diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
index 5417e35ff2f1..40bdbcd59149 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js
@@ -98,12 +98,14 @@ var Tool = Backbone.View.extend({
__class__: "RuntimeValue"
};
input.is_workflow =
- (input.options && input.options.length == 0) || ["integer", "float"].indexOf(input.type) != -1;
+ (input.options && input.options.length === 0) || ["integer", "float"].indexOf(input.type) != -1;
}
}
});
Utils.deepeach(options.inputs, input => {
- input.type == "conditional" && (input.test_param.collapsible_value = undefined);
+ if (input.type === "conditional") {
+ input.test_param.collapsible_value = undefined;
+ }
});
_addSections(form);
_addLabelAnnotation(form);
@@ -151,181 +153,185 @@ function _addLabelAnnotation(form) {
});
}
-/** Builds all sub sections */
-function _addSections(form) {
- var options = form.model.attributes;
- var inputs = options.inputs;
- var datatypes = options.datatypes;
- var node = options.node;
- var workflow = options.workflow;
- var post_job_actions = node.post_job_actions;
- var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
-
- /** Visit input nodes and enrich by name/value pairs from server data */
- function visit(head, head_list) {
- head_list = head_list || [];
- head_list.push(head);
- for (var i in head.inputs) {
- var input = head.inputs[i];
- var action = input.action;
- if (action) {
- input.name = `pja__${output_id}__${input.action}`;
- if (input.pja_arg) {
- input.name += `__${input.pja_arg}`;
+/** Visit input nodes and enrich by name/value pairs from server data */
+function _visit(head, head_list, output_id, options) {
+ var post_job_actions = options.node.post_job_actions;
+ head_list = head_list || [];
+ head_list.push(head);
+ for (var i in head.inputs) {
+ var input = head.inputs[i];
+ var action = input.action;
+ if (action) {
+ input.name = `pja__${output_id}__${input.action}`;
+ if (input.pja_arg) {
+ input.name += `__${input.pja_arg}`;
+ }
+ if (input.payload) {
+ for (var p_id in input.payload) {
+ input.payload[`${input.name}__${p_id}`] = input.payload[p_id];
+ delete input.payload[p_id];
}
- if (input.payload) {
- for (var p_id in input.payload) {
- input.payload[`${input.name}__${p_id}`] = input.payload[p_id];
- delete input.payload[p_id];
- }
+ }
+ var d = post_job_actions[input.action + output_id];
+ if (d) {
+ for (var j in head_list) {
+ head_list[j].expanded = true;
}
- var d = post_job_actions[input.action + output_id];
- if (d) {
- for (var j in head_list) {
- head_list[j].expanded = true;
- }
- if (input.pja_arg) {
- input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;
- } else {
- input.value = "true";
- }
+ if (input.pja_arg) {
+ input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;
+ } else {
+ input.value = "true";
}
}
- input.inputs && visit(input, head_list.slice(0));
+ }
+ if (input.inputs) {
+ _visit(input, head_list.slice(0), output_id, options);
}
}
+}
- /** Builds sub section with step actions/annotation */
- function _makeSection(output_id, datatypes) {
- var extensions = [];
- var input_terminal_names = [];
- for (var key in datatypes) {
- extensions.push({ 0: datatypes[key], 1: datatypes[key] });
- }
- for (key in node.input_terminals) {
- input_terminal_names.push(node.input_terminals[key].name);
- }
- extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));
- extensions.unshift({
- 0: "Sequences",
- 1: "Sequences"
- });
- extensions.unshift({
- 0: "Roadmaps",
- 1: "Roadmaps"
- });
- extensions.unshift({
- 0: "Leave unchanged",
- 1: "__empty__"
- });
- var output;
- var input_config = {
- title: `Configure Output: '${output_id}'`,
- type: "section",
- flat: true,
- inputs: [
- {
- label: "Label",
- type: "text",
- value: ((output = node.getWorkflowOutput(output_id)) && output.label) || "",
- help:
- "This will provide a short name to describe the output - this must be unique across workflows.",
- onchange: function(new_value) {
- workflow.attemptUpdateOutputLabel(node, output_id, new_value);
- }
- },
- {
- action: "RenameDatasetAction",
- pja_arg: "newname",
- label: "Rename dataset",
- type: "text",
- value: "",
- ignore: "",
- help: `This action will rename the output dataset. Click here for more information. Valid inputs are: ${input_terminal_names.join(
- ", "
- )}.`
- },
- {
- action: "ChangeDatatypeAction",
- pja_arg: "newtype",
- label: "Change datatype",
- type: "select",
- ignore: "__empty__",
- value: "__empty__",
- options: extensions,
- help: "This action will change the datatype of the output to the indicated value."
- },
- {
- action: "TagDatasetAction",
- pja_arg: "tags",
- label: "Add Tags",
- type: "text",
- value: "",
- ignore: "",
- help: "This action will set tags for the dataset."
- },
- {
- action: "RemoveTagDatasetAction",
- pja_arg: "tags",
- label: "Remove Tags",
- type: "text",
- value: "",
- ignore: "",
- help: "This action will remove tags for the dataset."
- },
- {
- title: "Assign columns",
- type: "section",
- flat: true,
- inputs: [
- {
- action: "ColumnSetAction",
- pja_arg: "chromCol",
- label: "Chrom column",
- type: "integer",
- value: "",
- ignore: ""
- },
- {
- action: "ColumnSetAction",
- pja_arg: "startCol",
- label: "Start column",
- type: "integer",
- value: "",
- ignore: ""
- },
- {
- action: "ColumnSetAction",
- pja_arg: "endCol",
- label: "End column",
- type: "integer",
- value: "",
- ignore: ""
- },
- {
- action: "ColumnSetAction",
- pja_arg: "strandCol",
- label: "Strand column",
- type: "integer",
- value: "",
- ignore: ""
- },
- {
- action: "ColumnSetAction",
- pja_arg: "nameCol",
- label: "Name column",
- type: "integer",
- value: "",
- ignore: ""
- }
- ],
- help: "This action will set column assignments in the output dataset. Blank fields are ignored."
- }
- ]
- };
- visit(input_config);
- return input_config;
+/** Builds sub section with step actions/annotation */
+function _makeSection(output_id, options) {
+ var extensions = [];
+ var input_terminal_names = [];
+ var datatypes = options.datatypes;
+ var node = options.node;
+ var workflow = options.workflow;
+
+ for (var key in datatypes) {
+ extensions.push({ 0: datatypes[key], 1: datatypes[key] });
+ }
+ for (key in node.input_terminals) {
+ input_terminal_names.push(node.input_terminals[key].name);
}
+ extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));
+ extensions.unshift({
+ 0: "Sequences",
+ 1: "Sequences"
+ });
+ extensions.unshift({
+ 0: "Roadmaps",
+ 1: "Roadmaps"
+ });
+ extensions.unshift({
+ 0: "Leave unchanged",
+ 1: "__empty__"
+ });
+ var output;
+ var input_config = {
+ title: `Configure Output: '${output_id}'`,
+ type: "section",
+ flat: true,
+ inputs: [
+ {
+ label: "Label",
+ type: "text",
+ value: ((output = node.getWorkflowOutput(output_id)) && output.label) || "",
+ help: "This will provide a short name to describe the output - this must be unique across workflows.",
+ onchange: function(new_value) {
+ workflow.attemptUpdateOutputLabel(node, output_id, new_value);
+ }
+ },
+ {
+ action: "RenameDatasetAction",
+ pja_arg: "newname",
+ label: "Rename dataset",
+ type: "text",
+ value: "",
+ ignore: "",
+ help: `This action will rename the output dataset. Click here for more information. Valid inputs are: ${input_terminal_names.join(
+ ", "
+ )}.`
+ },
+ {
+ action: "ChangeDatatypeAction",
+ pja_arg: "newtype",
+ label: "Change datatype",
+ type: "select",
+ ignore: "__empty__",
+ value: "__empty__",
+ options: extensions,
+ help: "This action will change the datatype of the output to the indicated value."
+ },
+ {
+ action: "TagDatasetAction",
+ pja_arg: "tags",
+ label: "Add Tags",
+ type: "text",
+ value: "",
+ ignore: "",
+ help: "This action will set tags for the dataset."
+ },
+ {
+ action: "RemoveTagDatasetAction",
+ pja_arg: "tags",
+ label: "Remove Tags",
+ type: "text",
+ value: "",
+ ignore: "",
+ help: "This action will remove tags for the dataset."
+ },
+ {
+ title: "Assign columns",
+ type: "section",
+ flat: true,
+ inputs: [
+ {
+ action: "ColumnSetAction",
+ pja_arg: "chromCol",
+ label: "Chrom column",
+ type: "integer",
+ value: "",
+ ignore: ""
+ },
+ {
+ action: "ColumnSetAction",
+ pja_arg: "startCol",
+ label: "Start column",
+ type: "integer",
+ value: "",
+ ignore: ""
+ },
+ {
+ action: "ColumnSetAction",
+ pja_arg: "endCol",
+ label: "End column",
+ type: "integer",
+ value: "",
+ ignore: ""
+ },
+ {
+ action: "ColumnSetAction",
+ pja_arg: "strandCol",
+ label: "Strand column",
+ type: "integer",
+ value: "",
+ ignore: ""
+ },
+ {
+ action: "ColumnSetAction",
+ pja_arg: "nameCol",
+ label: "Name column",
+ type: "integer",
+ value: "",
+ ignore: ""
+ }
+ ],
+ help: "This action will set column assignments in the output dataset. Blank fields are ignored."
