October 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 15 Oct '13

15 Oct '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/167437d3da2d/ Changeset: 167437d3da2d Branch: action_tpye_make_install User: BjoernGruening Date: 2013-09-16 12:12:10 Summary: Add <make_install> tag. make && make install in one tag. Affected #: 2 files diff -r 5b17d89780b381bfd53712f964e0b53137adc322 -r 167437d3da2d72f5a553ca0fc4a2259897a2560a lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -409,6 +409,14 @@ return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + elif action_type == 'make_install': + # make; make install; allow providing make options + with settings( warn_only=True ): + make_opts = action_dict.get( 'make_opts', '' ) + cmd = install_environment.build_command( 'make %s && make install' % make_opts ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) + if return_code: + return elif action_type == 'download_file': # Download a single file to the current working directory. url = action_dict[ 'url' ] diff -r 5b17d89780b381bfd53712f964e0b53137adc322 -r 167437d3da2d72f5a553ca0fc4a2259897a2560a lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -602,6 +602,11 @@ # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) + elif action_type == 'make_install': + # make; make install; allow providing make options + if action_elem.text: + make_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) + action_dict[ 'make_opts' ] = make_opts elif action_type == 'chmod': # Change the read, write, and execute bits on a file. # <action type="chmod"> https://bitbucket.org/galaxy/galaxy-central/commits/be307f53645c/ Changeset: be307f53645c Branch: action_tpye_make_install User: BjoernGruening Date: 2013-09-16 14:46:42 Summary: merge Affected #: 1 file diff -r 167437d3da2d72f5a553ca0fc4a2259897a2560a -r be307f53645c0125826bcd444d9f44b4fde35022 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -393,7 +393,7 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) + cmd = install_environment.build_command( action_dict[ 'command' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return https://bitbucket.org/galaxy/galaxy-central/commits/1f9ecea92261/ Changeset: 1f9ecea92261 User: Dave Bouvier Date: 2013-10-15 17:30:55 Summary: Merged in BjoernGruening/galaxy-central-bgruening/action_tpye_make_install (pull request #217) Affected #: 2 files diff -r 8de5aa8e59eff9acfccbdd961d4a8c6a3ff64e40 -r 1f9ecea922615ec3c231aa196a8b1785e7b148a4 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -486,6 +486,14 @@ return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + elif action_type == 'make_install': + # make; make install; allow providing make options + with settings( warn_only=True ): + make_opts = action_dict.get( 'make_opts', '' ) + cmd = install_environment.build_command( 'make %s && make install' % make_opts ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) + if return_code: + return elif action_type == 'download_file': # Download a single file to the current working directory. url = action_dict[ 'url' ] diff -r 8de5aa8e59eff9acfccbdd961d4a8c6a3ff64e40 -r 1f9ecea922615ec3c231aa196a8b1785e7b148a4 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -626,6 +626,11 @@ action_dict[ 'r_packages' ] = r_packages else: continue + elif action_type == 'make_install': + # make; make install; allow providing make options + if action_elem.text: + make_opts = td_common_util.evaluate_template( action_elem.text, install_dir ) + action_dict[ 'make_opts' ] = make_opts elif action_type == 'chmod': # Change the read, write, and execute bits on a file. # <action type="chmod"> https://bitbucket.org/galaxy/galaxy-central/commits/914cec313725/ Changeset: 914cec313725 Branch: action_tpye_make_install User: Dave Bouvier Date: 2013-10-15 17:32:42 Summary: Close branch action_tpye_make_install. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 15 Oct '13

15 Oct '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66f388d6a822/ Changeset: 66f388d6a822 Branch: R_environment User: BjoernGruening Date: 2013-09-16 12:18:00 Summary: Add an advanced R_environment. Setup an R environment with a special R version: <action type="setup_r_environment"><r_base name="package_r_3_0_1" owner="bgruening" /></action> Allow downloading and installing an R package: <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</r_package> Affected #: 2 files diff -r 5b17d89780b381bfd53712f964e0b53137adc322 -r 66f388d6a822628aab96f012621940e921f17de8 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -303,6 +303,37 @@ filename = url.split( '/' )[ -1 ] td_common_util.url_download( work_dir, filename, url ) dir = os.path.curdir + elif action_type == 'setup_r_environment': + # setup an R environment + # <action type="setup_r_environment"> + # <r_base name="package_r_3_0_1" owner="bgruening" /> + # </action> + # allow downloading and installing an R package + # <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</r_package> + if action_dict.get( 'env_shell_file_paths', False ): + install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) + else: + log.warning( 'Missing R environment. Please check your specified R installation exists.' ) + return + tarball_names = list() + for url in action_dict[ 'r_packages' ]: + filename = url.split( '/' )[ -1 ] + tarball_names.append( filename ) + common_util.url_download( work_dir, filename, url, extract=False ) + dir = os.path.curdir + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): + with settings( warn_only=True ): + for tarball_name in tarball_names: + cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && + Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % (tarball_name) + + cmd = install_environment.build_command( common_util.evaluate_template( cmd, install_dir ) ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) + if return_code: + return + + else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> diff -r 5b17d89780b381bfd53712f964e0b53137adc322 -r 66f388d6a822628aab96f012621940e921f17de8 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -602,6 +602,26 @@ # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) + elif action_type == 'setup_r_environment': + # setup an R environment + # <action type="setup_r_environment" name="package_r_3_0_1" owner="bgruening"> + # <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</r_package> + # </action> + + env_shell_file_paths = td_common_util.get_env_shell_file_paths( app, action_elem.find('repository') ) + + all_env_shell_file_paths.extend( env_shell_file_paths ) + if all_env_shell_file_paths: + action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths + r_packages = list() + for env_elem in action_elem: + if env_elem.tag == 'r_package': + r_packages.append( env_elem.text.strip() ) + + if r_packages: + action_dict[ 'r_packages' ] = r_packages + else: + continue elif action_type == 'chmod': # Change the read, write, and execute bits on a file. # <action type="chmod"> https://bitbucket.org/galaxy/galaxy-central/commits/8fe3988b1811/ Changeset: 8fe3988b1811 Branch: R_environment User: BjoernGruening Date: 2013-09-16 15:36:45 Summary: merge Affected #: 1 file diff -r 66f388d6a822628aab96f012621940e921f17de8 -r 8fe3988b181190c151c30c014e25fc4211f77b18 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -424,7 +424,7 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) + cmd = install_environment.build_command( action_dict[ 'command' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return https://bitbucket.org/galaxy/galaxy-central/commits/6cc367d73045/ Changeset: 6cc367d73045 Branch: R_environment User: BjoernGruening Date: 2013-09-16 17:01:29 Summary: Change the <r_package> tag to <package>, because we are already in a special <setup_r_environment> environment. Affected #: 2 files diff -r 8fe3988b181190c151c30c014e25fc4211f77b18 -r 6cc367d730457c01cfdfc457f5e3d8ecfa8e9ea1 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -309,7 +309,7 @@ # <r_base name="package_r_3_0_1" owner="bgruening" /> # </action> # allow downloading and installing an R package - # <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</r_package> + # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> if action_dict.get( 'env_shell_file_paths', False ): install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) else: @@ -319,7 +319,7 @@ for url in action_dict[ 'r_packages' ]: filename = url.split( '/' )[ -1 ] tarball_names.append( filename ) - common_util.url_download( work_dir, filename, url, extract=False ) + td_common_util.url_download( work_dir, filename, url, extract=False ) dir = os.path.curdir current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) with lcd( current_dir ): @@ -328,12 +328,10 @@ cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % (tarball_name) - cmd = install_environment.build_command( common_util.evaluate_template( cmd, install_dir ) ) + cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return - - else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> diff -r 8fe3988b181190c151c30c014e25fc4211f77b18 -r 6cc367d730457c01cfdfc457f5e3d8ecfa8e9ea1 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -605,7 +605,7 @@ elif action_type == 'setup_r_environment': # setup an R environment # <action type="setup_r_environment" name="package_r_3_0_1" owner="bgruening"> - # <r_package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</r_package> + # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> # </action> env_shell_file_paths = td_common_util.get_env_shell_file_paths( app, action_elem.find('repository') ) @@ -615,7 +615,7 @@ action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths r_packages = list() for env_elem in action_elem: - if env_elem.tag == 'r_package': + if env_elem.tag == 'package': r_packages.append( env_elem.text.strip() ) if r_packages: https://bitbucket.org/galaxy/galaxy-central/commits/e19c7819ea3c/ Changeset: e19c7819ea3c Branch: R_environment User: BjoernGruening Date: 2013-09-17 17:21:10 Summary: set the R_LIBS env var automatically Affected #: 1 file diff -r 6cc367d730457c01cfdfc457f5e3d8ecfa8e9ea1 -r e19c7819ea3c0b9d2ae97fa8bb8cafc722240a04 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -332,6 +332,14 @@ return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + + # R libraries are installed to $INSTALL_DIR (install_dir), we now set the R_LIBS path to that directory + # TODO: That code is used a lot for the different environments and should be refactored, once the environments are integrated + modify_env_command_dict = dict( name="R_LIBS", action="prepend_to", value=install_dir ) + modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) + return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + if return_code: + return else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> https://bitbucket.org/galaxy/galaxy-central/commits/8de5aa8e59ef/ Changeset: 8de5aa8e59ef User: inithello Date: 2013-10-15 17:24:21 Summary: Merged in BjoernGruening/galaxy-central-bgruening/R_environment (pull request #219) Implementation of the a r_environment to easily install R packages in a reproducible way. Affected #: 2 files diff -r 86573eb35eec9474ac4121875da321811f343994 -r 8de5aa8e59eff9acfccbdd961d4a8c6a3ff64e40 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -338,6 +338,43 @@ filename = url.split( '/' )[ -1 ] td_common_util.url_download( work_dir, filename, url ) dir = os.path.curdir + elif action_type == 'setup_r_environment': + # setup an R environment + # <action type="setup_r_environment"> + # <r_base name="package_r_3_0_1" owner="bgruening" /> + # </action> + # allow downloading and installing an R package + # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> + if action_dict.get( 'env_shell_file_paths', False ): + install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) + else: + log.warning( 'Missing R environment. Please check your specified R installation exists.' ) + return + tarball_names = list() + for url in action_dict[ 'r_packages' ]: + filename = url.split( '/' )[ -1 ] + tarball_names.append( filename ) + td_common_util.url_download( work_dir, filename, url, extract=False ) + dir = os.path.curdir + current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + with lcd( current_dir ): + with settings( warn_only=True ): + for tarball_name in tarball_names: + cmd = '''export PATH=$PATH:$R_HOME/bin && export R_LIBS=$INSTALL_DIR && + Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % (tarball_name) + + cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) + return_code = handle_command( app, tool_dependency, install_dir, cmd ) + if return_code: + return + + # R libraries are installed to $INSTALL_DIR (install_dir), we now set the R_LIBS path to that directory + # TODO: That code is used a lot for the different environments and should be refactored, once the environments are integrated + modify_env_command_dict = dict( name="R_LIBS", action="prepend_to", value=install_dir ) + modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) + return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + if return_code: + return else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> diff -r 86573eb35eec9474ac4121875da321811f343994 -r 8de5aa8e59eff9acfccbdd961d4a8c6a3ff64e40 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -606,6 +606,26 @@ # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) + elif action_type == 'setup_r_environment': + # setup an R environment + # <action type="setup_r_environment" name="package_r_3_0_1" owner="bgruening"> + # <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGe…</package> + # </action> + + env_shell_file_paths = td_common_util.get_env_shell_file_paths( app, action_elem.find('repository') ) + + all_env_shell_file_paths.extend( env_shell_file_paths ) + if all_env_shell_file_paths: + action_dict[ 'env_shell_file_paths' ] = all_env_shell_file_paths + r_packages = list() + for env_elem in action_elem: + if env_elem.tag == 'package': + r_packages.append( env_elem.text.strip() ) + + if r_packages: + action_dict[ 'r_packages' ] = r_packages + else: + continue elif action_type == 'chmod': # Change the read, write, and execute bits on a file. # <action type="chmod"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 6 new changesets
by commits-noreply＠bitbucket.org 15 Oct '13

15 Oct '13

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/67be8479c89d/ Changeset: 67be8479c89d User: BjoernGruening Date: 2013-09-16 10:54:21 Summary: move evaluate_template() to td_common_util and add the install_dir parameter Affected #: 2 files diff -r b65602624e257d96d90fe94de13b483fd70d2f7e -r 67be8479c89db565816a71edd41d69228b4e87ee lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -445,10 +445,6 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ): """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" - def evaluate_template( text ): - """ Substitute variables defined in XML blocks from dependencies file.""" - return Template( text ).safe_substitute( td_common_util.get_env_var_values( install_dir ) ) - sa_session = app.model.context.current if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -493,7 +489,7 @@ action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None ) elif action_type == 'shell_command': # <action type="shell_command">make</action> - action_elem_text = evaluate_template( action_elem.text ) + action_elem_text = td_common_util.evaluate_template( action_elem.text, install_dir ) if action_elem_text: action_dict[ 'command' ] = action_elem_text else: @@ -541,7 +537,7 @@ elif action_type == 'make_directory': # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: - action_dict[ 'full_path' ] = evaluate_template( action_elem.text ) + action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) else: continue elif action_type == 'change_directory': @@ -560,7 +556,7 @@ # <destination_directory>$INSTALL_DIR/bin</destination_directory> # </action> for move_elem in action_elem: - move_elem_text = evaluate_template( move_elem.text ) + move_elem_text = td_common_util.evaluate_template( move_elem.text, install_dir ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'set_environment': @@ -605,9 +601,12 @@ # <action type="setup_virtualenv">pyyaml==3.2.0 # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. - action_dict[ 'requirements' ] = evaluate_template( action_elem.text or 'requirements.txt' ) + action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) elif action_type == 'chmod': # Change the read, write, and execute bits on a file. + # <action type="chmod"> + # <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file> + # </action> file_elems = action_elem.findall( 'file' ) chmod_actions = [] # A unix octal mode is the sum of the following values: @@ -623,7 +622,7 @@ received_mode = int( file_elem.get( 'mode', 600 ), base=8 ) # For added security, ensure that the setuid and setgid bits are not set. mode = received_mode & ~( stat.S_ISUID | stat.S_ISGID ) - file = evaluate_template( file_elem.text ) + file = td_common_util.evaluate_template( file_elem.text, install_dir ) chmod_tuple = ( file, mode ) chmod_actions.append( chmod_tuple ) action_dict[ 'change_modes' ] = chmod_actions diff -r b65602624e257d96d90fe94de13b483fd70d2f7e -r 67be8479c89db565816a71edd41d69228b4e87ee lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -6,6 +6,7 @@ import traceback import urllib2 import zipfile +from string import Template import tool_shed.util.shed_util_common as suc from galaxy.datatypes import checkers from urllib2 import HTTPError @@ -415,3 +416,8 @@ def __shellquote(s): """Quote and escape the supplied string for use in shell expressions.""" return "'" + s.replace( "'", "'\\''" ) + "'" + +def evaluate_template( text, install_dir ): + """ Substitute variables defined in XML blocks from dependencies file.""" + return Template( text ).safe_substitute( get_env_var_values( install_dir ) ) + https://bitbucket.org/galaxy/galaxy-central/commits/d4e5ea66bd74/ Changeset: d4e5ea66bd74 Branch: action_type_misc User: BjoernGruening Date: 2013-09-16 10:59:47 Summary: touch Affected #: 1 file diff -r 67be8479c89db565816a71edd41d69228b4e87ee -r d4e5ea66bd74385e7eb2e76191566ebe5dd3109a lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -420,4 +420,3 @@ def evaluate_template( text, install_dir ): """ Substitute variables defined in XML blocks from dependencies file.""" return Template( text ).safe_substitute( get_env_var_values( install_dir ) ) - https://bitbucket.org/galaxy/galaxy-central/commits/5b17d89780b3/ Changeset: 5b17d89780b3 Branch: action_type_misc User: BjoernGruening Date: 2013-09-16 11:42:33 Summary: Add John Chilton's InstallEnvrionment() abstraction. Setup abstraction (InstallEnvrionment) in tool shed client for capturing the environment setup to during building and installations of packages. This simplifies install_and_build_package and provides a clear extension point for other customizations to the install process. Affected #: 1 file diff -r d4e5ea66bd74385e7eb2e76191566ebe5dd3109a -r 5b17d89780b381bfd53712f964e0b53137adc322 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -164,6 +164,54 @@ shutil.move( full_path_to_dir, venv_dir ) return True + +class InstallEnvironment( object ): + """ + Object describing the environment built up as part of the process of building + and installing a package. + """ + + def __init__( self ): + self.env_shell_file_paths = [] + + def build_command( self, command, action_type='shell_command' ): + """ + Build command line for execution from simple command, but + configuring environment described by this object. + """ + env_cmds = self.environment_commands(action_type) + return '\n'.join(env_cmds + [command]) + + def environment_commands(self, action_type): + """ + Build a list of commands used to construct the environment