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- 10008 discussions
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/66fda01625f3
changeset: 3482:66fda01625f3
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Thu Mar 04 13:49:09 2010 -0500
description:
Refactor page, history, workflow display code to use same security code as get() methods.
diffstat:
lib/galaxy/web/base/controller.py | 3 +--
lib/galaxy/web/controllers/history.py | 10 +++-------
lib/galaxy/web/controllers/page.py | 10 +++-------
lib/galaxy/web/controllers/workflow.py | 12 +++---------
4 files changed, 10 insertions(+), 25 deletions(-)
diffs (79 lines):
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/base/controller.py Thu Mar 04 13:49:09 2010 -0500
@@ -110,8 +110,7 @@
if check_accessible:
# Verify accessible.
if ( item.user != user ) and ( not item.importable ) and ( user not in item.users_shared_with_dot_users ):
- raise "hi"
- error( "%s is not accessible by current user" % item.__class__.__name__ )
+ error( "%s is not accessible to current user" % item.__class__.__name__ )
return item
class UsesHistoryDatasetAssociation:
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/history.py Thu Mar 04 13:49:09 2010 -0500
@@ -589,15 +589,11 @@
# Get history.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- history_query_base = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view history if it's importable or if it's shared with him/her.
- history = history_query_base.filter( or_( model.History.importable==True, model.History.users_shared_with.any( model.HistoryUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view history is if it's importable.
- history = history_query_base.filter_by( importable=True ).first()
+ history = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False ).first()
if history is None:
raise web.httpexceptions.HTTPNotFound()
+ # Security check raises error if user cannot access history.
+ self.security_check( trans.get_user(), history, False, True)
# Get datasets.
datasets = self.get_history_datasets( trans, history )
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/page.py
--- a/lib/galaxy/web/controllers/page.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/page.py Thu Mar 04 13:49:09 2010 -0500
@@ -555,15 +555,11 @@
# Get page.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- page_query_base = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view page if it's importable or if it's shared with him/her.
- page = page_query_base.filter( or_( model.Page.user==trans.get_user(), model.Page.importable==True, model.Page.users_shared_with.any( model.PageUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view page is if it's importable.
- page = page_query_base.filter_by( importable=True ).first()
+ page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False ).first()
if page is None:
raise web.httpexceptions.HTTPNotFound()
+ # Security check raises error if user cannot access page.
+ self.security_check( trans.get_user(), page, False, True)
# Process page content.
processor = _PageContentProcessor( trans, 'utf-8', 'text/html', self._get_embed_html )
diff -r 2e025a8d71d0 -r 66fda01625f3 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:19:14 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:49:09 2010 -0500
@@ -169,15 +169,9 @@
# Get workflow.
session = trans.sa_session
user = session.query( model.User ).filter_by( username=username ).first()
- workflow_query_base = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False )
- if user is not None:
- # User can view workflow if it's importable or if it's shared with him/her.
- stored_workflow = workflow_query_base.filter( or_( model.StoredWorkflow.importable==True, model.StoredWorkflow.users_shared_with.any( model.StoredWorkflowUserShareAssociation.user==trans.get_user() ) ) ).first()
- else:
- # User not logged in, so only way to view workflow is if it's importable.
- stored_workflow = workflow_query_base.filter_by( importable=True ).first()
- if stored_workflow is None:
- raise web.httpexceptions.HTTPNotFound()
+ stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False ).first()
+ # Security check raises error if user cannot access workflow.
+ self.security_check( trans.get_user(), stored_workflow, False, True)
# Get data for workflow's steps.
self.get_stored_workflow_steps( trans, stored_workflow )
1
0
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/2e025a8d71d0
changeset: 3481:2e025a8d71d0
user: Dan Blankenberg <dan(a)bx.psu.edu>
date: Thu Mar 04 13:19:14 2010 -0500
description:
Update default tool action execute() method to only wrap incoming values once per call. It was previously wrapping once per output data label generated and for each change_format tag.
