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commit/galaxy-central: dannon: Merged in jmchilton/galaxy-central-fork-1 (pull request #401)
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/646b5877871b/ Changeset: 646b5877871b User: dannon Date: 2014-06-12 17:09:04 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #401) Allow tools and deployers to specify optional Docker-based dependency resolution. Affected #: 10 files diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -97,6 +97,90 @@ elements. This empty block will simply disable job metrics for the corresponding destination. --></destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination><destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -582,6 +582,16 @@ import galaxy.tools.search self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + from galaxy.tools.deps import containers + galaxy_root_dir = os.path.abspath(self.config.root) + file_path = os.path.abspath(getattr(self.config, "file_path")) + app_info = containers.AppInfo( + galaxy_root_dir, + default_file_path=file_path, + outputs_to_working_directory=self.config.outputs_to_working_directory + ) + self.container_finder = galaxy.tools.deps.containers.ContainerFinder(app_info) + def _configure_tool_data_tables( self, from_shed_config ): from galaxy.tools.data import ToolDataTableManager diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -1,4 +1,6 @@ from os import getcwd +from os import chmod +from os.path import join from os.path import abspath CAPTURE_RETURN_CODE = "return_code=$?" @@ -8,7 +10,14 @@ log = getLogger( __name__ ) -def build_command( runner, job_wrapper, include_metadata=False, include_work_dir_outputs=True, remote_command_params={} ): +def build_command( + runner, + job_wrapper, + container=None, + include_metadata=False, + include_work_dir_outputs=True, + remote_command_params={} +): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -29,7 +38,35 @@ __handle_version_command(commands_builder, job_wrapper) __handle_task_splitting(commands_builder, job_wrapper) - __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + # One could imagine also allowing dependencies inside of the container but + # that is too sophisticated for a first crack at this - build your + # containers ready to go! + if not container: + __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + if container: + # Stop now and build command before handling metadata and copying + # working directory files back. These should always happen outside + # of docker container - no security implications when generating + # metadata and means no need for Galaxy to be available to container + # and not copying workdir outputs back means on can be more restrictive + # of where container can write to in some circumstances. + + local_container_script = join( job_wrapper.working_directory, "container.sh" ) + fh = file( local_container_script, "w" ) + fh.write( "#!/bin/sh\n%s" % commands_builder.build() ) + fh.close() + chmod( local_container_script, 0755 ) + + compute_container_script = local_container_script + if 'working_directory' in remote_command_params: + compute_container_script = "/bin/sh %s" % join(remote_command_params['working_directory'], "container.sh") + + run_in_container_command = container.containerize_command( + compute_container_script + ) + commands_builder = CommandsBuilder( run_in_container_command ) if include_work_dir_outputs: __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params) diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -177,7 +177,16 @@ raise NotImplementedError() def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): - return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) + # TODO: Eliminate extra kwds no longer used (since LWR skips + # abstraction and calls build_command directly). + container = self._find_container( job_wrapper ) + return build_command( + self, + job_wrapper, + include_metadata=include_metadata, + include_work_dir_outputs=include_work_dir_outputs, + container=container + ) def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ): """ @@ -276,6 +285,31 @@ if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) + def _find_container( + self, + job_wrapper, + compute_working_directory=None, + compute_tool_directory=None, + compute_job_directory=None + ): + if not compute_working_directory: + compute_working_directory = job_wrapper.working_directory + + if not compute_tool_directory: + compute_tool_directory = job_wrapper.tool.tool_dir + + tool = job_wrapper.tool + from galaxy.tools.deps import containers + tool_info = containers.ToolInfo(tool.containers, tool.requirements) + job_info = containers.JobInfo(compute_working_directory, compute_tool_directory, compute_job_directory) + + destination_info = job_wrapper.job_destination.params + return self.app.container_finder.find_container( + tool_info, + destination_info, + job_info + ) + class JobState( object ): """ diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -233,9 +233,21 @@ metadata_kwds=metadata_kwds, dependency_resolution=dependency_resolution, ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for LWR, always worked for LWR but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) command_line = build_command( self, job_wrapper=job_wrapper, + container=container, include_metadata=remote_metadata, include_work_dir_outputs=False, remote_command_params=remote_command_params, diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1346,7 +1346,9 @@ self.__tests_populated = False # Requirements (dependencies) - self.requirements = parse_requirements_from_xml( root ) + requirements, containers = parse_requirements_from_xml( root ) + self.requirements = requirements + self.containers = containers # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/containers.py --- /dev/null +++ b/lib/galaxy/tools/deps/containers.py @@ -0,0 +1,246 @@ +from abc import ( + ABCMeta, + abstractmethod +) +import os +import string + +from galaxy.util import asbool +from ..deps import docker_util + +import logging +log = logging.getLogger(__name__) + +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerFinder(object): + + def __init__(self, app_info): + self.app_info = app_info + self.container_registry = ContainerRegistry() + + def find_container(self, tool_info, destination_info, job_info): + def __destination_container(container_description=None, container_id=None, container_type=None): + if container_description: + container_id = container_description.identifier + container_type = container_description.type + container = self.__destination_container( + container_id, + container_type, + tool_info, + destination_info, + job_info + ) + return container + + # Is destination forcing Galaxy to use a particular container do it, + # this is likely kind of a corner case. For instance if deployers + # do not trust the containers annotated in tools. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__overridden_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + # Otherwise lets see if we can find container for the tool. + + # Exact matches first from explicitly listed containers in tools... + for container_description in tool_info.container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # Implement vague concept of looping through all containers + # matching requirements. Exact details need to be worked through + # but hopefully the idea that it sits below find_container somewhere + # external components to this module don't need to worry about it + # is good enough. + container_descriptions = self.container_registry.container_descriptions_for_requirements(tool_info.requirements) + for container_description in container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # If we still don't have a container, check to see if any container + # types define a default container id and use that. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__default_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + return NULL_CONTAINER + + def __overridden_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_container_id_override" % container_type) + + def __default_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_default_container_id" % container_type) + + def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info): + # TODO: ensure destination_info is dict-like + if not self.__container_type_enabled(container_type, destination_info): + return NULL_CONTAINER + + # TODO: Right now this assumes all containers available when a + # container type is - there should be more thought put into this. + # Checking which are availalbe - settings policies for what can be + # auto-fetched, etc.... + return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info) + + def __container_type_enabled(self, container_type, destination_info): + return asbool(destination_info.get("%s_enabled" % container_type, False)) + + +class ContainerRegistry(): + + def __init__(self): + pass + + def container_descriptions_for_requirements(self, requirements): + # Return lists of containers that would match requirements... + return [] + + +class AppInfo(object): + + def __init__(self, galaxy_root_dir=None, default_file_path=None, outputs_to_working_directory=False): + self.galaxy_root_dir = galaxy_root_dir + self.default_file_path = default_file_path + # TODO: Vary default value for docker_volumes based on this... + self.outputs_to_working_directory = outputs_to_working_directory + + +class ToolInfo(object): + # TODO: Introduce tool XML syntax to annotate the optional environment + # variables they can consume (e.g. JVM options, license keys, etc..) + # and add these to env_path_through + + def __init__(self, container_descriptions=[], requirements=[]): + self.container_descriptions = container_descriptions + self.requirements = requirements + self.env_pass_through = ["GALAXY_SLOTS"] + + +class JobInfo(object): + + def __init__(self, working_directory, tool_directory, job_directory): + self.working_directory = working_directory + self.job_directory = job_directory + # Tool files may be remote staged - so this is unintuitively a property + # of the job not of the tool. + self.tool_directory = tool_directory + + +class Container( object ): + __metaclass__ = ABCMeta + + def __init__(self, container_id, app_info, tool_info, destination_info, job_info): + self.container_id = container_id + self.app_info = app_info + self.tool_info = tool_info + self.destination_info = destination_info + self.job_info = job_info + + @abstractmethod + def containerize_command(self, command): + """ + Use destination supplied container configuration parameters, + container_id, and command to build a new command that runs + input command in container. + """ + + +class DockerContainer(Container): + + def containerize_command(self, command): + def prop(name, default): + destination_name = "docker_%s" % name + return self.destination_info.get(destination_name, default) + + env_directives = [] + for pass_through_var in self.tool_info.env_pass_through: + env_directives.append('"%s=$%s"' % (pass_through_var, pass_through_var)) + + # Allow destinations to explicitly set environment variables just for + # docker container. Better approach is to set for destination and then + # pass through only what tool needs however. (See todo in ToolInfo.) + for key, value in self.destination_info.iteritems(): + if key.startswith("docker_env_"): + env = key[len("docker_env_"):] + env_directives.append('"%s=%s"' % (env, value)) + + working_directory = self.job_info.working_directory + if not working_directory: + raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory) + + volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults")) + # TODO: Remove redundant volumes... + volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw) + return docker_util.build_docker_run_command( + command, + self.container_id, + volumes=volumes, + env_directives=env_directives, + working_directory=working_directory, + docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND), + sudo=asbool(prop("sudo", docker_util.DEFAULT_SUDO)), + sudo_cmd=prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND), + host=prop("host", docker_util.DEFAULT_HOST), + net=prop("net", "none") # By default, docker instance has networking disabled + ) + + def __expand_str(self, value): + template = string.Template(value) + variables = dict() + + def add_var(name, value): + if value: + variables[name] = os.path.abspath(value) + + add_var("working_directory", self.job_info.working_directory) + add_var("job_directory", self.job_info.job_directory) + add_var("tool_directory", self.job_info.tool_directory) + add_var("galaxy_root", self.app_info.galaxy_root_dir) + add_var("default_file_path", self.app_info.default_file_path) + + if self.job_info.job_directory: + # We have a job directory, so everything needed (excluding index + # files) should be available in job_directory... + defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw" + elif self.app_info.outputs_to_working_directory: + # Should need default_file_path (which is a course estimate given + # object stores anyway. + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro" + else: + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw" + + # Define $defaults that can easily be extended with external library and + # index data without deployer worrying about above details. + variables["defaults"] = string.Template(defaults).safe_substitute(variables) + + return template.safe_substitute(variables) + + +CONTAINER_CLASSES = dict( + docker=DockerContainer, +) + + +class NullContainer(object): + + def __init__(self): + pass + + def __nonzero__(self): + return False + + +NULL_CONTAINER = NullContainer() diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/docker_util.py --- /dev/null +++ b/lib/galaxy/tools/deps/docker_util.py @@ -0,0 +1,91 @@ + +DEFAULT_DOCKER_COMMAND = "docker" +DEFAULT_SUDO = True +DEFAULT_SUDO_COMMAND = "sudo" +DEFAULT_HOST = None +DEFAULT_VOLUME_MOUNT_TYPE = "rw" +DEFAULT_WORKING_DIRECTORY = None +DEFAULT_NET = None +DEFAULT_MEMORY = None + + +class DockerVolume(object): + + def __init__(self, path, to_path=None, how=DEFAULT_VOLUME_MOUNT_TYPE): + self.from_path = path + self.to_path = to_path or path + if not DockerVolume.__valid_how(how): + raise ValueError("Invalid way to specify docker volume %s" % how) + self.how = how + + @staticmethod + def volumes_from_str(volumes_as_str): + if not volumes_as_str: + return [] + volume_strs = [v.strip() for v in volumes_as_str.split(",")] + return map(DockerVolume.volume_from_str, volume_strs) + + @staticmethod + def volume_from_str(as_str): + if not as_str: + raise ValueError("Failed to parse docker volume from %s" % as_str) + parts = as_str.split(":", 2) + kwds = dict(path=parts[0]) + if len(parts) == 2: + if DockerVolume.