def update( self, trans, payload, **kwd ):
"""
PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.
"""
repository_metadata_id = kwd.get( 'id', None )
try:
repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id )
flush_needed = False
for key, new_value in payload.items():
if hasattr( repository_metadata, key ):
old_value = getattr( repository_metadata, key )
setattr( repository_metadata, key, new_value )
if key in [ 'tools_functionally_correct', 'time_last_tested' ]:
# Automatically update repository_metadata.time_last_tested.
repository_metadata.time_last_tested = datetime.datetime.utcnow()
flush_needed = True
if flush_needed:
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
except Exception, e:
message = "Error in the Tool Shed repository_revisions API in update: %s" % str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def update(self, trans, payload, **kwd):
"""
PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.
"""
repository_metadata_id = kwd.get('id', None)
try:
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans, repository_metadata_id)
flush_needed = False
for key, new_value in payload.items():
if hasattr(repository_metadata, key):
old_value = getattr(repository_metadata, key)
setattr(repository_metadata, key, new_value)
if key in [
'tools_functionally_correct', 'time_last_tested'
]:
# Automatically update repository_metadata.time_last_tested.
repository_metadata.time_last_tested = datetime.datetime.utcnow(
)
flush_needed = True
if flush_needed:
trans.sa_session.add(repository_metadata)
trans.sa_session.flush()
except Exception, e:
message = "Error in the Tool Shed repository_revisions API in update: %s" % str(
e)
log.error(message, exc_info=True)
trans.response.status = 500
return message
def delete_repository_metadata(self, trans, **kwd):
message = escape(kwd.get("message", ""))
status = kwd.get("status", "done")
id = kwd.get("id", None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = "error"
trans.response.send_redirect(
web.url_for(
controller="admin",
action="browse_repository_metadata",
message=util.sanitize_text(message),
status=status,
)
)
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, repository_metadata_id)
repository_id = trans.security.encode_id(repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = repository_util.get_tool_shed_repository_by_id(trans.app, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata['workflows']:
workflow_dict = workflow_tup[1]
if workflow_dict['name'] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata['tools']
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision)
workflow_canvas = WorkflowCanvas()
canvas = workflow_canvas.canvas
# Store px width for boxes of each step.
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step)
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps)
module_name = get_workflow_module_name(module, missing_tool_tups)
workflow_canvas.populate_data_for_step(
step,
module_name,
module_data_inputs,
module_data_outputs,
tool_errors=tool_errors
)
workflow_canvas.add_steps(highlight_errors=True)
workflow_canvas.finish()
trans.response.set_content_type("image/svg+xml")
return canvas.tostring()
def update(self, trans, payload, **kwd):
"""
PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.
:param id: the encoded id of the `RepositoryMetadata` object
"""
repository_metadata_id = kwd.get('id', None)
if repository_metadata_id is None:
raise HTTPBadRequest(detail="Missing required parameter 'id'.")
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, repository_metadata_id)
if repository_metadata is None:
decoded_repository_metadata_id = trans.security.decode_id(
repository_metadata_id)
log.debug('Cannot locate repository_metadata with id %s' %
str(decoded_repository_metadata_id))
return {}
else:
decoded_repository_metadata_id = repository_metadata.id
flush_needed = False
for key, new_value in payload.items():
if key == 'time_last_tested':
repository_metadata.time_last_tested = datetime.datetime.utcnow(
)
flush_needed = True
elif hasattr(repository_metadata, key):
# log information when setting attributes associated with the Tool Shed's install and test framework.
if key in [
'do_not_test', 'includes_tools',
'missing_test_components', 'test_install_error',
'tools_functionally_correct'
]:
log.debug(
'Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.'
% (str(key), str(new_value),
str(repository_metadata.changeset_revision)))
setattr(repository_metadata, key, new_value)
flush_needed = True
if flush_needed:
log.debug(
'Updating repository_metadata record with id %s and changeset_revision %s.'