described by + this object. + """ + cmds = [] + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmds.append( env_setting.strip( '\n' ) ) + else: + log.debug( 'Invalid file %s specified, ignoring %s action.', env_shell_file_path, action_type ) + return cmds + + def environment_dict(self, action_type='template_command'): + env_vars = dict() + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + else: + log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path ) + return env_vars + + def add_env_shell_file_paths(self, paths): + self.env_shell_file_paths.extend(paths) + + def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" sa_session = app.model.context.current @@ -171,7 +219,7 @@ package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) filtered_actions = [] - env_shell_file_paths = [] + install_environment = InstallEnvironment() if actions: with make_tmp_dir() as work_dir: with lcd( work_dir ): @@ -286,13 +334,7 @@ # Currently the only action supported in this category is "environment_variable". # Build a command line from the prior_installation_required, in case an environment variable is referenced # in the set_environment action. - cmds = [] - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmds.append( env_setting.strip( '\n' ) ) - else: - log.debug( 'Invalid file %s specified, ignoring set_environment action.', env_shell_file_path ) + cmds = install_environment.environment_commands( 'set_environment' ) env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. @@ -305,7 +347,7 @@ # Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files, # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. - env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] + install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) elif action_type == 'setup_virtualenv': # TODO: maybe should be configurable venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) @@ -351,27 +393,13 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - cmd = '' - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmd += '%s\n' % env_setting - else: - log.debug( 'Invalid file %s specified, ignoring shell_command action.', env_shell_file_path ) - cmd += action_dict[ 'command' ] + install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return elif action_type == 'template_command': env_vars = dict() - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - env_string = env_setting.split( ';' )[ 0 ] - env_name, env_path = env_string.split( '=' ) - env_vars[ env_name ] = env_path - else: - log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path ) + env_vars = install_environment.environment_dict() env_vars.update( td_common_util.get_env_var_values( install_dir ) ) language = action_dict[ 'language' ] with settings( warn_only=True, **env_vars ): https://bitbucket.org/galaxy/galaxy-central/commits/318dc55bd485/ Changeset: 318dc55bd485 Branch: action_type_misc User: BjoernGruening Date: 2013-09-16 14:30:11 Summary: bugfix Affected #: 1 file diff -r 5b17d89780b381bfd53712f964e0b53137adc322 -r 318dc55bd4859105a315d0d52de2e2ba032260eb lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -393,7 +393,7 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) + install_environment.add_env_shell_file_paths( action_dict[ 'command' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return https://bitbucket.org/galaxy/galaxy-central/commits/223f968a3b3c/ Changeset: 223f968a3b3c Branch: action_type_misc User: BjoernGruening Date: 2013-09-16 14:37:25 Summary: forgot the cmd variable Affected #: 1 file diff -r 318dc55bd4859105a315d0d52de2e2ba032260eb -r 223f968a3b3c35c709b7588bec33f4e183c8d906 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -393,7 +393,7 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - install_environment.add_env_shell_file_paths( action_dict[ 'command' ] ) + cmd = install_environment.build_command( action_dict[ 'command' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return https://bitbucket.org/galaxy/galaxy-central/commits/86573eb35eec/ Changeset: 86573eb35eec User: inithello Date: 2013-10-15 17:15:57 Summary: Merged in BjoernGruening/galaxy-central-bgruening/action_type_misc (pull request #216) Move the evaluate_template function to the td_common_util file. Affected #: 3 files diff -r 00d3bdc6e73d65126b97eb38289dc52688f810a3 -r 86573eb35eec9474ac4121875da321811f343994 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -199,6 +199,54 @@ shutil.move( full_path_to_dir, venv_dir ) return True + +class InstallEnvironment( object ): + """ + Object describing the environment built up as part of the process of building + and installing a package. + """ + + def __init__( self ): + self.env_shell_file_paths = [] + + def build_command( self, command, action_type='shell_command' ): + """ + Build command line for execution from simple command, but + configuring environment described by this object. + """ + env_cmds = self.environment_commands(action_type) + return '\n'.join(env_cmds + [command]) + + def environment_commands(self, action_type): + """ + Build a list of commands used to construct the environment described by + this object. + """ + cmds = [] + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + cmds.append( env_setting.strip( '\n' ) ) + else: + log.debug( 'Invalid file %s specified, ignoring %s action.', env_shell_file_path, action_type ) + return cmds + + def environment_dict(self, action_type='template_command'): + env_vars = dict() + for env_shell_file_path in self.env_shell_file_paths: + if os.path.exists( env_shell_file_path ): + for env_setting in open( env_shell_file_path ): + env_string = env_setting.split( ';' )[ 0 ] + env_name, env_path = env_string.split( '=' ) + env_vars[ env_name ] = env_path + else: + log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path ) + return env_vars + + def add_env_shell_file_paths(self, paths): + self.env_shell_file_paths.extend(paths) + + def install_and_build_package( app, tool_dependency, actions_dict ): """Install a Galaxy tool dependency package either via a url or a mercurial or git clone command.""" sa_session = app.model.context.current @@ -206,7 +254,7 @@ package_name = actions_dict[ 'package_name' ] actions = actions_dict.get( 'actions', None ) filtered_actions = [] - env_shell_file_paths = [] + install_environment = InstallEnvironment() if actions: with make_tmp_dir() as work_dir: with lcd( work_dir ): @@ -326,13 +374,7 @@ # Currently the only action supported in this category is "environment_variable". # Build a command line from the prior_installation_required, in case an environment variable is referenced # in