+ }
+ ]
+ };
+ _visit(input_config, [], output_id, options);
+ return input_config;
+}
+
+/** Builds all sub sections */
+function _addSections(form) {
+ var options = form.model.attributes;
+ var inputs = options.inputs;
+ var node = options.node;
+ var post_job_actions = node.post_job_actions;
+ var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
if (output_id) {
inputs.push({
@@ -349,7 +355,7 @@ function _addSections(form) {
"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."
});
for (var i in node.output_terminals) {
- inputs.push(_makeSection(i, datatypes));
+ inputs.push(_makeSection(i, options));
}
}
}
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 38fad8b1dfc0..a14919d35e32 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -14,7 +14,7 @@ var Node = Backbone.Model.extend({
});
},
isWorkflowOutput: function(outputName) {
- return this.getWorkflowOutput(outputName) != undefined;
+ return this.getWorkflowOutput(outputName) !== undefined;
},
removeWorkflowOutput: function(outputName) {
while (this.isWorkflowOutput(outputName)) {
@@ -25,7 +25,7 @@ var Node = Backbone.Model.extend({
if (!this.isWorkflowOutput(outputName)) {
var output = { output_name: outputName };
if (label) {
- output["label"] = label;
+ output.label = label;
}
this.workflow_outputs.push(output);
return true;
@@ -37,8 +37,8 @@ var Node = Backbone.Model.extend({
var oldLabel = null;
if (this.isWorkflowOutput(outputName)) {
var workflowOutput = this.getWorkflowOutput(outputName);
- oldLabel = workflowOutput["label"];
- workflowOutput["label"] = label;
+ oldLabel = workflowOutput.label;
+ workflowOutput.label = label;
changed = oldLabel != label;
} else {
changed = this.addWorkflowOutput(outputName, label);
@@ -239,7 +239,7 @@ var Node = Backbone.Model.extend({
this.config_form = data.config_form;
this.tool_version = this.config_form && this.config_form.version;
this.errors = data.errors;
- this.annotation = data["annotation"];
+ this.annotation = data.annotation;
this.label = data.label;
if ("post_job_actions" in data) {
// Won't be present in response for data inputs
@@ -271,7 +271,7 @@ var Node = Backbone.Model.extend({
old_body.replaceWith(new_body);
if ("workflow_outputs" in data) {
// Won't be present in response for data inputs
- this.workflow_outputs = workflow_outputs ? workflow_outputs : [];
+ this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];
}
// If active, reactivate with new config_form
this.markChanged();
diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 56437b395b6b..d1b1500c955e 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -146,6 +146,7 @@
+
@@ -677,6 +678,7 @@
+
diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index f5814dff02ce..1d69cbba5fb0 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -25,7 +25,6 @@
from galaxy.util.checkers import is_bz2, is_gzip
from . import data, dataproviders
-
log = logging.getLogger(__name__)
# Currently these supported binary data types must be manually set on upload
@@ -890,6 +889,60 @@ def display_peek(self, dataset):
return "Biom2 (HDF5) file (%s)" % (nice_size(dataset.get_size()))
+class Cool(H5):
+ """
+ Class describing the cool format (https://github.com/mirnylab/cooler)
+ """
+
+ file_ext = "cool"
+
+ def sniff(self, filename):
+ """
+ >>> from galaxy.datatypes.sniff import get_test_fname
+ >>> fname = get_test_fname( 'matrix.cool' )
+ >>> Cool().sniff( fname )
+ True
+ >>> fname = get_test_fname( 'test.mz5' )
+ >>> Cool().sniff( fname )
+ False
+ >>> fname = get_test_fname( 'wiggle.wig' )
+ >>> Cool().sniff( fname )
+ False
+ >>> fname = get_test_fname( 'biom2_sparse_otu_table_hdf5.biom' )
+ >>> Cool().sniff( fname )
+ False
+ """
+
+ MAGIC = "HDF5::Cooler"
+ URL = "https://github.com/mirnylab/cooler"
+
+ if super(Cool, self).sniff(filename):
+ keys = ['chroms', 'bins', 'pixels', 'indexes']
+ with h5py.File(filename, 'r') as handle:
+ fmt = handle.attrs.get('format', None)
+ url = handle.attrs.get('format-url', None)
+ if fmt == MAGIC or url == URL:
+ if not all(name in handle.keys() for name in keys):
+ return False
+ return True
+ return False
+
+ def set_peek(self, dataset, is_multi_byte=False):
+ if not dataset.dataset.purged:
+ dataset.peek = "Cool (HDF5) file for storing genomic interaction data."
+ dataset.blurb = nice_size(dataset.get_size())
+ else:
+ dataset.peek = 'file does not exist'
+ dataset.blurb = 'file purged from disk'
+
+ def display_peek(self, dataset):
+ try:
+ return dataset.peek
+ except Exception:
+ return "Cool (HDF5) file (%s)." % (nice_size(dataset.get_size()))
+
+
+Binary.register_sniffable_binary_format("cool", "cool", Cool)
Binary.register_sniffable_binary_format("biom2", "biom2", Biom2)
Binary.register_sniffable_binary_format("h5", "h5", H5)
diff --git a/lib/galaxy/datatypes/test/matrix.cool b/lib/galaxy/datatypes/test/matrix.cool
new file mode 100644
index 000000000000..91ec17bb85ff
Binary files /dev/null and b/lib/galaxy/datatypes/test/matrix.cool differ
diff --git a/lib/galaxy/jobs/metrics/instrumenters/core.py b/lib/galaxy/jobs/metrics/instrumenters/core.py
index 86c923d69b74..c17af4bc55d4 100644
--- a/lib/galaxy/jobs/metrics/instrumenters/core.py
+++ b/lib/galaxy/jobs/metrics/instrumenters/core.py
@@ -8,6 +8,7 @@
log = logging.getLogger(__name__)
GALAXY_SLOTS_KEY = "galaxy_slots"
+GALAXY_MEMORY_MB_KEY = "galaxy_memory_mb"
START_EPOCH_KEY = "start_epoch"
END_EPOCH_KEY = "end_epoch"
RUNTIME_SECONDS_KEY = "runtime_seconds"
@@ -19,6 +20,8 @@ def format(self, key, value):
value = int(value)
if key == GALAXY_SLOTS_KEY:
return ("Cores Allocated", "%d" % value)
+ elif key == GALAXY_MEMORY_MB_KEY:
+ return ("Memory Allocated (MB)", "%d" % value)
elif key == RUNTIME_SECONDS_KEY:
return ("Job Runtime (Wall Clock)", formatting.seconds_to_str(value))
else:
@@ -40,6 +43,7 @@ def __init__(self, **kwargs):
def pre_execute_instrument(self, job_directory):
commands = []
commands.append(self.__record_galaxy_slots_command(job_directory))
+ commands.append(self.__record_galaxy_memory_mb_command(job_directory))
commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "start"))
return commands
@@ -50,9 +54,11 @@ def post_execute_instrument(self, job_directory):
def job_properties(self, job_id, job_directory):
galaxy_slots_file = self.__galaxy_slots_file(job_directory)
+ galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
properties = {}
properties[GALAXY_SLOTS_KEY] = self.__read_integer(galaxy_slots_file)
+ properties[GALAXY_MEMORY_MB_KEY] = self.__read_integer(galaxy_memory_mb_file)
start = self.__read_seconds_since_epoch(job_directory, "start")
end = self.__read_seconds_since_epoch(job_directory, "end")
if start is not None and end is not None:
@@ -65,6 +71,10 @@ def __record_galaxy_slots_command(self, job_directory):
galaxy_slots_file = self.__galaxy_slots_file(job_directory)
return '''echo "$GALAXY_SLOTS" > '%s' ''' % galaxy_slots_file
+ def __record_galaxy_memory_mb_command(self, job_directory):
+ galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
+ return '''echo "$GALAXY_MEMORY_MB" > '%s' ''' % galaxy_memory_mb_file
+
def __record_seconds_since_epoch_to_file(self, job_directory, name):
path = self._instrument_file_path(job_directory, "epoch_%s" % name)
return 'date +"%s" > ' + path
@@ -76,6 +86,9 @@ def __read_seconds_since_epoch(self, job_directory, name):
def __galaxy_slots_file(self, job_directory):
return self._instrument_file_path(job_directory, "galaxy_slots")
+ def __galaxy_memory_mb_file(self, job_directory):
+ return self._instrument_file_path(job_directory, "galaxy_memory_mb")
+
def __read_integer(self, path):
value = None
try:
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 7f388828137f..0e6420a43c31 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -187,14 +187,17 @@ def update(self, trans, instance_type, id, payload):
changed = self._set_from_dict(trans, dataset_collection_instance, payload)
return changed
- def copy(self, trans, parent, source, encoded_source_id):
+ def copy(self, trans, parent, source, encoded_source_id, copy_elements=False):
"""
PRECONDITION: security checks on ability to add to parent occurred
during load.
"""
assert source == "hdca" # for now
source_hdca = self.__get_history_collection_instance(trans, encoded_source_id)
- new_hdca = source_hdca.copy()
+ copy_kwds = {}
+ if copy_elements:
+ copy_kwds["element_destination"] = parent
+ new_hdca = source_hdca.copy(**copy_kwds)
tags_str = self.tag_manager.get_tags_str(source_hdca.tags)
self.tag_manager.apply_item_tags(trans.get_user(), new_hdca, tags_str)
parent.add_dataset_collection(new_hdca)
diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py
index 63843062b991..25f4f8d9e96a 100644
--- a/lib/galaxy/webapps/galaxy/api/configuration.py
+++ b/lib/galaxy/webapps/galaxy/api/configuration.py
@@ -90,6 +90,18 @@ def dynamic_tool_confs(self, trans):
confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True)
return map(_tool_conf_to_dict, confs)
+ @expose_api
+ @require_admin
+ def decode_id(self, trans, encoded_id, **kwds):
+ """Decode a given id."""