% (str(decoded_repository_metadata_id),
str(repository_metadata.changeset_revision)))
trans.sa_session.add(repository_metadata)
trans.sa_session.flush()
trans.sa_session.refresh(repository_metadata)
repository_metadata_dict = repository_metadata.to_dict(
view='element', value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(
controller='repository_revisions',
action='show',
id=repository_metadata_id)
return repository_metadata_dict
def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode( workflow_name )
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
repository_id = trans.security.encode_id( repository_metadata.repository_id )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata[ 'workflows' ]:
workflow_dict = workflow_tup[1]
if workflow_dict[ 'name' ] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata[ 'tools' ]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict( trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision )
workflow_canvas = WorkflowCanvas()
canvas = workflow_canvas.canvas
# Store px width for boxes of each step.
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step )
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs( step, module )
module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps )
module_name = get_workflow_module_name( module, missing_tool_tups )
workflow_canvas.populate_data_for_step(
step,
module_name,
module_data_inputs,
module_data_outputs,
tool_errors=tool_errors
)
workflow_canvas.add_steps( highlight_errors=True )
workflow_canvas.finish( )
trans.response.set_content_type( "image/svg+xml" )
return canvas.tostring()
def browse_repository_metadata( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if operation == "delete":
return self.delete_repository_metadata( trans, **kwd )
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans, kwd[ 'id' ] )
repository = repository_metadata.repository
kwd[ 'id' ] = trans.security.encode_id( repository.id )
kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
kwd[ 'operation' ] = 'view_or_manage_repository'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
**kwd ) )
return self.repository_metadata_grid( trans, **kwd )
def browse_repository_metadata( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if operation == "delete":
return self.delete_repository_metadata( trans, **kwd )
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, kwd[ 'id' ] )
repository = repository_metadata.repository
kwd[ 'id' ] = trans.security.encode_id( repository.id )
kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
kwd[ 'operation' ] = 'view_or_manage_repository'
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
**kwd ) )
return self.repository_metadata_grid( trans, **kwd )
def show(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded_repository_metadata_id}
Displays information about a repository_metadata record in the Tool Shed.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
if repository_metadata is None:
log.debug('Cannot locate repository_metadata with id %s' % str(id))
return {}
encoded_repository_id = trans.security.encode_id(repository_metadata.repository_id)
repository_metadata_dict = repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(controller='repositories',
action='show',
id=encoded_repository_id)
return repository_metadata_dict
def show(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded_repository_metadata_id}
Displays information about a repository_metadata record in the Tool Shed.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
if repository_metadata is None:
log.debug('Cannot locate repository_metadata with id %s' % str(id))
return {}
encoded_repository_id = trans.security.encode_id(repository_metadata.repository_id)
repository_metadata_dict = repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(controller='repositories',
action='show',
id=encoded_repository_id)
return repository_metadata_dict
def update( self, trans, payload, **kwd ):
"""
PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload}
Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload.
:param id: the encoded id of the `RepositoryMetadata` object
"""
repository_metadata_id = kwd.get( 'id', None )
if repository_metadata_id is None:
raise HTTPBadRequest( detail="Missing required parameter 'id'." )
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
if repository_metadata is None:
decoded_repository_metadata_id = trans.security.decode_id( repository_metadata_id )
log.debug( 'Cannot locate repository_metadata with id %s' % str( decoded_repository_metadata_id ) )
return {}
else:
decoded_repository_metadata_id = repository_metadata.id
flush_needed = False
for key, new_value in payload.items():
if key == 'time_last_tested':
repository_metadata.time_last_tested = datetime.datetime.utcnow()
flush_needed = True
elif hasattr( repository_metadata, key ):
# log information when setting attributes associated with the Tool Shed's install and test framework.
if key in [ 'do_not_test', 'includes_tools', 'missing_test_components', 'test_install_error',
'tools_functionally_correct' ]:
log.debug( 'Setting repository_metadata column %s to value %s for changeset_revision %s via the Tool Shed API.' %
( str( key ), str( new_value ), str( repository_metadata.changeset_revision ) ) )
setattr( repository_metadata, key, new_value )
flush_needed = True
if flush_needed:
log.debug( 'Updating repository_metadata record with id %s and changeset_revision %s.' %
( str( decoded_repository_metadata_id ), str( repository_metadata.changeset_revision ) ) )