__valid_how(parts[1]): + kwds["how"] = parts[1] + else: + kwds["to_path"] = parts[1] + elif len(parts) == 3: + kwds["to_path"] = parts[1] + kwds["how"] = parts[2] + return DockerVolume(**kwds) + + @staticmethod + def __valid_how(how): + return how in ["ro", "rw"] + + def __str__(self): + return ":".join([self.from_path, self.to_path, self.how]) + + +def build_docker_run_command( + container_command, + image, + tag=None, + docker_cmd=DEFAULT_DOCKER_COMMAND, + volumes=[], + memory=DEFAULT_MEMORY, + env_directives=[], + working_directory=DEFAULT_WORKING_DIRECTORY, + sudo=DEFAULT_SUDO, + sudo_cmd=DEFAULT_SUDO_COMMAND, + name=None, + host=DEFAULT_HOST, + net=DEFAULT_NET, +): + command_parts = [] + if sudo: + command_parts.append(sudo_cmd) + command_parts.append(docker_cmd) + if host: + command_parts.append(["-H", host]) + command_parts.append("run") + for env_directive in env_directives: + command_parts.extend(["-e", env_directive]) + for volume in volumes: + command_parts.extend(["-v", str(volume)]) + if memory: + command_parts.extend(["-m", memory]) + if name: + command_parts.extend(["-name", name]) + if working_directory: + command_parts.extend(["-w", working_directory]) + if net: + command_parts.extend(["--net", net]) + full_image = image + if tag: + full_image = "%s:%s" % (full_image, tag) + command_parts.append(full_image) + command_parts.append(container_command) + return " ".join(command_parts) diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/requirements.py --- a/lib/galaxy/tools/deps/requirements.py +++ b/lib/galaxy/tools/deps/requirements.py @@ -26,6 +26,25 @@ return ToolRequirement( name=name, type=type, version=version ) +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerDescription( object ): + + def __init__( self, identifier=None, type="docker" ): + self.identifier = identifier + self.type = type + + def to_dict( self ): + return dict(identifier=self.identifier, type=self.type) + + @staticmethod + def from_dict( dict ): + identifier = dict["identifier"] + type = dict.get("type", DEFAULT_CONTAINER_TYPE) + return ContainerDescription( identifier=identifier, type=type ) + + def parse_requirements_from_xml( xml_root ): """ @@ -63,4 +82,15 @@ requirement = ToolRequirement( name=name, type=type, version=version ) requirements.append( requirement ) - return requirements + container_elems = [] + if requirements_elem is not None: + container_elems = requirements_elem.findall( 'container' ) + + containers = [] + for container_elem in container_elems: + identifier = xml_text( container_elem ) + type = container_elem.get( "type", DEFAULT_CONTAINER_TYPE ) + container = ContainerDescription( identifier=identifier, type=type ) + containers.append( container ) + + return requirements, containers diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 test/functional/tools/catDocker.xml --- /dev/null +++ b/test/functional/tools/catDocker.xml @@ -0,0 +1,28 @@ +<tool id="catdc" name="Concatenate datasets (in docker)"> + <description>tail-to-head</description> + <requirements> + <container type="docker">busybox:ubuntu-14.04</container> + </requirements> + <command> + echo "Galaxy slots passed through contain as \$GALAXY_SLOTS"; + cat $input1 + #for $q in $queries + ${q.input2} + #end for + > $out_file1; + echo "Work dir output" > working_file + + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + <repeat name="queries" title="Dataset"> + <param name="input2" type="data" label="Select" /> + </repeat> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + <data name="out_file2" format="txt" from_work_dir="working_file" /> + </outputs> + <help> + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60d8de457dd5/ Changeset: 60d8de457dd5 User: jmchilton Date: 2014-06-07 08:45:05 Summary: Allow tools and deployers to specify optional Docker-based dependency resolution. Testing it out: --------------- - Install [docker](http://docker.io) (tough, but getting easier). - Copy `test/functional/tools/catDocker.xml` to somewhere in `tools/` and add to `tool_conf.xml`. - Add `<param id="docker_enabled">true</param>` to your favorite job destination. - Run the tool. Description and Configuration: ------------------------------ Works with all stock job runners including remote jobs with the LWR. Supports file system isolation allowing deployer to determine what paths are exposed to container and optionally allowing these to be read-only. They can be overridden or extended but defaults are provided that attempt to guess what should be read-only and what should be writable based on Galaxy's configuration and the job destination. Lots of details and discussion in job_conf.xml.sample_advanced. `$GALAXY_SLOTS` (however it is configured for the given runner) is passed into the container at runtime and will be available. Tools are allowed to explicitly annotate what container should be used to run the tool. I added in hooks to allow a more expansive approach where containers could be linked to requirements and resolved that way. To be clear, this is not implemented at all but the class ContainerRegistry is instantiated, passed the list of requirements, and given the chance to return a list of potential containers... if someone wants to implement this someday. >From a reproducibility stand-point it makes sense for tool author's to have control over which container is selected, but there is this security and isolation aspect to these enhancements as well. So there are some more advanced options that allow deployers (instead of tool authors) to decide which containers are selected for jobs. `docker_default_container_id` can be added to a destination to cause that container to be used for all un-mapped tools - which will result in every job on that destination being run in a docker container. If the deployer does not even trust those tools annotated with image ids - they can go a step further and set `docker_container_id_override` instead. This will likewise cause all jobs to run in a container - but the tool details themselves will be ignored and *EVERY* tool will use the specified container. Additional advanced docker options are available to control memory, enable network access (disabled by default), where docker is found, if and how sudo is used, etc.... These are all documented in `job_conf.xml.sample_advanced`. Implementation Details: ----------------------- Metadata is set outside the container - so the container itself only needs to supply the underlying application and doesn't need to be configured with Galaxy for instance. Likewise - traditional `tool_dependency_dir` based dependency resolution is disabled when job is run in a container - for now it is assumed the container will supply these dependencies. What's Next: ------------ If implementation is merged, much is left to be discussed and worked through - how to fetch and control what images are fetched (right now the code just assumes if you have docker enabled all referenced images are available), where to fetch images from, tool shed integration (host a tool shed docker repository?, services to build docker images preconfigured with tool shed depedencies?), etc.... This is meant as more of a foundation for the dependency resolution and job runner portions of this. Affected #: 10 files diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -97,6 +97,90 @@ elements. This empty block will simply disable job metrics for the corresponding destination. --></destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination><destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -581,6 +581,16 @@ import galaxy.tools.search self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + from galaxy.tools.deps import containers + galaxy_root_dir = os.path.abspath(self.config.root) + file_path = os.path.abspath(getattr(self.config, "file_path")) + app_info = containers.AppInfo( + galaxy_root_dir, + default_file_path=file_path, + outputs_to_working_directory=self.config.outputs_to_working_directory + ) + self.container_finder = galaxy.tools.deps.containers.ContainerFinder(app_info) + def _configure_tool_data_tables( self, from_shed_config ): from galaxy.tools.data import ToolDataTableManager diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -1,4 +1,6 @@ from os import getcwd +from os import chmod +from os.path import join from os.path import abspath CAPTURE_RETURN_CODE = "return_code=$?" @@ -8,7 +10,14 @@ log = getLogger( __name__ ) -def build_command( runner, job_wrapper, include_metadata=False, include_work_dir_outputs=True, remote_command_params={} ): +def build_command( + runner, + job_wrapper, + container=None, + include_metadata=False, + include_work_dir_outputs=True, + remote_command_params={} +): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -29,7 +38,35 @@ __handle_version_command(commands_builder, job_wrapper) __handle_task_splitting(commands_builder, job_wrapper) - __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + # One could imagine also allowing dependencies inside of the container but + # that is too sophisticated for a first crack at this - build your + # containers ready to go! + if not container: + __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + if container: + # Stop now and build command before handling metadata and copying + # working directory files back. These should always happen outside + # of docker container - no security implications when generating + # metadata and means no need for Galaxy to be available to container + # and not copying workdir outputs back means on can be more restrictive + # of where container can write to in some circumstances. + + local_container_script = join( job_wrapper.working_directory, "container.sh" ) + fh = file( local_container_script, "w" ) + fh.write( "#!/bin/sh\n%s" % commands_builder.build() ) + fh.close() + chmod( local_container_script, 0755 ) + + compute_container_script = local_container_script + if 'working_directory' in remote_command_params: + compute_container_script = "/bin/sh %s" % join(remote_command_params['working_directory'], "container.sh") + + run_in_container_command = container.containerize_command( + compute_container_script + ) + commands_builder = CommandsBuilder( run_in_container_command ) if include_work_dir_outputs: __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params) diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -177,7 +177,16 @@ raise NotImplementedError() def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): - return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) + # TODO: Eliminate extra kwds no longer used (since LWR skips + # abstraction and calls build_command directly). + container = self._find_container( job_wrapper ) + return build_command( + self, + job_wrapper, + include_metadata=include_metadata, + include_work_dir_outputs=include_work_dir_outputs, + container=container + ) def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ): """ @@ -276,6 +285,31 @@ if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) + def _find_container( + self, + job_wrapper, + compute_working_directory=None, + compute_tool_directory=None, + compute_job_directory=None + ): + if not compute_working_directory: + compute_working_directory = job_wrapper.working_directory + + if not compute_tool_directory: + compute_tool_directory = job_wrapper.tool.tool_dir + + tool = job_wrapper.tool + from galaxy.tools.deps import containers + tool_info = containers.ToolInfo(tool.containers, tool.requirements) + job_info = containers.JobInfo(compute_working_directory, compute_tool_directory, compute_job_directory) + + destination_info = job_wrapper.job_destination.params + return self.app.container_finder.find_container( + tool_info, + destination_info, + job_info + ) + class JobState( object ): """ diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -227,9 +227,21 @@ metadata_kwds=metadata_kwds, dependency_resolution=dependency_resolution, ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for LWR, always worked for LWR but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) command_line = build_command( self, job_wrapper=job_wrapper, + container=container, include_metadata=remote_metadata, include_work_dir_outputs=False, remote_command_params=remote_command_params, diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1346,7 +1346,9 @@ self.__tests_populated = False # Requirements (dependencies) - self.requirements = parse_requirements_from_xml( root ) + requirements, containers = parse_requirements_from_xml( root ) + self.requirements = requirements + self.containers = containers # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/tools/deps/containers.py --- /dev/null +++ b/lib/galaxy/tools/deps/containers.py @@ -0,0 +1,246 @@ +from abc import ( + ABCMeta, + abstractmethod +) +import os +import string + +from galaxy.util import asbool +from ..deps import docker_util + +import logging +log = logging.getLogger(__name__) + +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerFinder(object): + + def __init__(self, app_info): + self.app_info = app_info + self.container_registry = ContainerRegistry() + + def find_container(self, tool_info, destination_info, job_info): + def __destination_container(container_description=None, container_id=None, container_type=None): + if container_description: + container_id = container_description.identifier + container_type = container_description.type + container = self.__destination_container( + container_id, + container_type, + tool_info, + destination_info, + job_info + ) + return container + + # Is destination forcing Galaxy to use a particular container do it, + # this is likely kind of a corner case. For instance if deployers + # do not trust the containers annotated in tools. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__overridden_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + # Otherwise lets see if we can find container for the tool. + + # Exact matches first from explicitly listed containers in tools... + for container_description in tool_info.container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # Implement vague concept of looping through all containers + # matching requirements. Exact details need to be worked through + # but hopefully the idea that it sits below find_container somewhere + # external components to this module don't need to worry about it + # is good enough. + container_descriptions = self.container_registry.container_descriptions_for_requirements(tool_info.requirements) + for container_description in container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # If we still don't have a container, check to see if any container + # types define a default container id and use that. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__default_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + return NULL_CONTAINER + + def __overridden_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_container_id_override" % container_type) + + def __default_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_default_container_id" % container_type) + + def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info): + # TODO: ensure destination_info is dict-like + if not self.