+ decoded_id = None
+ # Handle the special case for library folders
+ if ((len(encoded_id) % 16 == 1) and encoded_id.startswith('F')):
+ decoded_id = trans.security.decode_id(encoded_id[1:])
+ else:
+ decoded_id = trans.security.decode_id(encoded_id)
+ return {"decoded_id": decoded_id}
+
@expose_api
@require_admin
def tool_lineages(self, trans):
diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py
index 673a217b7270..f881fd8822fe 100644
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -252,6 +252,9 @@ def create(self, trans, history_id, payload, **kwd):
copy from history dataset collection (for type 'dataset_collection')
'source' = 'hdca'
'content' = [the encoded id from the HDCA]
+ 'copy_elements' = Copy child HDAs into the target history as well,
+ defaults to False but this is less than ideal and may
+ be changed in future releases.
create new history dataset collection (for type 'dataset_collection')
'source' = 'new_collection' (default 'source' if type is
@@ -434,11 +437,13 @@ def __create_dataset_collection(self, trans, history, payload, **kwd):
content = payload.get('content', None)
if content is None:
raise exceptions.RequestParameterMissingException("'content' id of target to copy is missing")
+ copy_elements = payload.get('copy_elements', False)
dataset_collection_instance = service.copy(
trans=trans,
parent=history,
source="hdca",
encoded_source_id=content,
+ copy_elements=copy_elements,
)
else:
message = "Invalid 'source' parameter in request %s" % source
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 3e0c2fc43a95..b50e489038fe 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -341,6 +341,10 @@ def populate_api_routes(webapp, app):
"/api/whoami", controller='configuration',
action='whoami',
conditions=dict(method=["GET"]))
+ webapp.mapper.connect("api_decode",
+ "/api/configuration/decode/{encoded_id}", controller='configuration',
+ action='decode_id',
+ conditions=dict(method=["GET"]))
webapp.mapper.resource('datatype',
'datatypes',
path_prefix='/api',
diff --git a/lib/galaxy/workflow/scheduling_manager.py b/lib/galaxy/workflow/scheduling_manager.py
index a815f6123238..8ce11db5601b 100644
--- a/lib/galaxy/workflow/scheduling_manager.py
+++ b/lib/galaxy/workflow/scheduling_manager.py
@@ -204,10 +204,10 @@ def __attempt_schedule(self, invocation_id, workflow_scheduler):
sa_session = self.app.model.context
workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
- if not workflow_invocation or not workflow_invocation.active:
- return False
-
try:
+ if not workflow_invocation or not workflow_invocation.active:
+ return False
+
# This ensures we're only ever working on the 'first' active
# workflow invocation in a given history, to force sequential
# activation.
@@ -220,6 +220,8 @@ def __attempt_schedule(self, invocation_id, workflow_scheduler):
# TODO: eventually fail this - or fail it right away?
log.exception("Exception raised while attempting to schedule workflow request.")
return False
+ finally:
+ sa_session.expunge_all()
# A workflow was obtained and scheduled...
return True
diff --git a/run_tests.sh b/run_tests.sh
index f03420f3ae5a..cbb7d3207a8e 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -76,6 +76,13 @@ Run all selenium tests (Under Linux using Docker):
Run a specific selenium test (under Linux or Mac OS X after installing geckodriver or chromedriver):
./run_tests.sh -selenium test/selenium_tests/test_registration.py:RegistrationTestCase.test_reregister_username_fails
+Run a selenium test against a running server while watching client (fastest iterating on client tests):
+ ./run.sh & # run Galaxy on 8080
+ make client-watch & # watch for client changes
+ export GALAXY_TEST_EXTERNAL=http://localhost:8080/ # Target tests at server.
+ . .venv/bin/activate # source the virtualenv so can skip run_tests.sh.
+ nosetests test/selenium_tests/test_workflow_editor.py:WorkflowEditorTestCase.test_data_input
+
Note About Selenium Tests:
If using a local selenium driver such as a Chrome or Firefox based one
diff --git a/static/maps/mvc/workflow/workflow-forms.js.map b/static/maps/mvc/workflow/workflow-forms.js.map
index 6dfe075acf1a..ac3d4d2d5bbc 100644
--- a/static/maps/mvc/workflow/workflow-forms.js.map
+++ b/static/maps/mvc/workflow/workflow-forms.js.map
@@ -1 +1 @@
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Utils from \"utils/utils\";\nimport Form from \"mvc/form/form-view\";\nimport ToolFormBase from \"mvc/tool/tool-form-base\";\n/** Default form wrapper for non-tool modules in the workflow editor. */\nvar Default = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new Form(\n Utils.merge(options, {\n onchange: function() {\n Utils.request({\n type: \"POST\",\n url: `${Galaxy.root}api/workflows/build_module`,\n data: {\n id: node.id,\n type: node.type,\n content_id: node.content_id,\n inputs: self.form.data.create()\n },\n success: function(data) {\n node.update_field_data(data);\n }\n });\n }\n })\n );\n _addLabelAnnotation(this.form);\n this.form.render();\n }\n});\n\n/** Tool form wrapper for the workflow editor. */\nvar Tool = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new ToolFormBase(\n Utils.merge(options, {\n text_enable: \"Set in Advance\",\n text_disable: \"Set at Runtime\",\n narrow: true,\n initial_errors: true,\n cls: \"ui-portlet-narrow\",\n initialmodel: function(process, form) {\n self._customize(form);\n process.resolve();\n },\n buildmodel: function(process, form) {\n form.model.get(\"postchange\")(process, form);\n },\n postchange: function(process, form) {\n var options = form.model.attributes;\n var current_state = {\n tool_id: options.id,\n tool_version: options.version,\n type: \"tool\",\n inputs: $.extend(true, {}, form.data.create())\n };\n Galaxy.emit.debug(\"tool-form-workflow::postchange()\", \"Sending current state.\", current_state);\n Utils.request({\n type: \"POST\",\n url: `${Galaxy.root}api/workflows/build_module`,\n data: current_state,\n success: function(data) {\n form.model.set(data.config_form);\n self._customize(form);\n form.update(data.config_form);\n form.errors(data.config_form);\n // This hasn't modified the workflow, just returned\n // module information for the tool to 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Annotations are available when a workflow is viewed.\"\n });\n options.inputs.unshift({\n type: \"text\",\n name: \"__label\",\n label: \"Label\",\n value: node.label,\n help: \"Add a step label.\",\n fixed: true,\n onchange: function(new_label) {\n var duplicate = false;\n for (var i in workflow.nodes) {\n var n = workflow.nodes[i];\n if (n.label && n.label == new_label && n.id != node.id) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match(\"__label\");\n var input_element = form.element_list[input_id];\n input_element.model.set(\n \"error_text\",\n duplicate && \"Duplicate label. Please fix this before saving the workflow.\"\n );\n form.trigger(\"change\");\n }\n });\n}\n\n/** Builds all sub sections */\nfunction _addSections(form) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n var post_job_actions = node.post_job_actions;\n var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];\n\n /** Visit input nodes and enrich by name/value pairs from server data */\n function visit(head, head_list) {\n head_list = head_list || [];\n head_list.push(head);\n for (var i in head.inputs) {\n var input = head.inputs[i];\n var action = input.action;\n if (action) {\n input.name = `pja__${output_id}__${input.action}`;\n if (input.pja_arg) {\n input.name += `__${input.pja_arg}`;\n }\n if (input.payload) {\n for (var p_id in input.payload) {\n input.payload[`${input.name}__${p_id}`] = input.payload[p_id];\n delete input.payload[p_id];\n }\n }\n var d = post_job_actions[input.action + output_id];\n if (d) {\n for (var j in head_list) {\n head_list[j].expanded = true;\n }\n if (input.pja_arg) {\n input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;\n } else {\n input.value = \"true\";\n }\n }\n }\n input.inputs && visit(input, head_list.slice(0));\n }\n }\n\n /** Builds sub section with step actions/annotation */\n function _makeSection(output_id, datatypes) {\n var extensions = [];\n var input_terminal_names = [];\n for (var key in datatypes) {\n extensions.push({ 0: datatypes[key], 1: datatypes[key] });\n }\n for (key in node.input_terminals) {\n input_terminal_names.push(node.input_terminals[key].name);\n }\n extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));\n extensions.unshift({\n 0: \"Sequences\",\n 1: \"Sequences\"\n });\n extensions.unshift({\n 0: \"Roadmaps\",\n 1: \"Roadmaps\"\n });\n extensions.unshift({\n 0: \"Leave unchanged\",\n 1: \"__empty__\"\n });\n var output;\n var input_config = {\n title: `Configure Output: '${output_id}'`,\n type: \"section\",\n flat: true,\n inputs: [\n {\n label: \"Label\",\n type: \"text\",\n value: ((output = node.getWorkflowOutput(output_id)) && output.label) || \"\",\n help:\n \"This will provide a short name to describe the output - this must be unique across workflows.\",\n onchange: function(new_value) {\n workflow.attemptUpdateOutputLabel(node, output_id, new_value);\n }\n },\n {\n action: \"RenameDatasetAction\",\n pja_arg: \"newname\",\n label: \"Rename dataset\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: `This action will rename the output dataset. Click here for more information. Valid inputs are: ${input_terminal_names.join(\n \", \"\n )}.`\n },\n {\n action: \"ChangeDatatypeAction\",\n pja_arg: \"newtype\",\n label: \"Change datatype\",\n type: \"select\",\n ignore: \"__empty__\",\n value: \"__empty__\",\n options: extensions,\n help: \"This action will change the datatype of the output to the indicated value.\"\n },\n {\n action: \"TagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Add Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will set tags for the dataset.