the set_environment action. - cmds = [] - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmds.append( env_setting.strip( '\n' ) ) - else: - log.debug( 'Invalid file %s specified, ignoring set_environment action.', env_shell_file_path ) + cmds = install_environment.environment_commands( 'set_environment' ) env_var_dicts = action_dict[ 'environment_variable' ] for env_var_dict in env_var_dicts: # Check for the presence of the $ENV[] key string and populate it if possible. @@ -345,7 +387,7 @@ # Currently the only action supported in this category is a list of paths to one or more tool dependency env.sh files, # the environment setting in each of which will be injected into the environment for all <action type="shell_command"> # tags that follow this <action type="set_environment_for_install"> tag set in the tool_dependencies.xml file. - env_shell_file_paths = action_dict[ 'env_shell_file_paths' ] + install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) elif action_type == 'setup_virtualenv': # TODO: maybe should be configurable venv_src_directory = os.path.abspath( os.path.join( app.config.tool_dependency_dir, '__virtualenv_src' ) ) @@ -391,27 +433,13 @@ return elif action_type == 'shell_command': with settings( warn_only=True ): - cmd = '' - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - cmd += '%s\n' % env_setting - else: - log.debug( 'Invalid file %s specified, ignoring shell_command action.', env_shell_file_path ) - cmd += action_dict[ 'command' ] + cmd = install_environment.build_command( action_dict[ 'command' ] ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return elif action_type == 'template_command': env_vars = dict() - for env_shell_file_path in env_shell_file_paths: - if os.path.exists( env_shell_file_path ): - for env_setting in open( env_shell_file_path ): - env_string = env_setting.split( ';' )[ 0 ] - env_name, env_path = env_string.split( '=' ) - env_vars[ env_name ] = env_path - else: - log.debug( 'Invalid file %s specified, ignoring template_command action.', env_shell_file_path ) + env_vars = install_environment.environment_dict() env_vars.update( td_common_util.get_env_var_values( install_dir ) ) language = action_dict[ 'language' ] with settings( warn_only=True, **env_vars ): diff -r 00d3bdc6e73d65126b97eb38289dc52688f810a3 -r 86573eb35eec9474ac4121875da321811f343994 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -445,10 +445,6 @@ def install_via_fabric( app, tool_dependency, install_dir, package_name=None, proprietary_fabfile_path=None, actions_elem=None, action_elem=None, **kwd ): """Parse a tool_dependency.xml file's <actions> tag set to gather information for the installation via fabric.""" - def evaluate_template( text ): - """ Substitute variables defined in XML blocks from dependencies file.""" - return Template( text ).safe_substitute( td_common_util.get_env_var_values( install_dir ) ) - sa_session = app.model.context.current if not os.path.exists( install_dir ): os.makedirs( install_dir ) @@ -493,7 +489,7 @@ action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None ) elif action_type == 'shell_command': # <action type="shell_command">make</action> - action_elem_text = evaluate_template( action_elem.text ) + action_elem_text = td_common_util.evaluate_template( action_elem.text, install_dir ) if action_elem_text: action_dict[ 'command' ] = action_elem_text else: @@ -541,7 +537,7 @@ elif action_type == 'make_directory': # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: - action_dict[ 'full_path' ] = evaluate_template( action_elem.text ) + action_dict[ 'full_path' ] = td_common_util.evaluate_template( action_elem.text, install_dir ) else: continue elif action_type == 'change_directory': @@ -556,7 +552,7 @@ # <destination_directory>$INSTALL_DIR/bin</destination_directory> # </action> for move_elem in action_elem: - move_elem_text = evaluate_template( move_elem.text ) + move_elem_text = td_common_util.evaluate_template( move_elem.text, install_dir ) if move_elem_text: action_dict[ move_elem.tag ] = move_elem_text elif action_type == 'move_file': @@ -609,9 +605,12 @@ # <action type="setup_virtualenv">pyyaml==3.2.0 # lxml==2.3.0</action> ## Manually specify contents of requirements.txt file to create dynamically. - action_dict[ 'requirements' ] = evaluate_template( action_elem.text or 'requirements.txt' ) + action_dict[ 'requirements' ] = td_common_util.evaluate_template( action_elem.text or 'requirements.txt', install_dir ) elif action_type == 'chmod': # Change the read, write, and execute bits on a file. + # <action type="chmod"> + # <file mode="750">$INSTALL_DIR/bin/faToTwoBit</file> + # </action> file_elems = action_elem.findall( 'file' ) chmod_actions = [] # A unix octal mode is the sum of the following values: @@ -627,7 +626,7 @@ received_mode = int( file_elem.get( 'mode', 600 ), base=8 ) # For added security, ensure that the setuid and setgid bits are not set. mode = received_mode & ~( stat.S_ISUID | stat.S_ISGID ) - file = evaluate_template( file_elem.text ) + file = td_common_util.evaluate_template( file_elem.text, install_dir ) chmod_tuple = ( file, mode ) chmod_actions.append( chmod_tuple ) action_dict[ 'change_modes' ] = chmod_actions diff -r 00d3bdc6e73d65126b97eb38289dc52688f810a3 -r 86573eb35eec9474ac4121875da321811f343994 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -7,6 +7,7 @@ import traceback import urllib2 import zipfile +from string import Template import tool_shed.util.shed_util_common as suc from galaxy.datatypes import checkers @@ -470,3 +471,7 @@ def __shellquote(s): """Quote and escape the supplied string for use in shell expressions.""" return "'" + s.replace( "'", "'\\''" ) + "'" + +def evaluate_template( text, install_dir ): + """ Substitute variables defined in XML blocks from dependencies file.""" + return Template( text ).safe_substitute( get_env_var_values( install_dir ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Make icon number in icon bar a little bit smaller
by commits-noreply＠bitbucket.org 15 Oct '13

