependencies.xml file > to package_confab_1_0_1that looks like this - notice that the owner > "hello" is invalid since the required package_atlas_3_10 repository is > actually owned by "test". > > > > > prior_installation_required="True" /> > > > > > type="download_by_url">http://confab.googlecode.com/files/Confab-1.0.1.tar.gz > > > > > owner="hello"> > > > > > > cmake . > -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR= > $EIGEN_SOURCE_PATH/ > make > make install > > action="prepend_to">$INSTALL_DIR/bin > > > > Compiling Confab requires g++, CMake 2.4+ and Eigen > version 2 (libeigen2-dev). Optional but required for a few features is > libxml2 and zlib. > > > > > The above upload raises a server error, and the following stack trace > is displayed in the borwser. > Internal Server Error > Galaxy was unable to sucessfully complete your request > URL: > http://localhost:9009/upload/upload?repository_id=cd0d8ada19d98f27 > Module galaxy.web.framework.middleware.error:149 in __call__ > >> app_iter = self.application(environ, sr_checker) > Module paste.debug.prints:106 in __call__ > >> environ, self.app) > Module paste.wsgilib:543 in intercept_output > >> app_iter = application(environ, replacement_start_response) > Module paste.recursive:84 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:190 in handle_request > >> body = method( trans, **kwargs ) > Module galaxy.web.framework:98 in decorator > >> return func( self, trans, *args, **kwargs ) > Module galaxy.webapps.tool_shed.controllers.upload:147 in upload > >> altered, root_elem = > commit_util.handle_tool_dependencies_definition( trans, > uploaded_file_name ) > Module tool_shed.util.commit_util:321 in > handle_tool_dependencies_definition > >> raise Exception( exception_message ) > Exception: The tool_dependencies.xml file contains an invalid > tag. Unable to locate repository with name > package_atlas_3_10 and owner hello. > > > > The raised exception did not allow the upload to succeed, and the > "package_confab_1_0_1" repository remains empty with no changeset > revisions. > > > Revision: -1: > > > Please let me know if I've misunderstood the steps you used to produce > the behavior you saw. > > > Thanks very much, > > > Greg Von Kuster > > > > > > On Aug 12, 2013, at 7:44 AM, Bjoern Gruening > wrote: > > > On Mon, 2013-08-12 at 12:41 +0100, Peter Cock wrote: > > > On Mon, Aug 12, 2013 at 12:27 PM, Bjoern Gruening > > > wrote: > > > > Hi, > > > > > > > > > Hi Bjoern & Greg, > > > > > > > > > > The Biopython package looks OK on the test tool sh
Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
Hello Peter and Bjoern, I believe this issue was handled in the August Galaxy release, but the main tool shed had not yet been upgraded to that release when you were seeing this behavior. Unless I misunderstand the steps necessary to reproduce the behavior, I am not able to do so. Here is what I've tried in my local tool shed: 1) Create a repopsitory named package_atlas_3_10 owned by username "test" with repository type "tool_dependency_definition". 2 Populate the package_atlas_3_10 repository with a tool_dependencies.xml file that looks like this: file:///var/chemicaltoolbox/atlas.tar . $INSTALL_DIR $INSTALL_DIR/lib $INSTALL_DIR/include ATLAS_LIB_DIR and ATLAS_INCLUDE_DIR will be set (including libatlas.a). During ATLAS library compilation, ATLAS performs code efficiency checks. These checks can only provide optimal results, if "frequency scaling" is disabled on the CPU, and no other load-intense processes are running. Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see "cpufreq-selector" or "cpufreq-set"). 3) Create a repository named package_confab_1_0_1owned by "test" with repository type "tool_dependency_definition". 4) Attempt to upload a tool_dependencies.xml file to package_confab_1_0_1that looks like this - notice that the owner "hello" is invalid since the required package_atlas_3_10 repository is actually owned by "test". http://confab.googlecode.com/files/Confab-1.0.1.tar.gz cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN_SOURCE_PATH/ make make install $INSTALL_DIR/bin Compiling Confab requires g++, CMake 2.4+ and Eigen version 2 (libeigen2-dev). Optional but required for a few features is libxml2 and zlib. The above upload raises a server error, and the following stack trace is displayed in the borwser. Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://localhost:9009/upload/upload?repository_id=cd0d8ada19d98f27 Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:147 in upload >> altered, root_elem = commit_util.handle_tool_dependencies_definition( >> trans, uploaded_file_name ) Module tool_shed.util.commit_util:321 in handle_tool_dependencies_definition >> raise Exception( exception_message ) Exception: The tool_dependencies.xml file contains an invalid tag. Unable to locate repository with name package_atlas_3_10 and owner hello. The raised exception did not allow the upload to succeed, and the "package_confab_1_0_1" repository remains empty with no changeset revisions. Revision: -1: Please let me know if I've misunderstood the steps you used to produce the behavior you saw. Thanks very much, Greg Von Kuster On Aug 12, 2013, at 7:44 AM, Bjoern Gruening wrote: > On Mon, 2013-08-12 at 12:41 +0100, Peter Cock wrote: >> On Mon, Aug 12, 2013 at 12:27 PM, Bjoern Gruening >> wrote: >>> Hi, >>> Hi Bjoern & Greg, The Biopython package looks OK on the test tool shed, http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 This includes the lines: >>> name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"; /> >>> name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"; /> Note that we plan to update those dependencies to point at the IUC account, not Bjoern's personal account. However, on the ma
Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