diffstat:
lib/galaxy/tools/actions/__init__.py | 20 ++++++++++++--------
1 files changed, 12 insertions(+), 8 deletions(-)
diffs (44 lines):
diff -r 39aac31a841b -r 2e025a8d71d0 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py Thu Mar 04 13:10:09 2010 -0500
+++ b/lib/galaxy/tools/actions/__init__.py Thu Mar 04 13:19:14 2010 -0500
@@ -182,6 +182,7 @@
on_text = ""
# Add the dbkey to the incoming parameters
incoming[ "dbkey" ] = input_dbkey
+ params = None #wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed
# Keep track of parent / child relationships, we'll create all the
# datasets first, then create the associations
parent_to_child_pairs = []
@@ -213,8 +214,9 @@
ext = input_ext
#process change_format tags
if output.change_format:
- params = make_dict_copy( incoming ) #FIXME: The wrapping of inputs should only be done once per call to execute; currently happens here and possibly when generating output dataset name
- wrap_values( tool.inputs, params )
+ if params is None:
+ params = make_dict_copy( incoming )
+ wrap_values( tool.inputs, params )
for change_elem in output.change_format:
for when_elem in change_elem.findall( 'when' ):
check = when_elem.get( 'input', None )
@@ -258,12 +260,14 @@
data.blurb = "queued"
# Set output label
if output.label:
- params = make_dict_copy( incoming )
- # wrapping the params allows the tool config to contain things like
- # <outputs>
- # <data format="input" name="output" label="Blat on ${<input_param>.name}" />
- # </outputs>
- wrap_values( tool.inputs, params )
+ if params is None:
+ params = make_dict_copy( incoming )
+ # wrapping the params allows the tool config to contain things like
+ # <outputs>
+ # <data format="input" name="output" label="Blat on ${<input_param>.name}" />
+ # </outputs>
+ wrap_values( tool.inputs, params )
+ #tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined
params['tool'] = tool
params['on_string'] = on_text
data.name = fill_template( output.label, context=params )
1
0
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/723de1e2dbe7
changeset: 3479:723de1e2dbe7
user: gua110
date: Thu Mar 04 13:02:56 2010 -0500
description:
Converted space to tab on mm5 declaration line in manual_builds.txt.
diffstat:
tool-data/shared/ucsc/manual_builds.txt | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diffs (10 lines):
diff -r 11dcd9d18663 -r 723de1e2dbe7 tool-data/shared/ucsc/manual_builds.txt
--- a/tool-data/shared/ucsc/manual_builds.txt Thu Mar 04 11:48:10 2010 -0500
+++ b/tool-data/shared/ucsc/manual_builds.txt Thu Mar 04 13:02:56 2010 -0500
@@ -668,4 +668,4 @@
arabidopsis Arabidopsis thaliana TAIR9
arabidopsis_tair8 Arabidopsis thaliana TAIR8
araTha1 Arabidopsis thaliana TAIR7
-mm5 Mouse May 2004 (mm5)
\ No newline at end of file
+mm5 Mouse May 2004 (mm5)
1
0
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/39aac31a841b
changeset: 3480:39aac31a841b
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Thu Mar 04 13:10:09 2010 -0500
description:
Provide workflow annotation field when creating a workflow.
diffstat:
lib/galaxy/web/controllers/workflow.py | 10 +++++++---
1 files changed, 7 insertions(+), 3 deletions(-)
diffs (34 lines):
diff -r 723de1e2dbe7 -r 39aac31a841b lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:02:56 2010 -0500
+++ b/lib/galaxy/web/controllers/workflow.py Thu Mar 04 13:10:09 2010 -0500
@@ -441,7 +441,7 @@
@web.expose
@web.require_login( "create workflows" )
- def create( self, trans, workflow_name=None ):
+ def create( self, trans, workflow_name=None, workflow_annotation="" ):
"""
Create a new stored workflow with name `workflow_name`.
"""
@@ -456,6 +456,9 @@
workflow.name = workflow_name
workflow.stored_workflow = stored_workflow
stored_workflow.latest_workflow = workflow
+ # Add annotation.
+ workflow_annotation = sanitize_html( workflow_annotation, 'utf-8', 'text/html' )
+ self.add_item_annotation( trans, stored_workflow, workflow_annotation )
# Persist
session = trans.sa_session
session.add( stored_workflow )
@@ -464,8 +467,9 @@
trans.set_message( "Workflow '%s' created" % stored_workflow.name )
return self.list( trans )
else:
- return form( url_for(), "Create new workflow", submit_text="Create" ) \
- .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" )
+ return form( url_for(), "Create New Workflow", submit_text="Create" ) \
+ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \
+ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." )
@web.expose
def delete( self, trans, id=None ):
1
0
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/d9afcaa386f6
changeset: 3477:d9afcaa386f6
user: jeremy goecks <jeremy.goecks(a)emory.edu>
date: Wed Mar 03 17:05:56 2010 -0500
description:
Provide minimum width for columns in published items grids so that tags/annotations do not squish other columns too much.
