1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/ca3fe3a5f94c/
changeset: r5405:ca3fe3a5f94c
user: natefoo
date: 2011-04-18 20:04:06
summary: Use Egg.fetch() instead of Egg.resolve() to get dependencies when dist-scrambling.
affected #: 1 file (121 bytes)
--- a/scripts/dist-scramble.py Fri Apr 15 16:37:56 2011 -0400
+++ b/scripts/dist-scramble.py Mon Apr 18 14:04:06 2011 -0400
@@ -34,10 +34,11 @@
for egg in eggs:
try:
for dependency in egg.dependencies:
- print "Checking %s dependency: %s" % ( egg.name, dependency )
+ print "Checking %s on %s dependency: %s" % ( egg.name, egg.platform, dependency )
# this could be in a better data structure...
dep = filter( lambda x: x.platform == egg.platform, c[dependency] )[0]
- dep.resolve()
+ if not os.path.exists( dep.distribution.location ):
+ dep.fetch( dep.distribution.as_requirement() )
except EggNotFetchable, e:
degg = e.eggs[0]
print "%s build dependency %s %s %s couldn't be" % ( egg.name, degg.name, degg.version, degg.platform )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/efe423619733/
changeset: r5404:efe423619733
user: greg
date: 2011-04-15 22:37:56
summary: Fixes for external service file browser.
affected #: 1 file (16 bytes)
--- a/lib/galaxy/web/controllers/requests_admin.py Fri Apr 15 13:55:45 2011 -0400
+++ b/lib/galaxy/web/controllers/requests_admin.py Fri Apr 15 16:37:56 2011 -0400
@@ -425,17 +425,18 @@
cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( scp_configs[ 'user_name' ],
scp_configs[ 'host' ],
folder_path )
- # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process
- # hangs. Add an event that handles the authentication message if keys are not set - the
- # message is something like: "Are you sure you want to continue connecting (yes/no)."
+ # Handle the authentication message if ssh keys are not set - the message is
+ # something like: "Are you sure you want to continue connecting (yes/no)."
output = pexpect.run( cmd,
- events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n',
+ events={ '\(yes\/no\)\.*' : 'yes\r\n',
+ '.ssword:*' : scp_configs[ 'password' ] + '\r\n',
pexpect.TIMEOUT : print_ticks },
timeout=10 )
- if 'Password:\r\n' in output:
+ for password_str in [ 'Password:\r\n', 'password:\r\n' ]:
# Eliminate the output created using ssh from the tree
- output = output.replace( 'Password:\r\n', '' )
- return unicode( output.replace( '\n', '<br/>' ) )
+ if password_str in output:
+ output = output.replace( password_str, '' )
+ return unicode( output.replace( '\r\n', '<br/>' ) )
@web.json
def open_folder( self, trans, request_id, external_service_id, key ):
# Avoid caching
@@ -448,15 +449,16 @@
folder_contents = []
for filename in files_list:
is_folder = False
- if filename[-1] == os.sep:
+ if filename and filename[-1] == os.sep:
is_folder = True
- full_path = os.path.join( folder_path, filename )
- node = { "title": filename,
- "isFolder": is_folder,
- "isLazy": is_folder,
- "tooltip": full_path,
- "key": full_path }
- folder_contents.append( node )
+ if filename:
+ full_path = os.path.join( folder_path, filename )
+ node = { "title": filename,
+ "isFolder": is_folder,
+ "isLazy": is_folder,
+ "tooltip": full_path,
+ "key": full_path }
+ folder_contents.append( node )
return folder_contents
def __get_files( self, trans, request, external_service, folder_path ):
# Retrieves the filenames to be transferred from the remote host.
@@ -470,11 +472,11 @@
def print_ticks( d ):
pass
cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( scp_configs[ 'user_name' ], scp_configs[ 'host' ], folder_path )
- # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process
- # hangs. Add an event that handles the authentication message if keys are not set - the
- # message is something like: "Are you sure you want to continue connecting (yes/no)."
+ # Handle the authentication message if keys are not set - the message is
+ # something like: "Are you sure you want to continue connecting (yes/no)."
output = pexpect.run( cmd,
- events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n',
+ events={ '\(yes\/no\)\.*' : 'yes\r\n',
+ '.ssword:*' : scp_configs[ 'password' ] + '\r\n',
pexpect.TIMEOUT : print_ticks },
timeout=10 )
if 'No such file or directory' in output:
@@ -482,10 +484,9 @@
message = "No folder named (%s) exists on the external service." % folder_path
ok = False
if ok:
- if 'Password:' in output:
+ if 'assword:' in output:
# Eliminate the output created using ssh from the tree
- output_as_list = output.splitlines()
- output_as_list.remove( 'Password:' )
+ output_as_list = output.splitlines()[ 1: ]
else:
output_as_list = output.splitlines()
return output_as_list
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c663af1979e4/
changeset: r5401:c663af1979e4
user: fubar
date: 2011-04-15 15:35:41
summary: title not alt for popups on thumbnails for Haploview outputs
affected #: 1 file (2 bytes)
--- a/tools/rgenetics/rgHaploView.py Thu Apr 14 23:40:19 2011 -0400
+++ b/tools/rgenetics/rgHaploView.py Fri Apr 15 09:35:41 2011 -0400
@@ -429,7 +429,7 @@
if not os.path.exists(os.path.join(self.outfpath,mainthumb)):
outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf))
else:
- outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb))
+ outf.write('<table><tr><td><a href="%s"><img src="%s" title="Main combined LD image" hspace="10" align="middle">' % (mainpdf,mainthumb))
outf.write('</td><td>Click the thumbnail at left to download the main combined LD image <a href=%s>%s</a></td></tr></table>\n' % (mainpdf,mainpdf))
else:
outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n')
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6cacf178a129/
changeset: r5400:6cacf178a129
user: dannon
date: 2011-04-15 05:40:19
summary: Workflow Parameter bugfix for the case when a parameter isn't used in
any workflow step, but should still be available for PJAs.
affected #: 1 file (62 bytes)
--- a/templates/workflow/run.mako Thu Apr 14 20:25:54 2011 -0400
+++ b/templates/workflow/run.mako Thu Apr 14 23:40:19 2011 -0400
@@ -165,7 +165,7 @@
wf_parms = {}
for step in steps:
- for v in step.state.inputs.itervalues():
+ for v in [ActionBox.get_short_str(pja) for pja in step.post_job_actions] + step.state.inputs.values():
if isinstance(v, basestring):
for rematch in re.findall('\$\{.+?\}', v):
if rematch[2:-1] not in wf_parms:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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