On Mon, 2013-08-12 at 12:41 +0100, Peter Cock wrote: > On Mon, Aug 12, 2013 at 12:27 PM, Bjoern Gruening > wrote: > > Hi, > > > >> Hi Bjoern & Greg, > >> > >> The Biopython package looks OK on the test tool shed, > >> http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 > >> > >> This includes the lines: > >> > >> > >> >> name="package_numpy_1_7" owner="bgruening" > >> prior_installation_required="True" > >> toolshed="http://testtoolshed.g2.bx.psu.edu"; /> > >> > >> > >> >> name="package_matplotlib_1_2" owner="bgruening" > >> prior_installation_required="True" > >> toolshed="http://testtoolshed.g2.bx.psu.edu"; /> > >> > >> > >> Note that we plan to update those dependencies to point > >> at the IUC account, not Bjoern's personal account. > >> > >> However, on the main Tool Shed something is broken with the > >> dependencies lacking relevant revisions: > >> http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 > >> > >> > >> >> prior_installation_required="True" > >> toolshed="http://toolshed.g2.bx.psu.edu"; /> > >> > >> > >> >> prior_installation_required="True" > >> toolshed="http://toolshed.g2.bx.psu.edu"; /> > >> > > > > Upps ... :( > > > >> My guess is the revisions failed because there is no such > >> repository on the main Tool Shed (they do exist under the > >> new IUC user through, while on the Test Tool Shed they > >> exist under both usernames for now). > >> > >> Bjoern, do you remember if this was a manual upload to > >> the Main Tool Shed, or done via the migration script? > > > > It was done manually. > > > >> Greg, if this was uploaded manually, the reference to > >> non-existent repositories should have shown up as an > >> error. If this was migrated, was there no error message? > >> > >> Bjoern, are you happy to update both the test & main > >> repositories to point at the IUC packages now? Or > >> should I do that myself? > > > > Done! Hope it works now. > > > > Thanks for pointing that out! > > Bjoern > > Great - that seems to have solve the Biopython issue, > although I'm curious if there is a glitch in the Tool Shed > failing to issue a warning in a case like this? Yes, a waning would be really great. I totally missed it :( > Thanks, > > Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
On Mon, Aug 12, 2013 at 12:27 PM, Bjoern Gruening wrote: > Hi, > >> Hi Bjoern & Greg, >> >> The Biopython package looks OK on the test tool shed, >> http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 >> >> This includes the lines: >> >> >> > name="package_numpy_1_7" owner="bgruening" >> prior_installation_required="True" >> toolshed="http://testtoolshed.g2.bx.psu.edu"; /> >> >> >> > name="package_matplotlib_1_2" owner="bgruening" >> prior_installation_required="True" >> toolshed="http://testtoolshed.g2.bx.psu.edu"; /> >> >> >> Note that we plan to update those dependencies to point >> at the IUC account, not Bjoern's personal account. >> >> However, on the main Tool Shed something is broken with the >> dependencies lacking relevant revisions: >> http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 >> >> >> > prior_installation_required="True" >> toolshed="http://toolshed.g2.bx.psu.edu"; /> >> >> >> > prior_installation_required="True" >> toolshed="http://toolshed.g2.bx.psu.edu"; /> >> > > Upps ... :( > >> My guess is the revisions failed because there is no such >> repository on the main Tool Shed (they do exist under the >> new IUC user through, while on the Test Tool Shed they >> exist under both usernames for now). >> >> Bjoern, do you remember if this was a manual upload to >> the Main Tool Shed, or done via the migration script? > > It was done manually. > >> Greg, if this was uploaded manually, the reference to >> non-existent repositories should have shown up as an >> error. If this was migrated, was there no error message? >> >> Bjoern, are you happy to update both the test & main >> repositories to point at the IUC packages now? Or >> should I do that myself? > > Done! Hope it works now. > > Thanks for pointing that out! > Bjoern Great - that seems to have solve the Biopython issue, although I'm curious if there is a glitch in the Tool Shed failing to issue a warning in a case like this? Thanks, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
Hi, > Hi Bjoern & Greg, > > The Biopython package looks OK on the test tool shed, > http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 > > This includes the lines: > > > name="package_numpy_1_7" owner="bgruening" > prior_installation_required="True" > toolshed="http://testtoolshed.g2.bx.psu.edu"; /> > > > name="package_matplotlib_1_2" owner="bgruening" > prior_installation_required="True" > toolshed="http://testtoolshed.g2.bx.psu.edu"; /> > > > Note that we plan to update those dependencies to point > at the IUC account, not Bjoern's personal account. > > However, on the main Tool Shed something is broken with the > dependencies lacking relevant revisions: > http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 > > > prior_installation_required="True" > toolshed="http://toolshed.g2.bx.psu.edu"; /> > > > prior_installation_required="True" > toolshed="http://toolshed.g2.bx.psu.edu"; /> > Upps ... :( > My guess is the revisions failed because there is no such > repository on the main Tool Shed (they do exist under the > new IUC user through, while on the Test Tool Shed they > exist under both usernames for now). > > Bjoern, do you remember if this was a manual upload to > the Main Tool Shed, or done via the migration script? It was done manually. > Greg, if this was uploaded manually, the reference to > non-existent repositories should have shown up as an > error. If this was migrated, was there no error message? > > Bjoern, are you happy to update both the test & main > repositories to point at the IUC packages now? Or > should I do that myself? Done! Hope it works now. Thanks for pointing that out! Bjoern > Thanks, > > Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