\"\n },\n {\n action: \"RemoveTagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Remove Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will remove tags for the dataset.\"\n },\n {\n title: \"Assign columns\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n action: \"ColumnSetAction\",\n pja_arg: \"chromCol\",\n label: \"Chrom column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"startCol\",\n label: \"Start column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"endCol\",\n label: \"End column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"strandCol\",\n label: \"Strand column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"nameCol\",\n label: \"Name column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n }\n ],\n help: \"This action will set column assignments in the output dataset. Blank fields are ignored.\"\n }\n ]\n };\n visit(input_config);\n return input_config;\n }\n\n if (output_id) {\n inputs.push({\n name: `pja__${output_id}__EmailAction`,\n label: \"Email notification\",\n type: \"boolean\",\n value: String(Boolean(post_job_actions[`EmailAction${output_id}`])),\n ignore: \"false\",\n help: \"An email notification will be sent when the job has completed.\",\n payload: {\n host: window.location.host\n }\n });\n inputs.push({\n name: `pja__${output_id}__DeleteIntermediatesAction`,\n label: \"Output cleanup\",\n type: \"boolean\",\n value: String(Boolean(post_job_actions[`DeleteIntermediatesAction${output_id}`])),\n ignore: \"false\",\n help:\n \"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.\"\n });\n for (var i in node.output_terminals) {\n inputs.push(_makeSection(i, datatypes));\n }\n }\n}\n\nexport default {\n Default: Default,\n Tool: Tool\n};\n"]}
\ No newline at end of file
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Utils from \"utils/utils\";\nimport Form from \"mvc/form/form-view\";\nimport ToolFormBase from \"mvc/tool/tool-form-base\";\n/** Default form wrapper for non-tool modules in the workflow editor. */\nvar Default = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new Form(\n Utils.merge(options, {\n onchange: function() {\n Utils.request({\n type: \"POST\",\n url: `${Galaxy.root}api/workflows/build_module`,\n data: {\n id: node.id,\n type: node.type,\n content_id: node.content_id,\n inputs: self.form.data.create()\n },\n success: function(data) {\n node.update_field_data(data);\n }\n });\n }\n })\n );\n _addLabelAnnotation(this.form);\n this.form.render();\n }\n});\n\n/** Tool form wrapper for the workflow editor. */\nvar Tool = Backbone.View.extend({\n initialize: function(options) {\n var self = this;\n var node = options.node;\n this.form = new ToolFormBase(\n Utils.merge(options, {\n text_enable: \"Set in Advance\",\n text_disable: \"Set at Runtime\",\n narrow: true,\n initial_errors: true,\n cls: \"ui-portlet-narrow\",\n initialmodel: function(process, form) {\n self._customize(form);\n process.resolve();\n },\n buildmodel: function(process, form) {\n form.model.get(\"postchange\")(process, form);\n },\n postchange: function(process, form) {\n var options = form.model.attributes;\n var current_state = {\n tool_id: options.id,\n tool_version: options.version,\n type: \"tool\",\n inputs: $.extend(true, {}, form.data.create())\n };\n Galaxy.emit.debug(\"tool-form-workflow::postchange()\", \"Sending current state.\", current_state);\n Utils.request({\n type: \"POST\",\n url: `${Galaxy.root}api/workflows/build_module`,\n data: current_state,\n success: function(data) {\n form.model.set(data.config_form);\n self._customize(form);\n form.update(data.config_form);\n form.errors(data.config_form);\n // This hasn't modified the workflow, just returned\n // module information for the tool to update the workflow\n // state stored on the client with. User needs to save\n // for this to take effect.\n node.update_field_data(data);\n Galaxy.emit.debug(\"tool-form-workflow::postchange()\", \"Received new model.\", data);\n process.resolve();\n },\n error: function(response) {\n Galaxy.emit.debug(\"tool-form-workflow::postchange()\", \"Refresh request failed.\", response);\n process.reject();\n }\n });\n }\n })\n );\n },\n\n _customize: function(form) {\n var options = form.model.attributes;\n Utils.deepeach(options.inputs, input => {\n if (input.type) {\n if ([\"data\", \"data_collection\"].indexOf(input.type) != -1) {\n input.type = \"hidden\";\n input.info = `Data input '${input.name}' (${Utils.textify(input.extensions)})`;\n input.value = { __class__: \"RuntimeValue\" };\n } else if (!input.fixed) {\n input.collapsible_value = {\n __class__: \"RuntimeValue\"\n };\n input.is_workflow =\n (input.options && input.options.length === 0) || [\"integer\", \"float\"].indexOf(input.type) != -1;\n }\n }\n });\n Utils.deepeach(options.inputs, input => {\n if (input.type === \"conditional\") {\n input.test_param.collapsible_value = undefined;\n }\n });\n _addSections(form);\n _addLabelAnnotation(form);\n }\n});\n\n/** Augments the module form definition by adding label and annotation fields */\nfunction _addLabelAnnotation(form) {\n var options = form.model.attributes;\n var workflow = options.workflow;\n var node = options.node;\n options.inputs.unshift({\n type: \"text\",\n name: \"__annotation\",\n label: \"Annotation\",\n fixed: true,\n value: node.annotation,\n area: true,\n help: \"Add an annotation or notes to this step. Annotations are available when a workflow is viewed.\"\n });\n options.inputs.unshift({\n type: \"text\",\n name: \"__label\",\n label: \"Label\",\n value: node.label,\n help: \"Add a step label.\",\n fixed: true,\n onchange: function(new_label) {\n var duplicate = false;\n for (var i in workflow.nodes) {\n var n = workflow.nodes[i];\n if (n.label && n.label == new_label && n.id != node.id) {\n duplicate = true;\n break;\n }\n }\n var input_id = form.data.match(\"__label\");\n var input_element = form.element_list[input_id];\n input_element.model.set(\n \"error_text\",\n duplicate && \"Duplicate label. Please fix this before saving the workflow.\"\n );\n form.trigger(\"change\");\n }\n });\n}\n\n/** Visit input nodes and enrich by name/value pairs from server data */\nfunction _visit(head, head_list, output_id, options) {\n var post_job_actions = options.node.post_job_actions;\n head_list = head_list || [];\n head_list.push(head);\n for (var i in head.inputs) {\n var input = head.inputs[i];\n var action = input.action;\n if (action) {\n input.name = `pja__${output_id}__${input.action}`;\n if (input.pja_arg) {\n input.name += `__${input.pja_arg}`;\n }\n if (input.payload) {\n for (var p_id in input.payload) {\n input.payload[`${input.name}__${p_id}`] = input.payload[p_id];\n delete input.payload[p_id];\n }\n }\n var d = post_job_actions[input.action + output_id];\n if (d) {\n for (var j in head_list) {\n head_list[j].expanded = true;\n }\n if (input.pja_arg) {\n input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;\n } else {\n input.value = \"true\";\n }\n }\n }\n if (input.inputs) {\n _visit(input, head_list.slice(0), output_id, options);\n }\n }\n}\n\n/** Builds sub section with step actions/annotation */\nfunction _makeSection(output_id, options) {\n var extensions = [];\n var input_terminal_names = [];\n var datatypes = options.datatypes;\n var node = options.node;\n var workflow = options.workflow;\n\n for (var key in datatypes) {\n extensions.push({ 0: datatypes[key], 1: datatypes[key] });\n }\n for (key in node.input_terminals) {\n input_terminal_names.push(node.input_terminals[key].name);\n }\n extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));\n extensions.unshift({\n 0: \"Sequences\",\n 1: \"Sequences\"\n });\n extensions.unshift({\n 0: \"Roadmaps\",\n 1: \"Roadmaps\"\n });\n extensions.unshift({\n 0: \"Leave unchanged\",\n 1: \"__empty__\"\n });\n var output;\n var input_config = {\n title: `Configure Output: '${output_id}'`,\n type: \"section\",\n flat: true,\n inputs: [\n {\n label: \"Label\",\n type: \"text\",\n value: ((output = node.getWorkflowOutput(output_id)) && output.label) || \"\",\n help: \"This will provide a short name to describe the output - this must be unique across workflows.\",\n onchange: function(new_value) {\n workflow.attemptUpdateOutputLabel(node, output_id, new_value);\n }\n },\n {\n action: \"RenameDatasetAction\",\n pja_arg: \"newname\",\n label: \"Rename dataset\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: `This action will rename the output dataset. Click here for more information. Valid inputs are: ${input_terminal_names.join(\n \", \"\n )}.`\n },\n {\n action: \"ChangeDatatypeAction\",\n pja_arg: \"newtype\",\n label: \"Change datatype\",\n type: \"select\",\n ignore: \"__empty__\",\n value: \"__empty__\",\n options: extensions,\n help: \"This action will change the datatype of the output to the indicated value.\"\n },\n {\n action: \"TagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Add Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will set tags for the dataset.\"\n },\n {\n action: \"RemoveTagDatasetAction\",\n pja_arg: \"tags\",\n label: \"Remove Tags\",\n type: \"text\",\n value: \"\",\n ignore: \"\",\n help: \"This action will remove tags for the dataset.\"\n },\n {\n title: \"Assign columns\",\n type: \"section\",\n flat: true,\n inputs: [\n {\n action: \"ColumnSetAction\",\n pja_arg: \"chromCol\",\n label: \"Chrom column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"startCol\",\n label: \"Start column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"endCol\",\n label: \"End column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"strandCol\",\n label: \"Strand column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n },\n {\n action: \"ColumnSetAction\",\n pja_arg: \"nameCol\",\n label: \"Name column\",\n type: \"integer\",\n value: \"\",\n ignore: \"\"\n }\n ],\n help: \"This action will set column assignments in the output dataset. Blank fields are ignored.\"\n }\n ]\n };\n _visit(input_config, [], output_id, options);\n return input_config;\n}\n\n/** Builds all sub sections */\nfunction _addSections(form) {\n var options = form.model.attributes;\n var inputs = options.inputs;\n var node = options.node;\n var post_job_actions = node.post_job_actions;\n var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];\n\n if (output_id) {\n inputs.push({\n name: `pja__${output_id}__EmailAction`,\n label: \"Email notification\",\n type: \"boolean\",\n value: String(Boolean(post_job_actions[`EmailAction${output_id}`])),\n ignore: \"false\",\n help: \"An email notification will be sent when the job has completed.\",\n payload: {\n host: window.location.host\n }\n });\n inputs.push({\n name: `pja__${output_id}__DeleteIntermediatesAction`,\n label: \"Output cleanup\",\n type: \"boolean\",\n value: String(Boolean(post_job_actions[`DeleteIntermediatesAction${output_id}`])),\n ignore: \"false\",\n help:\n \"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs.\"\n });\n for (var i in node.output_terminals) {\n inputs.push(_makeSection(i, options));\n }\n }\n}\n\nexport default {\n Default: Default,\n Tool: Tool\n};\n"]}