diffstat:
templates/history/list_published.mako | 9 +++++++++
templates/page/list_published.mako | 13 +++++++++++++
templates/workflow/list_published.mako | 9 +++++++++
3 files changed, 31 insertions(+), 0 deletions(-)
diffs (61 lines):
diff -r adda1b9e31fa -r d9afcaa386f6 templates/history/list_published.mako
--- a/templates/history/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/history/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -13,6 +13,15 @@
Galaxy :: Published Histories
</%def>
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
diff -r adda1b9e31fa -r d9afcaa386f6 templates/page/list_published.mako
--- a/templates/page/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/page/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -9,6 +9,19 @@
%>
</%def>
+<%def name="title()">
+ Galaxy :: Published Pages
+</%def>
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
diff -r adda1b9e31fa -r d9afcaa386f6 templates/workflow/list_published.mako
--- a/templates/workflow/list_published.mako Wed Mar 03 17:00:50 2010 -0500
+++ b/templates/workflow/list_published.mako Wed Mar 03 17:05:56 2010 -0500
@@ -13,6 +13,15 @@
Galaxy :: Published Workflows
</%def>
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ <style>
+ .grid td {
+ min-width: 100px;
+ }
+ </style>
+</%def>
+
<%def name="center_panel()">
## <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="page", action="list" )}"> </iframe>
1
0
08 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/11dcd9d18663
changeset: 3478:11dcd9d18663
user: gua110
date: Thu Mar 04 11:48:10 2010 -0500
description:
Added a new tool set for performing multivariate statistical analyses
diffstat:
test-data/cca_out1.tabular | 22 +
test-data/cca_out2.pdf | 858 +++++++++++++++++++++
test-data/iris.tabular | 151 +++
test-data/kcca_out1.tabular | 304 +++++++
test-data/kcca_out2.tabular | 304 +++++++
test-data/kpca_out1.tabular | 304 +++++++
test-data/kpca_out2.pdf | 1190 ++++++++++++++++++++++++++++++
test-data/kpca_out3.tabular | 304 +++++++
test-data/kpca_out4.pdf | 624 +++++++++++++++
test-data/pca_out1.tabular | 159 ++++
test-data/pca_out2.pdf | 705 +++++++++++++++++
test-data/pca_out3.tabular | 159 ++++
test-data/pca_out4.pdf | 705 +++++++++++++++++
tool_conf.xml.sample | 6 +
tools/multivariate_stats/cca.py | 159 ++++
tools/multivariate_stats/cca.xml | 95 ++
tools/multivariate_stats/kcca.py | 146 +++
tools/multivariate_stats/kcca.xml | 150 +++
tools/multivariate_stats/kpca.py | 134 +++
tools/multivariate_stats/kpca.xml | 151 +++
tools/multivariate_stats/pca.py | 98 ++
tools/multivariate_stats/pca.xml | 76 +
tools/regVariation/linear_regression.xml | 8 +-
23 files changed, 6809 insertions(+), 3 deletions(-)
diffs (truncated from 6932 to 3000 lines):
diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/cca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cca_out1.tabular Thu Mar 04 11:48:10 2010 -0500
@@ -0,0 +1,22 @@
+#Component 1 2
+#Correlation 0.940897180432 0.131074795925
+#F-statistic 144.410560578 2.5696974623
+#p-value 6.21285598619e-68 0.111075110551
+#X-Coefficients 1 2
+c3 1.50661351834 -3.37790409332
+c4 -0.537226204038 3.65944099051
+#Y-Coefficients 1 2
+c1 6.35046749378 3.37940792566
+c2 -2.6597206473 6.66976562808
+#X-Loadings 1 2
+c3 0.989395177676 0.145248691528
+c4 0.913276653253 0.407339851504
+#Y-Loadings 1 2
+c1 0.928869265104 0.370407732566
+c2 -0.469775462051 0.882785939656
+#X-CrossLoadings 1 2
+c3 0.930919133009 0.0190384426004
+c4 0.859299428 0.0533919879079
+#Y-CrossLoadings 1 2
+c1 0.873970472527 0.0485511179549
+c2 -0.44201040768 0.115710986885
diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/cca_out2.pdf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cca_out2.pdf Thu Mar 04 11:48:10 2010 -0500