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
trans.sa_session.refresh( repository_metadata )
repository_metadata_dict = repository_metadata.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
id=repository_metadata_id )
return repository_metadata_dict
def show( self, trans, id, **kwd ):
"""
GET /api/repository_revisions/{encoded_repository_metadata_id}
Displays information about a repository_metadata record in the Tool Shed.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
try:
repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id )
repository_metadata_dict = repository_metadata.as_dict( value_mapper=default_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
id=trans.security.encode_id( repository_metadata.id ) )
return repository_metadata_dict
except Exception, e:
message = "Error in the Tool Shed repository_revisions API in show: %s" % str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def delete_repository_metadata( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
ids = util.listify( id )
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id )
trans.sa_session.delete( repository_metadata )
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) )
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text( message ),
status=status ) )
def delete_repository_metadata( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
id = kwd.get( 'id', None )
if id:
ids = util.listify( id )
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
trans.sa_session.delete( repository_metadata )
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % ( count, inflector.cond_plural( len( ids ), "record" ) )
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text( message ),
status=status ) )
def show(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded_repository_metadata_id}
Displays information about a repository_metadata record in the Tool Shed.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620
try:
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans, id)
repository_metadata_dict = repository_metadata.as_dict(
value_mapper=default_value_mapper(trans, repository_metadata))
repository_metadata_dict['url'] = web.url_for(
controller='repository_revisions',
action='show',
id=trans.security.encode_id(repository_metadata.id))
return repository_metadata_dict
except Exception, e:
message = "Error in the Tool Shed repository_revisions API in show: %s" % str(
e)
log.error(message, exc_info=True)
trans.response.status = 500
return message
def generate_workflow_image(trans, workflow_name, repository_metadata_id=None, repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == "tool_shed":
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id(trans, repository_metadata_id)
repository_id = trans.security.encode_id(repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id(trans, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata["workflows"]:
workflow_dict = workflow_tup[1]
if workflow_dict["name"] == workflow_name:
break
if "tools" in metadata:
tools_metadata = metadata["tools"]
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(
trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision,
)
data = []
canvas = svgfig.canvas(style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left")
text = svgfig.SVG("g")
connectors = svgfig.SVG("g")
boxes = svgfig.SVG("g")
svgfig.Text.defaults["font-size"] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id, changeset_revision, tools_metadata, step)
tool_errors = module.type == "tool" and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(step, module, workflow.steps)
step_dict = {
"id": step.order_index,
"data_inputs": module_data_inputs,
"data_outputs": module_data_outputs,
"position": step.position,
"tool_errors": tool_errors,
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[conn.input_name] = dict(id=conn.output_step.order_index, output_name=conn.output_name)
step_dict["input_connections"] = input_conn_dict
data.append(step_dict)
x, y = step.position["left"], step.position["top"]
count = 0
module_name = get_workflow_module_name(module, missing_tool_tups)
max_len = len(module_name) * 1.5
text.append(svgfig.Text(x, y + 20, module_name, **{"font-size": "14px"}).SVG())
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[step.order_index] = {}
in_pos[step.order_index][di["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, di["label"]).SVG())
count += 1
max_len = max(max_len, len(di["label"]))
if len(module.get_data_inputs()) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[step.order_index] = {}
out_pos[step.order_index][do["name"]] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, do["name"]).SVG())
count += 1
max_len = max(max_len, len(do["name"]))
widths[step.order_index] = max_len * 5.5
max_x = max(max_x, step.position["left"])
max_y = max(max_y, step.position["top"])
max_width = max(max_width, widths[step.order_index])
for step_dict in data:
tool_unavailable = step_dict["tool_errors"]
width = widths[step_dict["id"]]
x, y = step_dict["position"]["left"], step_dict["position"]["top"]
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == "tool_shed" and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append(svgfig.Rect(x - margin, y, x + width - margin, y + 30, fill=fill).SVG())
box_height = (len(step_dict["data_inputs"]) + len(step_dict["data_outputs"])) * line_px + margin
# Draw separator line.
if len(step_dict["data_inputs"]) > 0:
box_height += 15
sep_y = y + len(step_dict["data_inputs"]) * line_px + 40
text.append(svgfig.Line(x - margin, sep_y, x + width - margin, sep_y).SVG())