\ No newline at end of file
diff --git a/static/maps/mvc/workflow/workflow-node.js.map b/static/maps/mvc/workflow/workflow-node.js.map
index afff34177b71..8252b1ff8638 100644
--- a/static/maps/mvc/workflow/workflow-node.js.map
+++ b/static/maps/mvc/workflow/workflow-node.js.map
@@ -1 +1 @@
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NodeView from \"mvc/workflow/workflow-view-node\";\nvar Node = Backbone.Model.extend({\n initialize: function(app, attr) {\n this.app = app;\n this.element = attr.element;\n this.input_terminals = {};\n this.output_terminals = {};\n this.errors = {};\n this.workflow_outputs = [];\n },\n getWorkflowOutput: function(outputName) {\n return _.findWhere(this.workflow_outputs, {\n output_name: outputName\n });\n },\n isWorkflowOutput: function(outputName) {\n return this.getWorkflowOutput(outputName) != undefined;\n },\n removeWorkflowOutput: function(outputName) {\n while (this.isWorkflowOutput(outputName)) {\n this.workflow_outputs.splice(this.getWorkflowOutput(outputName), 1);\n }\n },\n addWorkflowOutput: function(outputName, label) {\n if (!this.isWorkflowOutput(outputName)) {\n var output = { output_name: outputName };\n if (label) {\n output[\"label\"] = label;\n }\n this.workflow_outputs.push(output);\n return true;\n }\n return false;\n },\n labelWorkflowOutput: function(outputName, label) {\n var changed = false;\n var oldLabel = null;\n if (this.isWorkflowOutput(outputName)) {\n var workflowOutput = this.getWorkflowOutput(outputName);\n oldLabel = workflowOutput[\"label\"];\n workflowOutput[\"label\"] = label;\n changed = oldLabel != label;\n } else {\n changed = this.addWorkflowOutput(outputName, label);\n }\n if (changed) {\n this.app.workflow.updateOutputLabel(oldLabel, label);\n this.markChanged();\n this.nodeView.redrawWorkflowOutputs();\n }\n return changed;\n },\n connectedOutputTerminals: function() {\n return this._connectedTerminals(this.output_terminals);\n },\n _connectedTerminals: function(terminals) {\n var connectedTerminals = [];\n $.each(terminals, (_, t) => {\n if (t.connectors.length > 0) {\n connectedTerminals.push(t);\n }\n });\n return connectedTerminals;\n },\n hasConnectedOutputTerminals: function() {\n // return this.connectedOutputTerminals().length > 0; <- optimized this\n var outputTerminals = this.output_terminals;\n for (var 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},\n _mappedTerminals: function(terminals) {\n var mappedTerminals = [];\n $.each(terminals, (_, t) => {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n mappedTerminals.push(t);\n }\n });\n return mappedTerminals;\n },\n hasMappedOverInputTerminals: function() {\n var found = false;\n _.each(this.input_terminals, t => {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n found = true;\n }\n });\n return found;\n },\n redraw: function() {\n $.each(this.input_terminals, (_, t) => {\n t.redraw();\n });\n $.each(this.output_terminals, (_, t) => {\n t.redraw();\n });\n },\n destroy: function() {\n $.each(this.input_terminals, (k, t) => {\n t.destroy();\n });\n $.each(this.output_terminals, (k, t) => {\n t.destroy();\n });\n this.app.workflow.remove_node(this);\n $(this.element).remove();\n },\n make_active: function() {\n $(this.element).addClass(\"toolForm-active\");\n },\n make_inactive: function() {\n // Keep inactive nodes stacked from most to least recently active\n // by moving element to the end of parent's node list\n var element = this.element.get(0);\n (p => {\n p.removeChild(element);\n p.appendChild(element);\n })(element.parentNode);\n // Remove active class\n $(element).removeClass(\"toolForm-active\");\n },\n init_field_data: function(data) {\n if (data.type) {\n this.type = data.type;\n }\n this.name = data.name;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.tool_state = data.tool_state;\n this.errors = data.errors;\n this.tooltip = data.tooltip ? data.tooltip : \"\";\n this.annotation = data.annotation;\n this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};\n this.label = data.label;\n this.uuid = data.uuid;\n this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];\n var node = this;\n var nodeView = new NodeView({\n el: this.element[0],\n node: node\n });\n node.nodeView = nodeView;\n $.each(data.data_inputs, (i, input) => {\n nodeView.addDataInput(input);\n });\n if (data.data_inputs.length > 0 && data.data_outputs.length > 0) {\n nodeView.addRule();\n }\n $.each(data.data_outputs, (i, output) => {\n nodeView.addDataOutput(output);\n });\n nodeView.render();\n this.app.workflow.node_changed(this, true);\n },\n update_field_data: function(data) {\n var node = this;\n var nodeView = node.nodeView;\n // remove unused output views and remove pre-existing output views from data.data_outputs,\n // so that these are not added twice.\n var unused_outputs = [];\n // nodeView.outputViews contains pre-existing outputs,\n // while data.data_output contains what should be displayed.\n // Now we gather the unused outputs\n $.each(nodeView.outputViews, (i, output_view) => {\n var cur_name = output_view.output.name;\n var data_names = data.data_outputs;\n var cur_name_in_data_outputs = false;\n _.each(data_names, data_name => {\n if (data_name.name == cur_name) {\n cur_name_in_data_outputs = true;\n }\n });\n if (cur_name_in_data_outputs === false) {\n unused_outputs.push(cur_name);\n }\n });\n\n // Remove the unused outputs\n _.each(unused_outputs, unused_output => {\n _.each(nodeView.outputViews[unused_output].terminalElement.terminal.connectors, x => {\n if (x) {\n x.destroy(); // Removes the noodle connectors\n }\n });\n nodeView.outputViews[unused_output].remove(); // removes the rendered output\n delete nodeView.outputViews[unused_output]; // removes the reference to the output\n delete node.output_terminals[unused_output]; // removes the output terminal\n });\n $.each(node.workflow_outputs, (i, wf_output) => {\n if (wf_output && !node.output_terminals[wf_output.output_name]) {\n node.workflow_outputs.splice(i, 1); // removes output from list of workflow outputs\n }\n });\n $.each(data.data_outputs, (i, output) => {\n if (!nodeView.outputViews[output.name]) {\n nodeView.addDataOutput(output); // add data output if it does not yet exist\n } else {\n // the output already exists, but the output formats may have changed.\n // Therefore we update the datatypes and destroy invalid connections.\n node.output_terminals[output.name].datatypes = output.extensions;\n node.output_terminals[output.name].destroyInvalidConnections();\n }\n });\n this.tool_state = data.tool_state;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.errors = data.errors;\n this.annotation = data[\"annotation\"];\n this.label = data.label;\n if (\"post_job_actions\" in data) {\n // Won't be present in response for data inputs\n var pja_in = data.post_job_actions;\n this.post_job_actions = pja_in ? pja_in : {};\n }\n node.nodeView.renderToolErrors();\n // Update input rows\n var old_body = nodeView.$(\"div.inputs\");\n var new_body = nodeView.newInputsDiv();\n var newTerminalViews = {};\n _.each(data.data_inputs, input => {\n var terminalView = node.nodeView.addDataInput(input, new_body);\n newTerminalViews[input.name] = terminalView;\n });\n // Cleanup any leftover terminals\n _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), unusedView => {\n unusedView.el.terminal.destroy();\n });\n nodeView.terminalViews = newTerminalViews;\n node.nodeView.render();\n // In general workflow editor assumes tool outputs don't change in # or\n // type (not really valid right?) but adding special logic here for\n // data collection input parameters that can have their collection\n // change.\n if (data.data_outputs.length == 1 && \"collection_type\" in data.data_outputs[0]) {\n nodeView.updateDataOutput(data.data_outputs[0]);\n }\n old_body.replaceWith(new_body);\n if (\"workflow_outputs\" in data) {\n // Won't be present in response for data inputs\n this.workflow_outputs = workflow_outputs ? workflow_outputs : [];\n }\n // If active, reactivate with new config_form\n this.markChanged();\n this.redraw();\n },\n error: function(text) {\n var b = $(this.element).find(\".toolFormBody\");\n b.find(\"div\").remove();\n var tmp = `${text}
`;\n this.config_form = tmp;\n b.html(tmp);\n this.app.workflow.node_changed(this);\n },\n markChanged: function() {\n this.app.workflow.node_changed(this);\n }\n});\nexport default Node;\n"]}