__container_type_enabled(container_type, destination_info): + return NULL_CONTAINER + + # TODO: Right now this assumes all containers available when a + # container type is - there should be more thought put into this. + # Checking which are availalbe - settings policies for what can be + # auto-fetched, etc.... + return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info) + + def __container_type_enabled(self, container_type, destination_info): + return asbool(destination_info.get("%s_enabled" % container_type, False)) + + +class ContainerRegistry(): + + def __init__(self): + pass + + def container_descriptions_for_requirements(self, requirements): + # Return lists of containers that would match requirements... + return [] + + +class AppInfo(object): + + def __init__(self, galaxy_root_dir=None, default_file_path=None, outputs_to_working_directory=False): + self.galaxy_root_dir = galaxy_root_dir + self.default_file_path = default_file_path + # TODO: Vary default value for docker_volumes based on this... + self.outputs_to_working_directory = outputs_to_working_directory + + +class ToolInfo(object): + # TODO: Introduce tool XML syntax to annotate the optional environment + # variables they can consume (e.g. JVM options, license keys, etc..) + # and add these to env_path_through + + def __init__(self, container_descriptions=[], requirements=[]): + self.container_descriptions = container_descriptions + self.requirements = requirements + self.env_pass_through = ["GALAXY_SLOTS"] + + +class JobInfo(object): + + def __init__(self, working_directory, tool_directory, job_directory): + self.working_directory = working_directory + self.job_directory = job_directory + # Tool files may be remote staged - so this is unintuitively a property + # of the job not of the tool. + self.tool_directory = tool_directory + + +class Container( object ): + __metaclass__ = ABCMeta + + def __init__(self, container_id, app_info, tool_info, destination_info, job_info): + self.container_id = container_id + self.app_info = app_info + self.tool_info = tool_info + self.destination_info = destination_info + self.job_info = job_info + + @abstractmethod + def containerize_command(self, command): + """ + Use destination supplied container configuration parameters, + container_id, and command to build a new command that runs + input command in container. + """ + + +class DockerContainer(Container): + + def containerize_command(self, command): + def prop(name, default): + destination_name = "docker_%s" % name + return self.destination_info.get(destination_name, default) + + env_directives = [] + for pass_through_var in self.tool_info.env_pass_through: + env_directives.append('"%s=$%s"' % (pass_through_var, pass_through_var)) + + # Allow destinations to explicitly set environment variables just for + # docker container. Better approach is to set for destination and then + # pass through only what tool needs however. (See todo in ToolInfo.) + for key, value in self.destination_info.iteritems(): + if key.startswith("docker_env_"): + env = key[len("docker_env_"):] + env_directives.append('"%s=%s"' % (env, value)) + + working_directory = self.job_info.working_directory + if not working_directory: + raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory) + + volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults")) + # TODO: Remove redundant volumes... + volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw) + return docker_util.build_docker_run_command( + command, + self.container_id, + volumes=volumes, + env_directives=env_directives, + working_directory=working_directory, + docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND), + sudo=asbool(prop("sudo", docker_util.DEFAULT_SUDO)), + sudo_cmd=prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND), + host=prop("host", docker_util.DEFAULT_HOST), + net=prop("net", "none") # By default, docker instance has networking disabled + ) + + def __expand_str(self, value): + template = string.Template(value) + variables = dict() + + def add_var(name, value): + if value: + variables[name] = os.path.abspath(value) + + add_var("working_directory", self.job_info.working_directory) + add_var("job_directory", self.job_info.job_directory) + add_var("tool_directory", self.job_info.tool_directory) + add_var("galaxy_root", self.app_info.galaxy_root_dir) + add_var("default_file_path", self.app_info.default_file_path) + + if self.job_info.job_directory: + # We have a job directory, so everything needed (excluding index + # files) should be available in job_directory... + defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw" + elif self.app_info.outputs_to_working_directory: + # Should need default_file_path (which is a course estimate given + # object stores anyway. + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro" + else: + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw" + + # Define $defaults that can easily be extended with external library and + # index data without deployer worrying about above details. + variables["defaults"] = string.Template(defaults).safe_substitute(variables) + + return template.safe_substitute(variables) + + +CONTAINER_CLASSES = dict( + docker=DockerContainer, +) + + +class NullContainer(object): + + def __init__(self): + pass + + def __nonzero__(self): + return False + + +NULL_CONTAINER = NullContainer() diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/tools/deps/docker_util.py --- /dev/null +++ b/lib/galaxy/tools/deps/docker_util.py @@ -0,0 +1,91 @@ + +DEFAULT_DOCKER_COMMAND = "docker" +DEFAULT_SUDO = True +DEFAULT_SUDO_COMMAND = "sudo" +DEFAULT_HOST = None +DEFAULT_VOLUME_MOUNT_TYPE = "rw" +DEFAULT_WORKING_DIRECTORY = None +DEFAULT_NET = None +DEFAULT_MEMORY = None + + +class DockerVolume(object): + + def __init__(self, path, to_path=None, how=DEFAULT_VOLUME_MOUNT_TYPE): + self.from_path = path + self.to_path = to_path or path + if not DockerVolume.__valid_how(how): + raise ValueError("Invalid way to specify docker volume %s" % how) + self.how = how + + @staticmethod + def volumes_from_str(volumes_as_str): + if not volumes_as_str: + return [] + volume_strs = [v.strip() for v in volumes_as_str.split(",")] + return map(DockerVolume.volume_from_str, volume_strs) + + @staticmethod + def volume_from_str(as_str): + if not as_str: + raise ValueError("Failed to parse docker volume from %s" % as_str) + parts = as_str.split(":", 2) + kwds = dict(path=parts[0]) + if len(parts) == 2: + if DockerVolume.__valid_how(parts[1]): + kwds["how"] = parts[1] + else: + kwds["to_path"] = parts[1] + elif len(parts) == 3: + kwds["to_path"] = parts[1] + kwds["how"] = parts[2] + return DockerVolume(**kwds) + + @staticmethod + def __valid_how(how): + return how in ["ro", "rw"] + + def __str__(self): + return ":".join([self.from_path, self.to_path, self.how]) + + +def build_docker_run_command( + container_command, + image, + tag=None, + docker_cmd=DEFAULT_DOCKER_COMMAND, + volumes=[], + memory=DEFAULT_MEMORY, + env_directives=[], + working_directory=DEFAULT_WORKING_DIRECTORY, + sudo=DEFAULT_SUDO, + sudo_cmd=DEFAULT_SUDO_COMMAND, + name=None, + host=DEFAULT_HOST, + net=DEFAULT_NET, +): + command_parts = [] + if sudo: + command_parts.append(sudo_cmd) + command_parts.append(docker_cmd) + if host: + command_parts.append(["-H", host]) + command_parts.append("run") + for env_directive in env_directives: + command_parts.extend(["-e", env_directive]) + for volume in volumes: + command_parts.extend(["-v", str(volume)]) + if memory: + command_parts.extend(["-m", memory]) + if name: + command_parts.extend(["-name", name]) + if working_directory: + command_parts.extend(["-w", working_directory]) + if net: + command_parts.extend(["--net", net]) + full_image = image + if tag: + full_image = "%s:%s" % (full_image, tag) + command_parts.append(full_image) + command_parts.append(container_command) + return " ".join(command_parts) diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d lib/galaxy/tools/deps/requirements.py --- a/lib/galaxy/tools/deps/requirements.py +++ b/lib/galaxy/tools/deps/requirements.py @@ -26,6 +26,25 @@ return ToolRequirement( name=name, type=type, version=version ) +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerDescription( object ): + + def __init__( self, identifier=None, type="docker" ): + self.identifier = identifier + self.type = type + + def to_dict( self ): + return dict(identifier=self.identifier, type=self.type) + + @staticmethod + def from_dict( dict ): + identifier = dict["identifier"] + type = dict.get("type", DEFAULT_CONTAINER_TYPE) + return ContainerDescription( identifier=identifier, type=type ) + + def parse_requirements_from_xml( xml_root ): """ @@ -63,4 +82,15 @@ requirement = ToolRequirement( name=name, type=type, version=version ) requirements.append( requirement ) - return requirements + container_elems = [] + if requirements_elem is not None: + container_elems = requirements_elem.findall( 'container' ) + + containers = [] + for container_elem in container_elems: + identifier = xml_text( container_elem ) + type = container_elem.get( "type", DEFAULT_CONTAINER_TYPE ) + container = ContainerDescription( identifier=identifier, type=type ) + containers.append( container ) + + return requirements, containers diff -r 84a00e4f7d06e9adcec7297d8133ce70524dc242 -r 60d8de457dd57adb71e30725a6451126148edd6d test/functional/tools/catDocker.xml --- /dev/null +++ b/test/functional/tools/catDocker.xml @@ -0,0 +1,28 @@ +<tool id="catdc" name="Concatenate datasets (in docker)"> + <description>tail-to-head</description> + <requirements> + <container type="docker">busybox:ubuntu-14.04</container> + </requirements> + <command> + echo "Galaxy slots passed through contain as \$GALAXY_SLOTS"; + cat $input1 + #for $q in $queries + ${q.input2} + #end for + > $out_file1; + echo "Work dir output" > working_file + + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + <repeat name="queries" title="Dataset"> + <param name="input2" type="data" label="Select" /> + </repeat> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + <data name="out_file2" format="txt" from_work_dir="working_file" /> + </outputs> + <help> + </help> +</tool> https://bitbucket.org/galaxy/galaxy-central/commits/646b5877871b/ Changeset: 646b5877871b User: dannon Date: 2014-06-12 17:09:04 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #401) Allow tools and deployers to specify optional Docker-based dependency resolution. Affected #: 10 files diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -97,6 +97,90 @@ elements. This empty block will simply disable job metrics for the corresponding destination. --></destination> + <destination id="docker_local" runner="local"> + <param id="docker_enabled">true</param> +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  +  + +  +  + +  +  + + </destination><destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -582,6 +582,16 @@ import galaxy.tools.search self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + from galaxy.tools.deps import containers + galaxy_root_dir = os.path.abspath(self.config.root) + file_path = os.path.abspath(getattr(self.config, "file_path")) + app_info = containers.AppInfo( + galaxy_root_dir, + default_file_path=file_path, + outputs_to_working_directory=self.config.outputs_to_working_directory + ) + self.container_finder = galaxy.tools.deps.containers.ContainerFinder(app_info) + def _configure_tool_data_tables( self, from_shed_config ): from galaxy.tools.data import ToolDataTableManager diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/command_factory.py --- a/lib/galaxy/jobs/command_factory.py +++ b/lib/galaxy/jobs/command_factory.py @@ -1,4 +1,6 @@ from os import getcwd +from os import chmod +from os.path import join from os.path import abspath CAPTURE_RETURN_CODE = "return_code=$?" @@ -8,7 +10,14 @@ log = getLogger( __name__ ) -def build_command( runner, job_wrapper, include_metadata=False, include_work_dir_outputs=True, remote_command_params={} ): +def build_command( + runner, + job_wrapper, + container=None, + include_metadata=False, + include_work_dir_outputs=True, + remote_command_params={} +): """ Compose the sequence of commands necessary to execute a job. This will currently include: @@ -29,7 +38,35 @@ __handle_version_command(commands_builder, job_wrapper) __handle_task_splitting(commands_builder, job_wrapper) - __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + # One could imagine also allowing dependencies inside of the container but + # that is too sophisticated for a first crack at this - build your + # containers ready to go! + if not container: + __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) + + if container: + # Stop now and build command before handling metadata and copying + # working directory files back. These should always happen outside + # of docker container - no security implications when generating + # metadata and means no need for Galaxy to be available to container + # and not copying workdir outputs back means on can be more restrictive + # of where container can write to in some circumstances. + + local_container_script = join( job_wrapper.working_directory, "container.sh" ) + fh = file( local_container_script, "w" ) + fh.write( "#!/bin/sh\n%s" % commands_builder.build() ) + fh.close() + chmod( local_container_script, 0755 ) + + compute_container_script = local_container_script + if 'working_directory' in remote_command_params: + compute_container_script = "/bin/sh %s" % join(remote_command_params['working_directory'], "container.sh") + + run_in_container_command = container.containerize_command( + compute_container_script + ) + commands_builder = CommandsBuilder( run_in_container_command ) if include_work_dir_outputs: __handle_work_dir_outputs(commands_builder, job_wrapper, runner, remote_command_params) diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -177,7 +177,16 @@ raise NotImplementedError() def build_command_line( self, job_wrapper, include_metadata=False, include_work_dir_outputs=True ): - return build_command( self, job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) + # TODO: Eliminate extra kwds no longer used (since LWR skips + # abstraction and calls build_command directly). + container = self._find_container( job_wrapper ) + return build_command( + self, + job_wrapper, + include_metadata=include_metadata, + include_work_dir_outputs=include_work_dir_outputs, + container=container + ) def get_work_dir_outputs( self, job_wrapper, job_working_directory=None ): """ @@ -276,6 +285,31 @@ if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) + def _find_container( + self, + job_wrapper, + compute_working_directory=None, + compute_tool_directory=None, + compute_job_directory=None + ): + if not compute_working_directory: + compute_working_directory = job_wrapper.working_directory + + if not compute_tool_directory: + compute_tool_directory = job_wrapper.tool.tool_dir + + tool = job_wrapper.tool + from galaxy.tools.deps import containers + tool_info = containers.ToolInfo(tool.containers, tool.requirements) + job_info = containers.JobInfo(compute_working_directory, compute_tool_directory, compute_job_directory) + + destination_info = job_wrapper.job_destination.params + return self.app.container_finder.find_container( + tool_info, + destination_info, + job_info + ) + class JobState( object ): """ diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -233,9 +233,21 @@ metadata_kwds=metadata_kwds, dependency_resolution=dependency_resolution, ) + remote_working_directory = remote_job_config['working_directory'] + # TODO: Following defs work for LWR, always worked for LWR but should be + # calculated at some other level. + remote_job_directory = os.path.abspath(os.path.join(remote_working_directory, os.path.pardir)) + remote_tool_directory = os.path.abspath(os.path.join(remote_job_directory, "tool_files")) + container = self._find_container( + job_wrapper, + compute_working_directory=remote_working_directory, + compute_tool_directory=remote_tool_directory, + compute_job_directory=remote_job_directory, + ) command_line = build_command( self, job_wrapper=job_wrapper, + container=container, include_metadata=remote_metadata, include_work_dir_outputs=False, remote_command_params=remote_command_params, diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1346,7 +1346,9 @@ self.