# Define an input/output box.
boxes.append(svgfig.Rect(x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff").SVG())
for conn, output_dict in step_dict["input_connections"].iteritems():
in_coords = in_pos[step_dict["id"]][conn]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict["id"]
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict["output_name"]
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[out_pos_index]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[out_pos_index][out_pos_name]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[out_pos_index][key]
adjusted = (out_conn_pos[0] + widths[output_dict["id"]], out_conn_pos[1])
text.append(
svgfig.SVG(
"circle",
cx=out_conn_pos[0] + widths[output_dict["id"]] - margin,
cy=out_conn_pos[1] - margin,
r=5,
fill="#ffffff",
)
)
connectors.append(
svgfig.Line(adjusted[0], adjusted[1] - margin, in_coords[0] - 10, in_coords[1], arrow_end="true").SVG()
)
canvas.append(connectors)
canvas.append(boxes)
canvas.append(text)
width, height = (max_x + max_width + 50), max_y + 300
canvas["width"] = "%s px" % width
canvas["height"] = "%s px" % height
canvas["viewBox"] = "0 0 %s %s" % (width, height)
trans.response.set_content_type("image/svg+xml")
return canvas.standalone_xml()
def repository_dependencies(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, id)
if repository_metadata is None:
log.debug('Invalid repository_metadata id received: %s' % str(id))
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug(
'The repository_metadata record with id %s has no metadata.' %
str(id))
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
rd_tups = metadata['repository_dependencies'][
'repository_dependencies']
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision = rd_tup[0:4]
repository_dependency = repository_util.get_repository_by_name_and_owner(
trans.app, name, owner)
if repository_dependency is None:
log.dbug(
'Cannot locate repository dependency %s owned by %s.' %
(name, owner))
continue
repository_dependency_id = trans.security.encode_id(
repository_dependency.id)
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
if repository_dependency_repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(
trans.app, repository_dependency, changeset_revision)
if new_changeset_revision != changeset_revision:
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
repository_dependency_id,
new_changeset_revision)
changeset_revision = new_changeset_revision
else:
decoded_repository_dependency_id = trans.security.decode_id(
repository_dependency_id)
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
(decoded_repository_dependency_id, str(name), str(owner))
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
(str(changeset_revision), str(new_changeset_revision))
log.debug(debug_msg)
continue
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_dependency_dict = repository_dependency.to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[k] = v
repository_dependency_metadata_dict['url'] = web.url_for(
controller='repositories',
action='show',
id=repository_dependency_id)
repository_dependencies_dicts.append(
repository_dependency_metadata_dict)
return repository_dependencies_dicts
def generate_workflow_image(trans,
workflow_name,
repository_metadata_id=None,
repository_id=None):
"""
Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called
from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id
will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value.
"""
workflow_name = encoding_util.tool_shed_decode(workflow_name)
if trans.webapp.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans, repository_metadata_id)
repository_id = trans.security.encode_id(
repository_metadata.repository_id)
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id(trans, repository_id)
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata['workflows']:
workflow_dict = workflow_tup[1]
if workflow_dict['name'] == workflow_name:
break
if 'tools' in metadata:
tools_metadata = metadata['tools']
else:
tools_metadata = []
workflow, missing_tool_tups = get_workflow_from_dict(
trans=trans,
workflow_dict=workflow_dict,
tools_metadata=tools_metadata,
repository_id=repository_id,
changeset_revision=changeset_revision)
data = []
canvas = svgfig.canvas(
style=
"stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left"
)
text = svgfig.SVG("g")
connectors = svgfig.SVG("g")
boxes = svgfig.SVG("g")
svgfig.Text.defaults["font-size"] = "10px"
in_pos = {}
out_pos = {}
margin = 5
# Spacing between input/outputs.
line_px = 16
# Store px width for boxes of each step.
widths = {}
max_width, max_x, max_y = 0, 0, 0
for step in workflow.steps:
step.upgrade_messages = {}
module = module_factory.from_workflow_step(trans, repository_id,
changeset_revision,
tools_metadata, step)
tool_errors = module.type == 'tool' and not module.tool
module_data_inputs = get_workflow_data_inputs(step, module)
module_data_outputs = get_workflow_data_outputs(
step, module, workflow.steps)
step_dict = {
'id': step.order_index,
'data_inputs': module_data_inputs,
'data_outputs': module_data_outputs,
'position': step.position,
'tool_errors': tool_errors
}
input_conn_dict = {}
for conn in step.input_connections:
input_conn_dict[conn.input_name] = dict(
id=conn.output_step.order_index, output_name=conn.output_name)
step_dict['input_connections'] = input_conn_dict
data.append(step_dict)
x, y = step.position['left'], step.position['top']
count = 0
module_name = get_workflow_module_name(module, missing_tool_tups)
max_len = len(module_name) * 1.5
text.append(
svgfig.Text(x, y + 20, module_name, **{
"font-size": "14px"
}).SVG())
y += 45
for di in module_data_inputs:
cur_y = y + count * line_px
if step.order_index not in in_pos:
in_pos[step.order_index] = {}
in_pos[step.order_index][di['name']] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, di['label']).SVG())
count += 1
max_len = max(max_len, len(di['label']))
if len(module.get_data_inputs()) > 0:
y += 15
for do in module_data_outputs:
cur_y = y + count * line_px
if step.order_index not in out_pos:
out_pos[step.order_index] = {}
out_pos[step.order_index][do['name']] = (x, cur_y)
text.append(svgfig.Text(x, cur_y, do['name']).SVG())
count += 1
max_len = max(max_len, len(do['name']))
widths[step.order_index] = max_len * 5.5
max_x = max(max_x, step.position['left'])
max_y = max(max_y, step.position['top'])
max_width = max(max_width, widths[step.order_index])
for step_dict in data:
tool_unavailable = step_dict['tool_errors']
width = widths[step_dict['id']]
x, y = step_dict['position']['left'], step_dict['position']['top']