\ No newline at end of file
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NodeView from \"mvc/workflow/workflow-view-node\";\nvar Node = Backbone.Model.extend({\n initialize: function(app, attr) {\n this.app = app;\n this.element = attr.element;\n this.input_terminals = {};\n this.output_terminals = {};\n this.errors = {};\n this.workflow_outputs = [];\n },\n getWorkflowOutput: function(outputName) {\n return _.findWhere(this.workflow_outputs, {\n output_name: outputName\n });\n },\n isWorkflowOutput: function(outputName) {\n return this.getWorkflowOutput(outputName) !== undefined;\n },\n removeWorkflowOutput: function(outputName) {\n while (this.isWorkflowOutput(outputName)) {\n this.workflow_outputs.splice(this.getWorkflowOutput(outputName), 1);\n }\n },\n addWorkflowOutput: function(outputName, label) {\n if (!this.isWorkflowOutput(outputName)) {\n var output = { output_name: outputName };\n if (label) {\n output.label = label;\n }\n this.workflow_outputs.push(output);\n return true;\n }\n return false;\n },\n labelWorkflowOutput: function(outputName, label) {\n var changed = false;\n var oldLabel = null;\n if (this.isWorkflowOutput(outputName)) {\n var workflowOutput = this.getWorkflowOutput(outputName);\n oldLabel = workflowOutput.label;\n workflowOutput.label = label;\n changed = oldLabel != label;\n } else {\n changed = this.addWorkflowOutput(outputName, label);\n }\n if (changed) {\n this.app.workflow.updateOutputLabel(oldLabel, label);\n this.markChanged();\n this.nodeView.redrawWorkflowOutputs();\n }\n return changed;\n },\n connectedOutputTerminals: function() {\n return this._connectedTerminals(this.output_terminals);\n },\n _connectedTerminals: function(terminals) {\n var connectedTerminals = [];\n $.each(terminals, (_, t) => {\n if (t.connectors.length > 0) {\n connectedTerminals.push(t);\n }\n });\n return connectedTerminals;\n },\n hasConnectedOutputTerminals: function() {\n // return this.connectedOutputTerminals().length > 0; <- optimized this\n var outputTerminals = this.output_terminals;\n for (var outputName in outputTerminals) {\n if (outputTerminals[outputName].connectors.length > 0) {\n return true;\n }\n }\n return false;\n },\n connectedMappedInputTerminals: function() {\n return this._connectedMappedTerminals(this.input_terminals);\n },\n hasConnectedMappedInputTerminals: function() {\n // return this.connectedMappedInputTerminals().length > 0; <- optimized this\n var inputTerminals = this.input_terminals;\n for (var inputName in inputTerminals) {\n var inputTerminal = inputTerminals[inputName];\n if (inputTerminal.connectors.length > 0 && inputTerminal.isMappedOver()) {\n return true;\n }\n }\n return false;\n },\n _connectedMappedTerminals: function(terminals) {\n var mapped_outputs = [];\n $.each(terminals, (_, t) => {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n if (t.connectors.length > 0) {\n mapped_outputs.push(t);\n }\n }\n });\n return mapped_outputs;\n },\n mappedInputTerminals: function() {\n return this._mappedTerminals(this.input_terminals);\n },\n _mappedTerminals: function(terminals) {\n var mappedTerminals = [];\n $.each(terminals, (_, t) => {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n mappedTerminals.push(t);\n }\n });\n return mappedTerminals;\n },\n hasMappedOverInputTerminals: function() {\n var found = false;\n _.each(this.input_terminals, t => {\n var mapOver = t.mapOver();\n if (mapOver.isCollection) {\n found = true;\n }\n });\n return found;\n },\n redraw: function() {\n $.each(this.input_terminals, (_, t) => {\n t.redraw();\n });\n $.each(this.output_terminals, (_, t) => {\n t.redraw();\n });\n },\n destroy: function() {\n $.each(this.input_terminals, (k, t) => {\n t.destroy();\n });\n $.each(this.output_terminals, (k, t) => {\n t.destroy();\n });\n this.app.workflow.remove_node(this);\n $(this.element).remove();\n },\n make_active: function() {\n $(this.element).addClass(\"toolForm-active\");\n },\n make_inactive: function() {\n // Keep inactive nodes stacked from most to least recently active\n // by moving element to the end of parent's node list\n var element = this.element.get(0);\n (p => {\n p.removeChild(element);\n p.appendChild(element);\n })(element.parentNode);\n // Remove active class\n $(element).removeClass(\"toolForm-active\");\n },\n init_field_data: function(data) {\n if (data.type) {\n this.type = data.type;\n }\n this.name = data.name;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.tool_state = data.tool_state;\n this.errors = data.errors;\n this.tooltip = data.tooltip ? data.tooltip : \"\";\n this.annotation = data.annotation;\n this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};\n this.label = data.label;\n this.uuid = data.uuid;\n this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];\n var node = this;\n var nodeView = new NodeView({\n el: this.element[0],\n node: node\n });\n node.nodeView = nodeView;\n $.each(data.data_inputs, (i, input) => {\n nodeView.addDataInput(input);\n });\n if (data.data_inputs.length > 0 && data.data_outputs.length > 0) {\n nodeView.addRule();\n }\n $.each(data.data_outputs, (i, output) => {\n nodeView.addDataOutput(output);\n });\n nodeView.render();\n this.app.workflow.node_changed(this, true);\n },\n update_field_data: function(data) {\n var node = this;\n var nodeView = node.nodeView;\n // remove unused output views and remove pre-existing output views from data.data_outputs,\n // so that these are not added twice.\n var unused_outputs = [];\n // nodeView.outputViews contains pre-existing outputs,\n // while data.data_output contains what should be displayed.\n // Now we gather the unused outputs\n $.each(nodeView.outputViews, (i, output_view) => {\n var cur_name = output_view.output.name;\n var data_names = data.data_outputs;\n var cur_name_in_data_outputs = false;\n _.each(data_names, data_name => {\n if (data_name.name == cur_name) {\n cur_name_in_data_outputs = true;\n }\n });\n if (cur_name_in_data_outputs === false) {\n unused_outputs.push(cur_name);\n }\n });\n\n // Remove the unused outputs\n _.each(unused_outputs, unused_output => {\n _.each(nodeView.outputViews[unused_output].terminalElement.terminal.connectors, x => {\n if (x) {\n x.destroy(); // Removes the noodle connectors\n }\n });\n nodeView.outputViews[unused_output].remove(); // removes the rendered output\n delete nodeView.outputViews[unused_output]; // removes the reference to the output\n delete node.output_terminals[unused_output]; // removes the output terminal\n });\n $.each(node.workflow_outputs, (i, wf_output) => {\n if (wf_output && !node.output_terminals[wf_output.output_name]) {\n node.workflow_outputs.splice(i, 1); // removes output from list of workflow outputs\n }\n });\n $.each(data.data_outputs, (i, output) => {\n if (!nodeView.outputViews[output.name]) {\n nodeView.addDataOutput(output); // add data output if it does not yet exist\n } else {\n // the output already exists, but the output formats may have changed.\n // Therefore we update the datatypes and destroy invalid connections.\n node.output_terminals[output.name].datatypes = output.extensions;\n node.output_terminals[output.name].destroyInvalidConnections();\n }\n });\n this.tool_state = data.tool_state;\n this.config_form = data.config_form;\n this.tool_version = this.config_form && this.config_form.version;\n this.errors = data.errors;\n this.annotation = data.annotation;\n this.label = data.label;\n if (\"post_job_actions\" in data) {\n // Won't be present in response for data inputs\n var pja_in = data.post_job_actions;\n this.post_job_actions = pja_in ? pja_in : {};\n }\n node.nodeView.renderToolErrors();\n // Update input rows\n var old_body = nodeView.$(\"div.inputs\");\n var new_body = nodeView.newInputsDiv();\n var newTerminalViews = {};\n _.each(data.data_inputs, input => {\n var terminalView = node.nodeView.addDataInput(input, new_body);\n newTerminalViews[input.name] = terminalView;\n });\n // Cleanup any leftover terminals\n _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), unusedView => {\n unusedView.el.terminal.destroy();\n });\n nodeView.terminalViews = newTerminalViews;\n node.nodeView.render();\n // In general workflow editor assumes tool outputs don't change in # or\n // type (not really valid right?) but adding special logic here for\n // data collection input parameters that can have their collection\n // change.\n if (data.data_outputs.length == 1 && \"collection_type\" in data.data_outputs[0]) {\n nodeView.updateDataOutput(data.data_outputs[0]);\n }\n old_body.replaceWith(new_body);\n if (\"workflow_outputs\" in data) {\n // Won't be present in response for data inputs\n this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];\n }\n // If active, reactivate with new config_form\n this.markChanged();\n this.redraw();\n },\n error: function(text) {\n var b = $(this.element).find(\".toolFormBody\");\n b.find(\"div\").remove();\n var tmp = `${text}
`;\n this.config_form = tmp;\n b.html(tmp);\n this.app.workflow.node_changed(this);\n },\n markChanged: function() {\n this.app.workflow.node_changed(this);\n }\n});\nexport default Node;\n"]}
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-forms.js b/static/scripts/mvc/workflow/workflow-forms.js
index f15c5db689dc..1774d6553576 100644
--- a/static/scripts/mvc/workflow/workflow-forms.js
+++ b/static/scripts/mvc/workflow/workflow-forms.js
@@ -1,2 +1,2 @@