@@ -0,0 +1,858 @@
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diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/iris.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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+4.9 2.4 3.3 1.0 Iris-versicolor
+6.6 2.9 4.6 1.3 Iris-versicolor
+5.2 2.7 3.9 1.4 Iris-versicolor
+5.0 2.0 3.5 1.0 Iris-versicolor
+5.9 3.0 4.2 1.5 Iris-versicolor
+6.0 2.2 4.0 1.0 Iris-versicolor
+6.1 2.9 4.7 1.4 Iris-versicolor
+5.6 2.9 3.6 1.3 Iris-versicolor
+6.7 3.1 4.4 1.4 Iris-versicolor
+5.6 3.0 4.5 1.5 Iris-versicolor
+5.8 2.7 4.1 1.0 Iris-versicolor
+6.2 2.2 4.5 1.5 Iris-versicolor
+5.6 2.5 3.9 1.1 Iris-versicolor
+5.9 3.2 4.8 1.8 Iris-versicolor
+6.1 2.8 4.0 1.3 Iris-versicolor
+6.3 2.5 4.9 1.5 Iris-versicolor
+6.1 2.8 4.7 1.2 Iris-versicolor
+6.4 2.9 4.3 1.3 Iris-versicolor
+6.6 3.0 4.4 1.4 Iris-versicolor
+6.8 2.8 4.8 1.4 Iris-versicolor
+6.7 3.0 5.0 1.7 Iris-versicolor
+6.0 2.9 4.5 1.5 Iris-versicolor
+5.7 2.6 3.5 1.0 Iris-versicolor
+5.5 2.4 3.8 1.1 Iris-versicolor
+5.5 2.4 3.7 1.0 Iris-versicolor
+5.8 2.7 3.9 1.2 Iris-versicolor
+6.0 2.7 5.1 1.6 Iris-versicolor
+5.4 3.0 4.5 1.5 Iris-versicolor
+6.0 3.4 4.5 1.6 Iris-versicolor
+6.7 3.1 4.7 1.5 Iris-versicolor
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+6.3 3.3 6.0 2.5 Iris-virginica
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+6.3 2.8 5.1 1.5 Iris-virginica
+6.1 2.6 5.6 1.4 Iris-virginica
+7.7 3.0 6.1 2.3 Iris-virginica
+6.3 3.4 5.6 2.4 Iris-virginica
+6.4 3.1 5.5 1.8 Iris-virginica
+6.0 3.0 4.8 1.8 Iris-virginica
+6.9 3.1 5.4 2.1 Iris-virginica
+6.7 3.1 5.6 2.4 Iris-virginica
+6.9 3.1 5.1 2.3 Iris-virginica
+5.8 2.7 5.1 1.9 Iris-virginica
+6.8 3.2 5.9 2.3 Iris-virginica
+6.7 3.3 5.7 2.5 Iris-virginica
+6.7 3.0 5.2 2.3 Iris-virginica
+6.3 2.5 5.0 1.9 Iris-virginica
+6.5 3.0 5.2 2.0 Iris-virginica
+6.2 3.4 5.4 2.3 Iris-virginica
+5.9 3.0 5.1 1.8 Iris-virginica
+
diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/kcca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kcca_out1.tabular Thu Mar 04 11:48:10 2010 -0500
@@ -0,0 +1,304 @@
+#Component 1 2 3 4
+#Correlation -0.999499965799 0.999499965799 -0.937388978867 0.937388978867
+#Estimated X-coefficients 1 2 3 4
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+145 3.23787858251e-05 3.23787858432e-05 0.0537581665472 0.0537581665472
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+150 -0.00315200955113 -0.00315200955116 -0.0846780840986 -0.0846780840986
+#Estimated Y-coefficients 1 2 3 4
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diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/kcca_out2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kcca_out2.tabular Thu Mar 04 11:48:10 2010 -0500
@@ -0,0 +1,304 @@
+#Component 1 2
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diff -r d9afcaa386f6 -r 11dcd9d18663 test-data/kpca_out1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kpca_out1.tabular Thu Mar 04 11:48:10 2010 -0500
@@ -0,0 +1,304 @@
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1
0
Begin forwarded message:
> From: webb(a)bx.psu.edu
> Date: March 5, 2010 1:44:01 PM EST
> To: Tjaart de Beer <tdebeer(a)gmail.com>
> Cc: Anton Nekrutenko <anton(a)bx.psu.edu>, Webb Miller
> <webb(a)bx.psu.edu>, Aakrosh Ratan <ratan(a)cse.psu.edu>
> Subject: Re: Fwd: [galaxy-user] Protein names
>
> Hi,
>
> The gene annotations are from RefSeq. As we processed the SNPs with
> tools such as PolyPhen and Sift, we sometimes had to use other
> names. My assumption was that people would load their favorite gene
> annotations into Galaxy and use an "interval" join to attach the
> desired names. Can you do something like that? Or is the problem
> that you need to deal with alternate splice forms?