__tests_populated = False # Requirements (dependencies) - self.requirements = parse_requirements_from_xml( root ) + requirements, containers = parse_requirements_from_xml( root ) + self.requirements = requirements + self.containers = containers # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/containers.py --- /dev/null +++ b/lib/galaxy/tools/deps/containers.py @@ -0,0 +1,246 @@ +from abc import ( + ABCMeta, + abstractmethod +) +import os +import string + +from galaxy.util import asbool +from ..deps import docker_util + +import logging +log = logging.getLogger(__name__) + +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerFinder(object): + + def __init__(self, app_info): + self.app_info = app_info + self.container_registry = ContainerRegistry() + + def find_container(self, tool_info, destination_info, job_info): + def __destination_container(container_description=None, container_id=None, container_type=None): + if container_description: + container_id = container_description.identifier + container_type = container_description.type + container = self.__destination_container( + container_id, + container_type, + tool_info, + destination_info, + job_info + ) + return container + + # Is destination forcing Galaxy to use a particular container do it, + # this is likely kind of a corner case. For instance if deployers + # do not trust the containers annotated in tools. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__overridden_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + # Otherwise lets see if we can find container for the tool. + + # Exact matches first from explicitly listed containers in tools... + for container_description in tool_info.container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # Implement vague concept of looping through all containers + # matching requirements. Exact details need to be worked through + # but hopefully the idea that it sits below find_container somewhere + # external components to this module don't need to worry about it + # is good enough. + container_descriptions = self.container_registry.container_descriptions_for_requirements(tool_info.requirements) + for container_description in container_descriptions: + container = __destination_container(container_description) + if container: + return container + + # If we still don't have a container, check to see if any container + # types define a default container id and use that. + for container_type in CONTAINER_CLASSES.keys(): + container_id = self.__default_container_id(container_type, destination_info) + if container_id: + container = __destination_container(container_type=container_type, container_id=container_id) + if container: + return container + + return NULL_CONTAINER + + def __overridden_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_container_id_override" % container_type) + + def __default_container_id(self, container_type, destination_info): + if not self.__container_type_enabled(container_type, destination_info): + return None + return destination_info.get("%s_default_container_id" % container_type) + + def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info): + # TODO: ensure destination_info is dict-like + if not self.__container_type_enabled(container_type, destination_info): + return NULL_CONTAINER + + # TODO: Right now this assumes all containers available when a + # container type is - there should be more thought put into this. + # Checking which are availalbe - settings policies for what can be + # auto-fetched, etc.... + return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info) + + def __container_type_enabled(self, container_type, destination_info): + return asbool(destination_info.get("%s_enabled" % container_type, False)) + + +class ContainerRegistry(): + + def __init__(self): + pass + + def container_descriptions_for_requirements(self, requirements): + # Return lists of containers that would match requirements... + return [] + + +class AppInfo(object): + + def __init__(self, galaxy_root_dir=None, default_file_path=None, outputs_to_working_directory=False): + self.galaxy_root_dir = galaxy_root_dir + self.default_file_path = default_file_path + # TODO: Vary default value for docker_volumes based on this... + self.outputs_to_working_directory = outputs_to_working_directory + + +class ToolInfo(object): + # TODO: Introduce tool XML syntax to annotate the optional environment + # variables they can consume (e.g. JVM options, license keys, etc..) + # and add these to env_path_through + + def __init__(self, container_descriptions=[], requirements=[]): + self.container_descriptions = container_descriptions + self.requirements = requirements + self.env_pass_through = ["GALAXY_SLOTS"] + + +class JobInfo(object): + + def __init__(self, working_directory, tool_directory, job_directory): + self.working_directory = working_directory + self.job_directory = job_directory + # Tool files may be remote staged - so this is unintuitively a property + # of the job not of the tool. + self.tool_directory = tool_directory + + +class Container( object ): + __metaclass__ = ABCMeta + + def __init__(self, container_id, app_info, tool_info, destination_info, job_info): + self.container_id = container_id + self.app_info = app_info + self.tool_info = tool_info + self.destination_info = destination_info + self.job_info = job_info + + @abstractmethod + def containerize_command(self, command): + """ + Use destination supplied container configuration parameters, + container_id, and command to build a new command that runs + input command in container. + """ + + +class DockerContainer(Container): + + def containerize_command(self, command): + def prop(name, default): + destination_name = "docker_%s" % name + return self.destination_info.get(destination_name, default) + + env_directives = [] + for pass_through_var in self.tool_info.env_pass_through: + env_directives.append('"%s=$%s"' % (pass_through_var, pass_through_var)) + + # Allow destinations to explicitly set environment variables just for + # docker container. Better approach is to set for destination and then + # pass through only what tool needs however. (See todo in ToolInfo.) + for key, value in self.destination_info.iteritems(): + if key.startswith("docker_env_"): + env = key[len("docker_env_"):] + env_directives.append('"%s=%s"' % (env, value)) + + working_directory = self.job_info.working_directory + if not working_directory: + raise Exception("Cannot containerize command [%s] without defined working directory." % working_directory) + + volumes_raw = self.