-define("mvc/workflow/workflow-forms",["exports","utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(e,t,a,o){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}function i(e){var t=e.model.attributes,a=t.workflow,o=t.node;t.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:o.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),t.inputs.unshift({type:"text",name:"__label",label:"Label",value:o.label,help:"Add a step label.",fixed:!0,onchange:function(t){var n=!1;for(var i in a.nodes){var l=a.nodes[i];if(l.label&&l.label==t&&l.id!=o.id){n=!0;break}}var r=e.data.match("__label");e.element_list[r].model.set("error_text",n&&"Duplicate label. Please fix this before saving the workflow."),e.trigger("change")}})}function l(e){function t(e,a){(a=a||[]).push(e);for(var o in e.inputs){var n=e.inputs[o];if(n.action){if(n.name="pja__"+s+"__"+n.action,n.pja_arg&&(n.name+="__"+n.pja_arg),n.payload)for(var i in n.payload)n.payload[n.name+"__"+i]=n.payload[i],delete n.payload[i];var l=r[n.action+s];if(l){for(var u in a)a[u].expanded=!0;n.pja_arg?n.value=l.action_arguments&&l.action_arguments[n.pja_arg]||n.value:n.value="true"}}n.inputs&&t(n,a.slice(0))}}var a=e.model.attributes,o=a.inputs,n=a.datatypes,i=a.node,l=a.workflow,r=i.post_job_actions,s=i.output_terminals&&Object.keys(i.output_terminals)[0];if(s){o.push({name:"pja__"+s+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+s])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),o.push({name:"pja__"+s+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+s])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var u in i.output_terminals)o.push(function(e,a){var o=[],n=[];for(var r in a)o.push({0:a[r],1:a[r]});for(r in i.input_terminals)n.push(i.input_terminals[r].name);o.sort(function(e,t){return e.label>t.label?1:e.labelhere for more information. Valid inputs are: '+n.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:o,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return t(u),u}(u,n))}}Object.defineProperty(e,"__esModule",{value:!0});var r=n(t),s=n(a),u=n(o),p=Backbone.View.extend({initialize:function(e){var t=this,a=e.node;this.form=new s.default(r.default.merge(e,{onchange:function(){r.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:a.id,type:a.type,content_id:a.content_id,inputs:t.form.data.create()},success:function(e){a.update_field_data(e)}})}})),i(this.form),this.form.render()}}),c=Backbone.View.extend({initialize:function(e){var t=this,a=e.node;this.form=new u.default(r.default.merge(e,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(e,a){t._customize(a),e.resolve()},buildmodel:function(e,t){t.model.get("postchange")(e,t)},postchange:function(e,o){var n=o.model.attributes,i={tool_id:n.id,tool_version:n.version,type:"tool",inputs:$.extend(!0,{},o.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",i),r.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:i,success:function(n){o.model.set(n.config_form),t._customize(o),o.update(n.config_form),o.errors(n.config_form),a.update_field_data(n),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",n),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",t),e.reject()}})}}))},_customize:function(e){var t=e.model.attributes;r.default.deepeach(t.inputs,function(e){e.type&&(-1!=["data","data_collection"].indexOf(e.type)?(e.type="hidden",e.info="Data input '"+e.name+"' ("+r.default.textify(e.extensions)+")",e.value={__class__:"RuntimeValue"}):e.fixed||(e.collapsible_value={__class__:"RuntimeValue"},e.is_workflow=e.options&&0==e.options.length||-1!=["integer","float"].indexOf(e.type)))}),r.default.deepeach(t.inputs,function(e){"conditional"==e.type&&(e.test_param.collapsible_value=void 0)}),l(e),i(e)}});e.default={Default:p,Tool:c}});
+define("mvc/workflow/workflow-forms",["exports","utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(e,t,a,o){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}function i(e){var t=e.model.attributes,a=t.workflow,o=t.node;t.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:o.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),t.inputs.unshift({type:"text",name:"__label",label:"Label",value:o.label,help:"Add a step label.",fixed:!0,onchange:function(t){var n=!1;for(var i in a.nodes){var l=a.nodes[i];if(l.label&&l.label==t&&l.id!=o.id){n=!0;break}}var r=e.data.match("__label");e.element_list[r].model.set("error_text",n&&"Duplicate label. Please fix this before saving the workflow."),e.trigger("change")}})}function l(e,t,a,o){var n=o.node.post_job_actions;(t=t||[]).push(e);for(var i in e.inputs){var r=e.inputs[i];if(r.action){if(r.name="pja__"+a+"__"+r.action,r.pja_arg&&(r.name+="__"+r.pja_arg),r.payload)for(var s in r.payload)r.payload[r.name+"__"+s]=r.payload[s],delete r.payload[s];var u=n[r.action+a];if(u){for(var p in t)t[p].expanded=!0;r.pja_arg?r.value=u.action_arguments&&u.action_arguments[r.pja_arg]||r.value:r.value="true"}}r.inputs&&l(r,t.slice(0),a,o)}}function r(e,t){var a=[],o=[],n=t.datatypes,i=t.node,r=t.workflow;for(var s in n)a.push({0:n[s],1:n[s]});for(s in i.input_terminals)o.push(i.input_terminals[s].name);a.sort(function(e,t){return e.label>t.label?1:e.labelhere for more information. Valid inputs are: '+o.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:a,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return l(p,[],e,t),p}function s(e){var t=e.model.attributes,a=t.inputs,o=t.node,n=o.post_job_actions,i=o.output_terminals&&Object.keys(o.output_terminals)[0];if(i){a.push({name:"pja__"+i+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(n["EmailAction"+i])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),a.push({name:"pja__"+i+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(n["DeleteIntermediatesAction"+i])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var l in o.output_terminals)a.push(r(l,t))}}Object.defineProperty(e,"__esModule",{value:!0});var u=n(t),p=n(a),d=n(o),c=Backbone.View.extend({initialize:function(e){var t=this,a=e.node;this.form=new p.default(u.default.merge(e,{onchange:function(){u.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:a.id,type:a.type,content_id:a.content_id,inputs:t.form.data.create()},success:function(e){a.update_field_data(e)}})}})),i(this.form),this.form.render()}}),f=Backbone.View.extend({initialize:function(e){var t=this,a=e.node;this.form=new d.default(u.default.merge(e,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(e,a){t._customize(a),e.resolve()},buildmodel:function(e,t){t.model.get("postchange")(e,t)},postchange:function(e,o){var n=o.model.attributes,i={tool_id:n.id,tool_version:n.version,type:"tool",inputs:$.extend(!0,{},o.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",i),u.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:i,success:function(n){o.model.set(n.config_form),t._customize(o),o.update(n.config_form),o.errors(n.config_form),a.update_field_data(n),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",n),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",t),e.reject()}})}}))},_customize:function(e){var t=e.model.attributes;u.default.deepeach(t.inputs,function(e){e.type&&(-1!=["data","data_collection"].indexOf(e.type)?(e.type="hidden",e.info="Data input '"+e.name+"' ("+u.default.textify(e.extensions)+")",e.value={__class__:"RuntimeValue"}):e.fixed||(e.collapsible_value={__class__:"RuntimeValue"},e.is_workflow=e.options&&0===e.options.length||-1!=["integer","float"].indexOf(e.type)))}),u.default.deepeach(t.inputs,function(e){"conditional"===e.type&&(e.test_param.collapsible_value=void 0)}),s(e),i(e)}});e.default={Default:c,Tool:f}});
//# sourceMappingURL=../../../maps/mvc/workflow/workflow-forms.js.map
diff --git a/static/scripts/mvc/workflow/workflow-node.js b/static/scripts/mvc/workflow/workflow-node.js
index 747c3d6e7e8a..71313055eb71 100644
--- a/static/scripts/mvc/workflow/workflow-node.js
+++ b/static/scripts/mvc/workflow/workflow-node.js
@@ -1,2 +1,2 @@
-define("mvc/workflow/workflow-node",["exports","mvc/workflow/workflow-view-node"],function(t,e){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var o=function(t){return t&&t.__esModule?t:{default:t}}(e),n=Backbone.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return _.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!=this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var o={output_name:t};return e&&(o.label=e),this.workflow_outputs.push(o),!0}return!1},labelWorkflowOutput:function(t,e){var o=!1,n=null;if(this.isWorkflowOutput(t)){var i=this.getWorkflowOutput(t);n=i.label,i.label=e,o=n!=e}else o=this.addWorkflowOutput(t,e);return o&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),o},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.connectors.length>0&&e.push(o)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var o=t[e];if(o.connectors.length>0&&o.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.mapOver().isCollection&&o.connectors.length>0&&e.push(o)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.mapOver().isCollection&&e.push(o)}),e},hasMappedOverInputTerminals:function(){var t=!1;return _.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){$.each(this.input_terminals,function(t,e){e.redraw()}),$.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){$.each(this.input_terminals,function(t,e){e.destroy()}),$.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),$(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,n=new o.default({el:this.element[0],node:e});e.nodeView=n,$.each(t.data_inputs,function(t,e){n.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&n.addRule(),$.each(t.data_outputs,function(t,e){n.addDataOutput(e)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,o=e.nodeView,n=[];if($.each(o.outputViews,function(e,o){var i=o.output.name,r=t.data_outputs,a=!1;_.each(r,function(t){t.name==i&&(a=!0)}),!1===a&&n.push(i)}),_.each(n,function(t){_.each(o.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),o.outputViews[t].remove(),delete o.outputViews[t],delete e.output_terminals[t]}),$.each(e.workflow_outputs,function(t,o){o&&!e.output_terminals[o.output_name]&&e.workflow_outputs.splice(t,1)}),$.each(t.data_outputs,function(t,n){o.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):o.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var i=t.post_job_actions;this.post_job_actions=i||{}}e.nodeView.renderToolErrors();var r=o.$("div.inputs"),a=o.newInputsDiv(),u={};_.each(t.data_inputs,function(t){var o=e.nodeView.addDataInput(t,a);u[t.name]=o}),_.each(_.difference(_.values(o.terminalViews),_.values(u)),function(t){t.el.terminal.destroy()}),o.terminalViews=u,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&o.updateDataOutput(t.data_outputs[0]),r.replaceWith(a),"workflow_outputs"in t&&(this.workflow_outputs=workflow_outputs||[]),this.markChanged(),this.redraw()},error:function(t){var e=$(this.element).find(".toolFormBody");e.find("div").remove();var o=""+t+"