15 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/00d3bdc6e73d/ Changeset: 00d3bdc6e73d User: guerler Date: 2013-10-15 17:14:23 Summary: Make icon number in icon bar a little bit smaller Affected #: 2 files diff -r 01b94ad2c37734c2692744861948eb79c3d32af2 -r 00d3bdc6e73d65126b97eb38289dc52688f810a3 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1182,7 +1182,7 @@ #masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top} #masthead .navbar-brand a{color:white;text-decoration:none} #masthead .iconbar{position:absolute;top:2px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px} -#masthead .iconbar .symbol .number{font-weight:bold;font-size:12px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-18px} +#masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-16px} #masthead .iconbar .toggle{color:#BCC800} .quota-meter-container{position:absolute;top:0;right:0;height:32px} .quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#f5f5f5} @@ -1462,3 +1462,4 @@ .icon-button.arrow-split:hover{background-image:url(sprite-fugue.png);background-position:0px -128px;width:16px;height:16px;height:16px} .icon-button.chevron-expand:hover{background-image:url(sprite-fugue.png);background-position:0px -336px;width:16px;height:16px;height:16px} .icon-button.chevron-expand{background-image:url(sprite-fugue.png);background-position:0px -320px;width:16px;height:16px;height:16px} +#for_bears{display:none} diff -r 01b94ad2c37734c2692744861948eb79c3d32af2 -r 00d3bdc6e73d65126b97eb38289dc52688f810a3 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -423,11 +423,11 @@ .symbol .number { font-weight : bold; - font-size : 12px; + font-size : 10px; font-family : @font-family-sans-serif; position : relative; left : 23px; - top : -18px; + top : -16px; } .toggle Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Add onbeforeunload functions to iconbar item
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01b94ad2c377/ Changeset: 01b94ad2c377 User: guerler Date: 2013-10-15 06:12:08 Summary: Add onbeforeunload functions to iconbar item Affected #: 4 files diff -r 31442bf4317bf2d8841255a36a42292f319f60e6 -r 01b94ad2c37734c2692744861948eb79c3d32af2 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -87,7 +87,11 @@ { icon : 'fa-icon-th', tooltip : 'Enable/Disable Scratchbook', - on_click : function(e) { self.event_panel_active(e) } + on_click : function(e) { self.event_panel_active(e) }, + on_unload : function() { + if (self.frame_counter > 0) + return "You opened " + self.frame_counter + " frame(s) which will be lost."; + } }); // add to master @@ -157,13 +161,6 @@ if (self.visible) self.panel_refresh(); }); - - // catch window close - window.onbeforeunload = function() - { - if (self.frame_counter > 0) - return "You opened " + self.frame_counter + " frame(s) which will be lost."; - }; }, /* diff -r 31442bf4317bf2d8841255a36a42292f319f60e6 -r 01b94ad2c37734c2692744861948eb79c3d32af2 static/scripts/galaxy.master.js --- a/static/scripts/galaxy.master.js +++ b/static/scripts/galaxy.master.js @@ -1,5 +1,5 @@ /* - galaxy master v1.0 + galaxy master */ // dependencies @@ -11,6 +11,9 @@ // base element el_master: '#masthead', + // item list + list : [], + // initialize initialize : function(options) { @@ -19,6 +22,21 @@ // append to master $(this.el_master).append($(this.el)); + + // loop through item specific unload functions + var self = this; + window.onbeforeunload = function() + { + var text = ""; + for (key in self.list) + if (self.list[key].options.on_unload) + { + var q = self.list[key].options.on_unload(); + if (q) text += q + " "; + } + if (text != "") + return text; + }; }, // prevent default @@ -27,16 +45,18 @@ 'mousedown' : function(e) {e.preventDefault()} }, - // adds and displays a new frame/window + // adds a new item to the master append : function(item) { $(this.el).append($(item.el)); + this.list.push(item); }, - // adds and displays a new frame/window + // adds a new item to the master prepend : function(item) { $(this.el).prepend($(item.el)); + this.list.push(item); }, /* @@ -61,6 +81,7 @@ tooltip : "galaxy-icon", with_number : false, on_click : function() { alert ('clicked') }, + on_unload : null, visible : true }, diff -r 31442bf4317bf2d8841255a36a42292f319f60e6 -r 01b94ad2c37734c2692744861948eb79c3d32af2 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -68,6 +68,10 @@ icon : 'fa-icon-upload', tooltip : 'Upload Files', on_click : function(e) { self.event_show(e) }, + on_unload : function() { + if (self.counter.running > 0) + return "Currently uploads are running."; + }, with_number : true }); @@ -83,7 +87,6 @@ self.select_extension[filetype] = filetype; } }); - }, // mouse over diff -r 31442bf4317bf2d8841255a36a42292f319f60e6 -r 01b94ad2c37734c2692744861948eb79c3d32af2 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -23,7 +23,7 @@ complete : function() {}, error_filesize : "File exceeds 2GB. Please use an FTP client.", error_default : "Please make sure the file is available.", - error_server : "The server is unavailable.", + error_server : "Upload request failed.", error_toomany : "You can only queue <20 files per upload session.", error_login : "Uploads require you to log in." } @@ -200,8 +200,7 @@ if (filesize < maxfilesize) { // send data - var data = opts.initialize(index, file); - send(index, file, data) + send(index, file, opts.initialize(index, file)) } else { // skip file error(index, file, opts.error_filesize); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97ad9d937454/ Changeset: 97ad9d937454 User: jmchilton Date: 2013-10-15 04:50:12 Summary: Bug fix in test exception handling code. Affected #: 1 file diff -r 6342b2fa44e5dc27d72868a93a536d5f9fe48375 -r 97ad9d937454d58413125c72608aaf4b1fa933d3 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1308,6 +1308,6 @@ # This timeout currently defaults to 180 seconds, or 3 minutes. if timeout_counter > common.repository_installation_timeout: raise AssertionError( 'Repository installation timed out, %d seconds elapsed, repository state is %s.' % \ - ( timeout_counter, repository.status ) ) + ( timeout_counter, galaxy_repository.status ) ) break time.sleep( 1 ) https://bitbucket.org/galaxy/galaxy-central/commits/31442bf4317b/ Changeset: 31442bf4317b User: jmchilton Date: 2013-10-15 04:50:12 Summary: Bug fix in scripts/functional_tests.py. A tempdir is referenced before it is created in certain cases. Affected #: 1 file diff -r 97ad9d937454d58413125c72608aaf4b1fa933d3 -r 31442bf4317bf2d8841255a36a42292f319f60e6 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -230,11 +230,11 @@ default_cluster_job_runner = default_cluster_job_runner ) psu_production = True else: + tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) # Configure the database path. if 'GALAXY_TEST_DBPATH' in os.environ: galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ] else: - tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) galaxy_db_path = os.path.join( tempdir, 'database' ) # Configure the paths Galaxy needs to test tools. file_path = os.path.join( galaxy_db_path, 'files' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Explicitly uninstall tool dependencies that are in an error state.
