1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9e90faf2cb1c/
changeset: 9e90faf2cb1c
user: John Duddy
date: 2011-11-02 22:15:08
summary: Fix signature of slit method
affected #: 1 file
diff -r 9a9479f7e53f31b7296dce641a8c3dd0ed2e230c -r 9e90faf2cb1c58b19dc715243f4766223a6b3a47 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -462,15 +462,16 @@
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
- def split( input_files, subdir_generator_function, split_params):
+ def split( cls, input_datasets, subdir_generator_function, split_params):
"""
Split the input files by line.
"""
if split_params is None:
return
- if len(input_files) > 1:
+ if len(input_datasets) > 1:
raise Exception("Text file splitting does not support multiple files")
+ input_files = [ds.file_name for ds in input_datasets]
lines_per_file = None
chunk_size = None
@@ -534,7 +535,7 @@
part_file.close()
raise
f.close()
- split = staticmethod(split)
+ split = classmethod(split)
class LineCount( Text ):
"""
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9a9479f7e53f/
changeset: 9a9479f7e53f
user: natefoo
date: 2011-11-02 21:39:08
summary: The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.
affected #: 2 files
diff -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda -r 9a9479f7e53f31b7296dce641a8c3dd0ed2e230c templates/webapps/galaxy/base_panels.mako
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -114,7 +114,7 @@
['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ],
['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
- ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
+ ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ]
]
tab( "help", "Help", None, menu_options=menu_options)
%>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3e2cebfac37f/
changeset: 3e2cebfac37f
user: natefoo
date: 2011-11-02 18:37:33
summary: Allow administrators to impersonate other users. Useful for debugging, but be aware that this gives said administrator a full session as the user, with the ability to do anything as that user (the user does not gain the administrator's privileges, however).
affected #: 4 files
diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -71,6 +71,7 @@
self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) )
+ self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) )
self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) )
self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -1029,6 +1029,27 @@
id=trans.security.encode_id( repository.id ),
message=message,
status=status ) )
+ @web.expose
+ @web.require_admin
+ def impersonate( self, trans, email=None, **kwd ):
+ if not trans.app.config.allow_user_impersonation:
+ return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." )
+ message = ''
+ status = 'done'
+ emails = None
+ if email is not None:
+ user = trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first()
+ if user:
+ trans.set_user( user )
+ message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % ( email, url_for( controller='root' ) )
+ emails = []
+ else:
+ message = 'Invalid user selected'
+ status = 'error'
+ if emails is None:
+ emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ]
+ return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status )
+
def __get_relative_install_dir( self, trans, repository ):
# Get the directory where the repository is install.
tool_shed = self.__clean_tool_shed_url( repository.tool_shed )
diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda templates/webapps/galaxy/admin/index.mako
--- a/templates/webapps/galaxy/admin/index.mako
+++ b/templates/webapps/galaxy/admin/index.mako
@@ -46,6 +46,9 @@
<div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp=webapp )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp=webapp )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp=webapp )}" target="galaxy_main">Manage roles</a></div>
+ %if trans.app.config.allow_user_impersonation:
+ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate', webapp=webapp )}" target="galaxy_main">Impersonate a user</a></div>
+ %endif
</div></div><div class="toolSectionPad"></div>
diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -405,6 +405,9 @@
# Allow administrators to delete accounts.
#allow_user_deletion = False
+# Allow administrators to log in as other users (useful for debugging)
+#allow_user_impersonation = False
+
# Allow users to remove their datasets from disk immediately (otherwise,
# datasets will be removed after a time period specified by an administrator in
# the cleanup scripts run via cron)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1bae407d0d51/
changeset: 1bae407d0d51
user: natefoo
date: 2011-11-02 18:28:43
summary: Fix a typo in tasks.
affected #: 1 file
diff -r b22ee1d4143247e2b0d8f0974e71cc4682efa401 -r 1bae407d0d51aa07e026896fee8db5f525e71eac lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1123,7 +1123,7 @@
def __get_runner_name( self, job_wrapper ):
if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper):
- runnner_name = "tasks"
+ runner_name = "tasks"
else:
runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0]
return runner_name
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9c7e4bb081b5/
changeset: 9c7e4bb081b5
user: jgoecks
date: 2011-11-01 18:40:21
summary: Fix bug introduced in f34a17e508e5.
affected #: 1 file
diff -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 -r 9c7e4bb081b5db8850d4ad7854f721c4c9376552 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -925,7 +925,7 @@
else:
message = 'Attributes updated'
new_dataset.set_meta()
- new_dataset.datatype.after_setting_metadata( data )
+ new_dataset.datatype.after_setting_metadata( new_dataset )
trans.sa_session.flush()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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