# Only highlight missing tools if displaying in the tool shed.
if trans.webapp.name == 'tool_shed' and tool_unavailable:
fill = "#EBBCB2"
else:
fill = "#EBD9B2"
boxes.append(
svgfig.Rect(x - margin, y, x + width - margin, y + 30,
fill=fill).SVG())
box_height = (len(step_dict['data_inputs']) +
len(step_dict['data_outputs'])) * line_px + margin
# Draw separator line.
if len(step_dict['data_inputs']) > 0:
box_height += 15
sep_y = y + len(step_dict['data_inputs']) * line_px + 40
text.append(
svgfig.Line(x - margin, sep_y, x + width - margin,
sep_y).SVG())
# Define an input/output box.
boxes.append(
svgfig.Rect(x - margin,
y + 30,
x + width - margin,
y + 30 + box_height,
fill="#ffffff").SVG())
for conn, output_dict in step_dict['input_connections'].iteritems():
in_coords = in_pos[step_dict['id']][conn]
# out_pos_index will be a step number like 1, 2, 3...
out_pos_index = output_dict['id']
# out_pos_name will be a string like 'o', 'o2', etc.
out_pos_name = output_dict['output_name']
if out_pos_index in out_pos:
# out_conn_index_dict will be something like:
# 7: {'o': (824.5, 618)}
out_conn_index_dict = out_pos[out_pos_index]
if out_pos_name in out_conn_index_dict:
out_conn_pos = out_pos[out_pos_index][out_pos_name]
else:
# Take any key / value pair available in out_conn_index_dict.
# A problem will result if the dictionary is empty.
if out_conn_index_dict.keys():
key = out_conn_index_dict.keys()[0]
out_conn_pos = out_pos[out_pos_index][key]
adjusted = (out_conn_pos[0] + widths[output_dict['id']],
out_conn_pos[1])
text.append(
svgfig.SVG("circle",
cx=out_conn_pos[0] + widths[output_dict['id']] -
margin,
cy=out_conn_pos[1] - margin,
r=5,
fill="#ffffff"))
connectors.append(
svgfig.Line(adjusted[0],
adjusted[1] - margin,
in_coords[0] - 10,
in_coords[1],
arrow_end="true").SVG())
canvas.append(connectors)
canvas.append(boxes)
canvas.append(text)
width, height = (max_x + max_width + 50), max_y + 300
canvas['width'] = "%s px" % width
canvas['height'] = "%s px" % height
canvas['viewBox'] = "0 0 %s %s" % (width, height)
trans.response.set_content_type("image/svg+xml")
return canvas.standalone_xml()
def repository_dependencies(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id(trans.app, id)
if repository_metadata is None:
log.debug('Invalid repository_metadata id received: %s' % str(id))
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug('The repository_metadata record with id %s has no metadata.' % str(id))
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
rd_tups = metadata['repository_dependencies']['repository_dependencies']
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision = rd_tup[0:4]
repository_dependency = repository_util.get_repository_by_name_and_owner(trans.app, name, owner)
if repository_dependency is None:
log.dbug('Cannot locate repository dependency %s owned by %s.' % (name, owner))
continue
repository_dependency_id = trans.security.encode_id(repository_dependency.id)
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app, repository_dependency_id, changeset_revision)
if repository_dependency_repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
repo = hg_util.get_repo_for_repository(trans.app,
repository=repository_dependency,
repo_path=None,
create=False)
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision(repository_dependency,
repo,
changeset_revision)
if new_changeset_revision != changeset_revision:
repository_dependency_repository_metadata = \
metadata_util.get_repository_metadata_by_changeset_revision(trans.app,
repository_dependency_id,
new_changeset_revision)
changeset_revision = new_changeset_revision
else:
decoded_repository_dependency_id = trans.security.decode_id(repository_dependency_id)
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
(decoded_repository_dependency_id, str(name), str(owner))
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
(str(changeset_revision), str(new_changeset_revision))
log.debug(debug_msg)
continue
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
repository_dependency_dict = repository_dependency.to_dict(view='element',
value_mapper=self.__get_value_mapper(trans))
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[k] = v
repository_dependency_metadata_dict['url'] = web.url_for(controller='repositories',
action='show',
id=repository_dependency_id)
repository_dependencies_dicts.append(repository_dependency_metadata_dict)
return repository_dependencies_dicts