>
> Please keep asking until you have everything working. If necessary,
> I can regenerate the file with other protein names. Thanks for your
> patience.
>
> --Webb
>
>
> Quoting Anton Nekrutenko <anton(a)bx.psu.edu>:
>
>> Webb:
>>
>> The question here is on where the protein names come from. Can you
>> elaborate, so I send him a reply.
>>
>> Thanks,
>>
>> anton
>>
>>
>>
>> Begin forwarded message:
>>
>>> From: Tjaart de Beer <tdebeer(a)gmail.com>
>>> Date: March 5, 2010 7:34:13 AM EST
>>> To: galaxy-user(a)bx.psu.edu
>>> Subject: [galaxy-user] Protein names
>>>
>>> Hi
>>>
>>> I am trying to parse some data from the Bushmen dataset and have
>>> a question.
>>>
>>> Where do you get the protein names from? It does not correspond 100%
>>> to the UniProt ID field in Uniprot entries nor is it Uniprot AC
>>> numbers. Is there some kind of mapping I can use to get the
>>> appropriate names or Uniprot entries? Would you be able to provide
>>> with this mapping? I have been going through the Uniprot website
>>> rather extensively and have failed to find any such downloadable
>>> mapping. Hope you can help!
>>>
>>> Thanks!
>>>
>>> Dr. Tjaart de Beer
>>> Thornton group
>>> EMBL-EBI
>>> Cambridge
>>> _______________________________________________
>>> galaxy-user mailing list
>>> galaxy-user(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-user
>>
>> Anton Nekrutenko
>> http://nekrut.bx.psu.edu
>> http://usegalaxy.org
>>
>>
>>
>>
>
>
>
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
1
0
Dear Galaxy Team,
I would like to visualize a wiggle format file in my galaxy instance. I made
initial set up for visualization and I am not able to find my track display.
Here I am attaching my screen shot, please find it.
less from my wiggle file,
track type=wiggle_0 name=test
variableStep chrom=I
I 3749 1
I 3750 1
I 3751 1
I 3752 1
I 3753 1
I 3754 1
I 3755 1
I 3756 1
I 3757 1
I 3758 1
I 3759 1
I 3760 1
I 3761 1
I 3762 1
I 3763 1
I 3764 1
I 3765 1
I 3766 3
I 3767 5
I 3768 6
I 3769 6
I 3770 6
I 3771 6
I 3772 6
It will be great if you can suggest me a way to solve the display problem.
Many thanks, Vipin
3
3
Hi,
I just wanted to check if Galaxy is now fully compatible with Python 2.6.
Thanks for your help
Shaun webb
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
2
1
03 Mar '10
details: http://www.bx.psu.edu/hg/galaxy/rev/adda1b9e31fa
changeset: 3476:adda1b9e31fa
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Mar 03 17:00:50 2010 -0500
description:
Fix for sharing histories that include restricted datasets.
diffstat:
lib/galaxy/web/controllers/history.py | 12 +++++++-----
1 files changed, 7 insertions(+), 5 deletions(-)
diffs (31 lines):
diff -r a2cb4b0ccf6b -r adda1b9e31fa lib/galaxy/web/controllers/history.py
--- a/lib/galaxy/web/controllers/history.py Wed Mar 03 15:37:43 2010 -0500
+++ b/lib/galaxy/web/controllers/history.py Wed Mar 03 17:00:50 2010 -0500
@@ -908,7 +908,7 @@
else:
# Only deal with datasets that have not been purged
for hda in history.activatable_datasets:
- if trans.app.security_agent.dataset_is_public( hda.dataset ):
+ if trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
# The no_change_needed dictionary is a special case. If both of can_change
# and cannot_change are empty, no_change_needed will used for sharing. Otherwise
# unique_no_change_needed will be used for displaying, so we need to populate both.
@@ -924,12 +924,14 @@
no_change_needed[ send_to_user ][ history ] = [ hda ]
else:
no_change_needed[ send_to_user ][ history ].append( hda )
- elif not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
+ else:
# The user with which we are sharing the history does not have access permission on the current dataset
- if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations:
+ if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ):
# The current user has authority to change permissions on the current dataset because
- # they have permission to manage permissions on the dataset and the dataset is not associated
- # with a library.
+ # they have permission to manage permissions on the dataset.
+ # NOTE: ( gvk )There may be problems if the dataset also has an ldda, but I don't think so
+ # because the user with which we are sharing will not have the "manage permission" permission
+ # on the dataset in their history. Keep an eye on this though...
if unique:
# Build the dictionaries for display, containing unique histories only
if history not in can_change:
1
0