";this.config_form=o,e.html(o),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});t.default=n});
+define("mvc/workflow/workflow-node",["exports","mvc/workflow/workflow-view-node"],function(t,e){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var o=function(t){return t&&t.__esModule?t:{default:t}}(e),n=Backbone.Model.extend({initialize:function(t,e){this.app=t,this.element=e.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(t){return _.findWhere(this.workflow_outputs,{output_name:t})},isWorkflowOutput:function(t){return void 0!==this.getWorkflowOutput(t)},removeWorkflowOutput:function(t){for(;this.isWorkflowOutput(t);)this.workflow_outputs.splice(this.getWorkflowOutput(t),1)},addWorkflowOutput:function(t,e){if(!this.isWorkflowOutput(t)){var o={output_name:t};return e&&(o.label=e),this.workflow_outputs.push(o),!0}return!1},labelWorkflowOutput:function(t,e){var o=!1,n=null;if(this.isWorkflowOutput(t)){var i=this.getWorkflowOutput(t);n=i.label,i.label=e,o=n!=e}else o=this.addWorkflowOutput(t,e);return o&&(this.app.workflow.updateOutputLabel(n,e),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),o},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.connectors.length>0&&e.push(o)}),e},hasConnectedOutputTerminals:function(){var t=this.output_terminals;for(var e in t)if(t[e].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var t=this.input_terminals;for(var e in t){var o=t[e];if(o.connectors.length>0&&o.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.mapOver().isCollection&&o.connectors.length>0&&e.push(o)}),e},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(t){var e=[];return $.each(t,function(t,o){o.mapOver().isCollection&&e.push(o)}),e},hasMappedOverInputTerminals:function(){var t=!1;return _.each(this.input_terminals,function(e){e.mapOver().isCollection&&(t=!0)}),t},redraw:function(){$.each(this.input_terminals,function(t,e){e.redraw()}),$.each(this.output_terminals,function(t,e){e.redraw()})},destroy:function(){$.each(this.input_terminals,function(t,e){e.destroy()}),$.each(this.output_terminals,function(t,e){e.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var t=this.element.get(0);!function(e){e.removeChild(t),e.appendChild(t)}(t.parentNode),$(t).removeClass("toolForm-active")},init_field_data:function(t){t.type&&(this.type=t.type),this.name=t.name,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=t.tool_state,this.errors=t.errors,this.tooltip=t.tooltip?t.tooltip:"",this.annotation=t.annotation,this.post_job_actions=t.post_job_actions?t.post_job_actions:{},this.label=t.label,this.uuid=t.uuid,this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[];var e=this,n=new o.default({el:this.element[0],node:e});e.nodeView=n,$.each(t.data_inputs,function(t,e){n.addDataInput(e)}),t.data_inputs.length>0&&t.data_outputs.length>0&&n.addRule(),$.each(t.data_outputs,function(t,e){n.addDataOutput(e)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(t){var e=this,o=e.nodeView,n=[];if($.each(o.outputViews,function(e,o){var i=o.output.name,r=t.data_outputs,u=!1;_.each(r,function(t){t.name==i&&(u=!0)}),!1===u&&n.push(i)}),_.each(n,function(t){_.each(o.outputViews[t].terminalElement.terminal.connectors,function(t){t&&t.destroy()}),o.outputViews[t].remove(),delete o.outputViews[t],delete e.output_terminals[t]}),$.each(e.workflow_outputs,function(t,o){o&&!e.output_terminals[o.output_name]&&e.workflow_outputs.splice(t,1)}),$.each(t.data_outputs,function(t,n){o.outputViews[n.name]?(e.output_terminals[n.name].datatypes=n.extensions,e.output_terminals[n.name].destroyInvalidConnections()):o.addDataOutput(n)}),this.tool_state=t.tool_state,this.config_form=t.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=t.errors,this.annotation=t.annotation,this.label=t.label,"post_job_actions"in t){var i=t.post_job_actions;this.post_job_actions=i||{}}e.nodeView.renderToolErrors();var r=o.$("div.inputs"),u=o.newInputsDiv(),a={};_.each(t.data_inputs,function(t){var o=e.nodeView.addDataInput(t,u);a[t.name]=o}),_.each(_.difference(_.values(o.terminalViews),_.values(a)),function(t){t.el.terminal.destroy()}),o.terminalViews=a,e.nodeView.render(),1==t.data_outputs.length&&"collection_type"in t.data_outputs[0]&&o.updateDataOutput(t.data_outputs[0]),r.replaceWith(u),"workflow_outputs"in t&&(this.workflow_outputs=t.workflow_outputs?t.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(t){var e=$(this.element).find(".toolFormBody");e.find("div").remove();var o=""+t+"
";this.config_form=o,e.html(o),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});t.default=n});
//# sourceMappingURL=../../../maps/mvc/workflow/workflow-node.js.map
diff --git a/test/api/test_configuration.py b/test/api/test_configuration.py
index c6927a3d8d46..48ba5310a2ce 100644
--- a/test/api/test_configuration.py
+++ b/test/api/test_configuration.py
@@ -3,6 +3,9 @@
assert_has_keys,
assert_not_has_keys,
)
+from base.populators import (
+ LibraryPopulator
+)
TEST_KEYS_FOR_ALL_USERS = [
'enable_unique_workflow_defaults',
@@ -24,6 +27,10 @@
class ConfigurationApiTestCase(api.ApiTestCase):
+ def setUp(self):
+ super(ConfigurationApiTestCase, self).setUp()
+ self.library_populator = LibraryPopulator(self)
+
def test_normal_user_configuration(self):
config = self._get_configuration()
assert_has_keys(config, *TEST_KEYS_FOR_ALL_USERS)
@@ -34,6 +41,22 @@ def test_admin_user_configuration(self):
assert_has_keys(config, *TEST_KEYS_FOR_ALL_USERS)
assert_has_keys(config, *TEST_KEYS_FOR_ADMIN_ONLY)
+ def test_admin_decode_id(self):
+ new_lib = self.library_populator.new_library('DecodeTestLibrary')
+ decode_response = self._get("configuration/decode/" + new_lib["id"], admin=True)
+ response_id = decode_response.json()["decoded_id"]
+ decoded_library_id = self.security.decode_id(new_lib["id"])
+ assert decoded_library_id == response_id
+ # fake valid folder id by prepending F
+ valid_encoded_folder_id = 'F' + new_lib["id"]
+ folder_decode_response = self._get("configuration/decode/" + valid_encoded_folder_id, admin=True)
+ folder_response_id = folder_decode_response.json()["decoded_id"]
+ assert decoded_library_id == folder_response_id
+
+ def test_normal_user_decode_id(self):
+ decode_response = self._get("configuration/decode/badhombre", admin=False)
+ self._assert_status_code_is(decode_response, 403)
+
def _get_configuration(self, data={}, admin=False):
response = self._get("configuration", data=data, admin=admin)
self._assert_status_code_is(response, 200)
diff --git a/test/api/test_history_contents.py b/test/api/test_history_contents.py
index bc2d59824a43..5cb2822556bd 100644
--- a/test/api/test_history_contents.py
+++ b/test/api/test_history_contents.py
@@ -221,7 +221,42 @@ def test_hdca_copy(self):
assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0
create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data)
self.__check_create_collection_response(create_response)
- assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 1
+ contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json()
+ assert len(contents) == 1
+ new_forward, _ = self.__get_paired_response_elements(contents[0])
+ self._assert_has_keys(new_forward, "history_id")
+ assert new_forward["history_id"] == self.history_id
+
+ def test_hdca_copy_and_elements(self):
+ hdca = self.dataset_collection_populator.create_pair_in_history(self.history_id).json()
+ hdca_id = hdca["id"]
+ second_history_id = self._new_history()
+ create_data = dict(
+ source='hdca',
+ content=hdca_id,
+ copy_elements=True,
+ )
+ assert len(self._get("histories/%s/contents/dataset_collections" % second_history_id).json()) == 0
+ create_response = self._post("histories/%s/contents/dataset_collections" % second_history_id, create_data)
+ self.__check_create_collection_response(create_response)
+
+ contents = self._get("histories/%s/contents/dataset_collections" % second_history_id).json()
+ assert len(contents) == 1
+ new_forward, _ = self.__get_paired_response_elements(contents[0])
+ self._assert_has_keys(new_forward, "history_id")
+ assert new_forward["history_id"] == second_history_id
+
+ def __get_paired_response_elements(self, contents):
+ hdca = self.__show(contents).json()
+ self._assert_has_keys(hdca, "name", "deleted", "visible", "elements")
+ elements = hdca["elements"]
+ assert len(elements) == 2
+ element0 = elements[0]
+ element1 = elements[1]
+ self._assert_has_keys(element0, "object")
+ self._assert_has_keys(element1, "object")
+
+ return element0["object"], element1["object"]
def test_hdca_from_library_datasets(self):
ld = self.library_populator.new_library_dataset("el1")
diff --git a/tools/stats/gsummary.py b/tools/stats/gsummary.py
index 44ea737d6722..276a30f93493 100755
--- a/tools/stats/gsummary.py
+++ b/tools/stats/gsummary.py
@@ -59,7 +59,7 @@ def main():
except Exception:
pass
- tmp_file = tempfile.NamedTemporaryFile('w+b')
+ tmp_file = tempfile.NamedTemporaryFile('w+')
# Write the R header row to the temporary file
hdr_str = "\t".join("c%s" % str(col + 1) for col in cols)
tmp_file.write("%s\n" % hdr_str)