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7416872890b/ Changeset: f7416872890b User: Dave Bouvier Date: 2013-10-14 22:46:41 Summary: Explicitly uninstall tool dependencies that are in an error state. Affected #: 2 files diff -r 2b92d545d02e6db34ce6459fa5d7b681d61021d6 -r f7416872890b78201d622746261a7ff34e915932 test/install_and_test_tool_shed_repositories/base/test_db_util.py --- a/test/install_and_test_tool_shed_repositories/base/test_db_util.py +++ b/test/install_and_test_tool_shed_repositories/base/test_db_util.py @@ -8,39 +8,59 @@ def delete_obj( obj ): sa_session.delete( obj ) sa_session.flush() + def delete_user_roles( user ): for ura in user.roles: sa_session.delete( ura ) sa_session.flush() + def flush( obj ): sa_session.add( obj ) sa_session.flush() + def get_repository( repository_id ): return sa_session.query( model.ToolShedRepository ) \ .filter( model.ToolShedRepository.table.c.id == repository_id ) \ .first() + def get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ): return sa_session.query( model.ToolShedRepository ) \ .filter( and_( model.ToolShedRepository.table.c.name == name, model.ToolShedRepository.table.c.owner == owner, model.ToolShedRepository.table.c.installed_changeset_revision == changeset_revision ) ) \ .one() + def get_private_role( user ): for role in user.all_roles(): if role.name == user.email and role.description == 'Private Role for %s' % user.email: return role raise AssertionError( "Private role not found for user '%s'" % user.email ) + +def get_tool_dependencies_for_installed_repository( repository_id, status=None ): + if status is not None: + return sa_session.query( model.ToolDependency ) \ + .filter( and_( model.ToolDependency.table.c.tool_shed_repository_id == repository_id, + model.ToolDependency.table.c.status == status ) ) \ + .all() + else: + return sa_session.query( model.ToolDependency ) \ + .filter( model.ToolDependency.table.c.tool_shed_repository_id == repository_id ) \ + .all() + def mark_obj_deleted( obj ): obj.deleted = True sa_session.add( obj ) sa_session.flush() + def refresh( obj ): sa_session.refresh( obj ) + def get_private_role( user ): for role in user.all_roles(): if role.name == user.email and role.description == 'Private Role for %s' % user.email: return role raise AssertionError( "Private role not found for user '%s'" % user.email ) + def get_user( email ): return sa_session.query( model.User ) \ .filter( model.User.table.c.email==email ) \ diff -r 2b92d545d02e6db34ce6459fa5d7b681d61021d6 -r f7416872890b78201d622746261a7ff34e915932 test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -149,4 +149,20 @@ strings_displayed.append( 'has been deactivated' ) else: strings_displayed.append( 'has been uninstalled' ) - self.check_for_strings( strings_displayed, strings_not_displayed=[] ) \ No newline at end of file + self.check_for_strings( strings_displayed, strings_not_displayed=[] ) + # Get all tool dependencies that are in an error state and uninstall them explicitly, so that the next installation attempt + # may succeed. + error_state = model.ToolDependency.installation_status.ERROR + tool_dependencies = test_db_util.get_tool_dependencies_for_installed_repository( installed_repository.id, status=error_state ) + if len( tool_dependencies ) > 0: + encoded_tool_dependency_ids = [ self.security.encode_id( tool_dependency.id ) for tool_dependency in tool_dependencies ] + self.uninstall_tool_dependencies( self.security.encode_id( installed_repository.id ), encoded_tool_dependency_ids ) + + def uninstall_tool_dependencies( self, encoded_repository_id, encoded_tool_dependency_ids ): + tool_dependency_ids = ','.join( encoded_tool_dependency_ids ) + url = '/admin_toolshed/uninstall_tool_dependencies?repository_id=%s&inst_td_ids=%s&operation=uninstall' % \ + ( encoded_repository_id, tool_dependency_ids ) + self.visit_url( url ) + tc.fv( 'uninstall_tool_dependencies', 'tool_dependency_ids', tool_dependency_ids ) + tc.submit( 'uninstall_tool_dependencies_button' ) + \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Improvements for the upload box
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b92d545d02e/ Changeset: 2b92d545d02e User: guerler Date: 2013-10-14 22:35:09 Summary: Improvements for the upload box Affected #: 1 file diff -r 5b95febb92c60babdc94882700124a8467662cf4 -r 2b92d545d02e6db34ce6459fa5d7b681d61021d6 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -50,9 +50,6 @@ // xml request element var xhr = null; - // file reader - var reader = null; - // attach to element $.fn.uploadbox = function(options) { @@ -163,7 +160,7 @@ function process() { // log - console.log("Processing queue..." + queue_length + " (" + queue_running + " / " + queue_pause + ")"); + //console.log("Processing queue..." + queue_length + " (" + queue_running + " / " + queue_pause + ")"); // validate if (queue_length == 0 || queue_pause) @@ -176,7 +173,7 @@ queue_running = true; // log - console.log("Looking for file..."); + //console.log("Looking for file..."); // get an identifier from the queue var index = -1; @@ -193,60 +190,21 @@ remove(index) // log - console.log("Initializing ('" + file.name + "')."); + //console.log("Initializing ('" + file.name + "')."); - // start - var data = opts.initialize(index, file); + // identify maximum file size + var filesize = file.size; + var maxfilesize = 1048576 * opts.maxfilesize; - // add file to queue - try + // check file size + if (filesize < maxfilesize) { - // load file read - reader = new FileReader(); - - // identify maximum file size - var filesize = file.size; - var maxfilesize = 1048576 * opts.maxfilesize; - - // set index - reader.index = index; - if (filesize < maxfilesize) - { - // link load - reader.onload = function(e) - { - // file read succesfully - console.log("Preparing submission ('" + file.name + "')."); - - // sending file - send(index, file, data) - }; - - // link error - reader.onerror = function(e) - { - error(index, file, opts.error_default); - }; - - // link abort - reader.onabort = function(e) - { - error(index, file, opts.error_default); - }; - - // reading file - console.log("Reading ('" + file.name + "')."); - - // read data - reader.readAsDataURL(file); - } else { - // skip file - error(index, file, opts.error_filesize); - } - } catch (err) - { - // parse error - error(index, file, err); + // send data + var data = opts.initialize(index, file); + send(index, file, data) + } else { + // skip file + error(index, file, opts.error_filesize); } } @@ -270,7 +228,7 @@ xhr.onreadystatechange = function() { // status change - console.log("Status changed: " + xhr.readyState + "."); + //console.log("Status changed: " + xhr.readyState + "."); // check for request completed, server connection closed if (xhr.readyState != xhr.DONE) @@ -291,20 +249,14 @@ // pass any error to the error option if (xhr.status < 200 || xhr.status > 299) { - // format error + // format status var text = xhr.statusText; - - // format status if (xhr.status == 403) text = opts.error_login; - - // text - if (!text) { - if (xhr.status == 0) - text = opts.error_server; - else - text = opts.error_default; - } + else if (xhr.status == 0) + text = opts.error_server; + else if (!text) + text = opts.error_default; // request error error(index, file, text + " (" + xhr.status + ")"); @@ -322,7 +274,7 @@ xhr.send(formData); // sending file - console.log("Sending file ('" + file.name + "')."); + //console.log("Sending file ('" + file.name + "')."); } // success @@ -392,7 +344,7 @@ // verify browser compatibility function compatible() { - return window.File && window.FileReader && window.FormData && window.XMLHttpRequest && window.FileList; + return window.File && window.FormData && window.XMLHttpRequest && window.FileList; } // export functions Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Upload box add user validation
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b95febb92c6/ Changeset: 5b95febb92c6 User: guerler Date: 2013-10-14 21:11:49 Summary: Upload box add user validation Affected #: 2 files diff -r 43cc213c5d8e531a2c31d06531a7566c2df43366 -r 5b95febb92c60babdc94882700124a8467662cf4 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -57,6 +57,10 @@ return; } + // check if logged in + if (!Galaxy.currUser.get('id')) + return; + // add activate icon var self = this; this.button_show = new mod_master.GalaxyMasterIcon ( diff -r 43cc213c5d8e531a2c31d06531a7566c2df43366 -r 5b95febb92c60babdc94882700124a8467662cf4 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -24,7 +24,8 @@ error_filesize : "File exceeds 2GB. Please use an FTP client.", error_default : "Please make sure the file is available.", error_server : "The server is unavailable.", - error_toomany : "You can only queue <20 files per upload session." + error_toomany : "You can only queue <20 files per upload session.", + error_login : "Uploads require you to log in." } // options @@ -292,7 +293,13 @@ { // format error var text = xhr.statusText; - if (!xhr.statusText) { + + // format status + if (xhr.status == 403) + text = opts.error_login; + + // text + if (!text) { if (xhr.status == 0) text = opts.error_server; else Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fill form by name instead of number.
by commits-noreply＠bitbucket.org 14 Oct '13

14 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43cc213c5d8e/ Changeset: 43cc213c5d8e User: Dave Bouvier Date: 2013-10-14 19:55:39 Summary: Fill form by name instead of number. Affected #: 1 file diff -r 7642e520cbb6767b2aba379b1681447c186a00ee -r 43cc213c5d8e531a2c31d06531a7566c2df43366 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -952,11 +952,11 @@ # HACK: don't use panels because late_javascripts() messes up the twill browser and it # can't find form fields (and hence user can't be logged in). self.visit_url( "%s/user/create?cntrller=%s&use_panels=False" % ( self.url, cntrller ) ) - tc.fv( '1', 'email', email ) - tc.fv( '1', 'redirect', redirect ) - tc.fv( '1', 'password', password ) - tc.fv( '1', 'confirm', password ) - tc.fv( '1', 'username', username ) + tc.fv( 'registration', 'email', email ) + tc.fv( 'registration', 'redirect', redirect ) + tc.fv( 'registration', 'password', password ) + tc.fv( 'registration', 'confirm', password ) + tc.fv( 'registration', 'username', username ) tc.submit( 'create_user_button' ) previously_created = False username_taken = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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