__expand_str(self.destination_info.get("docker_volumes", "$defaults")) + # TODO: Remove redundant volumes... + volumes = docker_util.DockerVolume.volumes_from_str(volumes_raw) + return docker_util.build_docker_run_command( + command, + self.container_id, + volumes=volumes, + env_directives=env_directives, + working_directory=working_directory, + docker_cmd=prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND), + sudo=asbool(prop("sudo", docker_util.DEFAULT_SUDO)), + sudo_cmd=prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND), + host=prop("host", docker_util.DEFAULT_HOST), + net=prop("net", "none") # By default, docker instance has networking disabled + ) + + def __expand_str(self, value): + template = string.Template(value) + variables = dict() + + def add_var(name, value): + if value: + variables[name] = os.path.abspath(value) + + add_var("working_directory", self.job_info.working_directory) + add_var("job_directory", self.job_info.job_directory) + add_var("tool_directory", self.job_info.tool_directory) + add_var("galaxy_root", self.app_info.galaxy_root_dir) + add_var("default_file_path", self.app_info.default_file_path) + + if self.job_info.job_directory: + # We have a job directory, so everything needed (excluding index + # files) should be available in job_directory... + defaults = "$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw" + elif self.app_info.outputs_to_working_directory: + # Should need default_file_path (which is a course estimate given + # object stores anyway. + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:ro" + else: + defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw" + + # Define $defaults that can easily be extended with external library and + # index data without deployer worrying about above details. + variables["defaults"] = string.Template(defaults).safe_substitute(variables) + + return template.safe_substitute(variables) + + +CONTAINER_CLASSES = dict( + docker=DockerContainer, +) + + +class NullContainer(object): + + def __init__(self): + pass + + def __nonzero__(self): + return False + + +NULL_CONTAINER = NullContainer() diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/docker_util.py --- /dev/null +++ b/lib/galaxy/tools/deps/docker_util.py @@ -0,0 +1,91 @@ + +DEFAULT_DOCKER_COMMAND = "docker" +DEFAULT_SUDO = True +DEFAULT_SUDO_COMMAND = "sudo" +DEFAULT_HOST = None +DEFAULT_VOLUME_MOUNT_TYPE = "rw" +DEFAULT_WORKING_DIRECTORY = None +DEFAULT_NET = None +DEFAULT_MEMORY = None + + +class DockerVolume(object): + + def __init__(self, path, to_path=None, how=DEFAULT_VOLUME_MOUNT_TYPE): + self.from_path = path + self.to_path = to_path or path + if not DockerVolume.__valid_how(how): + raise ValueError("Invalid way to specify docker volume %s" % how) + self.how = how + + @staticmethod + def volumes_from_str(volumes_as_str): + if not volumes_as_str: + return [] + volume_strs = [v.strip() for v in volumes_as_str.split(",")] + return map(DockerVolume.volume_from_str, volume_strs) + + @staticmethod + def volume_from_str(as_str): + if not as_str: + raise ValueError("Failed to parse docker volume from %s" % as_str) + parts = as_str.split(":", 2) + kwds = dict(path=parts[0]) + if len(parts) == 2: + if DockerVolume.__valid_how(parts[1]): + kwds["how"] = parts[1] + else: + kwds["to_path"] = parts[1] + elif len(parts) == 3: + kwds["to_path"] = parts[1] + kwds["how"] = parts[2] + return DockerVolume(**kwds) + + @staticmethod + def __valid_how(how): + return how in ["ro", "rw"] + + def __str__(self): + return ":".join([self.from_path, self.to_path, self.how]) + + +def build_docker_run_command( + container_command, + image, + tag=None, + docker_cmd=DEFAULT_DOCKER_COMMAND, + volumes=[], + memory=DEFAULT_MEMORY, + env_directives=[], + working_directory=DEFAULT_WORKING_DIRECTORY, + sudo=DEFAULT_SUDO, + sudo_cmd=DEFAULT_SUDO_COMMAND, + name=None, + host=DEFAULT_HOST, + net=DEFAULT_NET, +): + command_parts = [] + if sudo: + command_parts.append(sudo_cmd) + command_parts.append(docker_cmd) + if host: + command_parts.append(["-H", host]) + command_parts.append("run") + for env_directive in env_directives: + command_parts.extend(["-e", env_directive]) + for volume in volumes: + command_parts.extend(["-v", str(volume)]) + if memory: + command_parts.extend(["-m", memory]) + if name: + command_parts.extend(["-name", name]) + if working_directory: + command_parts.extend(["-w", working_directory]) + if net: + command_parts.extend(["--net", net]) + full_image = image + if tag: + full_image = "%s:%s" % (full_image, tag) + command_parts.append(full_image) + command_parts.append(container_command) + return " ".join(command_parts) diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 lib/galaxy/tools/deps/requirements.py --- a/lib/galaxy/tools/deps/requirements.py +++ b/lib/galaxy/tools/deps/requirements.py @@ -26,6 +26,25 @@ return ToolRequirement( name=name, type=type, version=version ) +DEFAULT_CONTAINER_TYPE = "docker" + + +class ContainerDescription( object ): + + def __init__( self, identifier=None, type="docker" ): + self.identifier = identifier + self.type = type + + def to_dict( self ): + return dict(identifier=self.identifier, type=self.type) + + @staticmethod + def from_dict( dict ): + identifier = dict["identifier"] + type = dict.get("type", DEFAULT_CONTAINER_TYPE) + return ContainerDescription( identifier=identifier, type=type ) + + def parse_requirements_from_xml( xml_root ): """ @@ -63,4 +82,15 @@ requirement = ToolRequirement( name=name, type=type, version=version ) requirements.append( requirement ) - return requirements + container_elems = [] + if requirements_elem is not None: + container_elems = requirements_elem.findall( 'container' ) + + containers = [] + for container_elem in container_elems: + identifier = xml_text( container_elem ) + type = container_elem.get( "type", DEFAULT_CONTAINER_TYPE ) + container = ContainerDescription( identifier=identifier, type=type ) + containers.append( container ) + + return requirements, containers diff -r a19ef9da5e470d14a31ad8385f14168a14556224 -r 646b5877871b3b15c6fc6a9ecf111fceb23ea270 test/functional/tools/catDocker.xml --- /dev/null +++ b/test/functional/tools/catDocker.xml @@ -0,0 +1,28 @@ +<tool id="catdc" name="Concatenate datasets (in docker)"> + <description>tail-to-head</description> + <requirements> + <container type="docker">busybox:ubuntu-14.04</container> + </requirements> + <command> + echo "Galaxy slots passed through contain as \$GALAXY_SLOTS"; + cat $input1 + #for $q in $queries + ${q.input2} + #end for + > $out_file1; + echo "Work dir output" > working_file + + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + <repeat name="queries" title="Dataset"> + <param name="input2" type="data" label="Select" /> + </repeat> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + <data name="out_file2" format="txt" from_work_dir="working_file" /> + </outputs> + <help> + </help> +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: natefoo: Merge stable.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a19ef9da5e47/ Changeset: a19ef9da5e47 User: natefoo Date: 2014-06-12 16:00:39 Summary: Merge stable. Affected #: 2 files diff -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 -r a19ef9da5e470d14a31ad8385f14168a14556224 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -128,6 +128,7 @@ from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log ) + self.heartbeat.daemon = True self.heartbeat.start() # Enable the memdump signal catcher if configured and available if self.config.use_memdump: @@ -150,6 +151,7 @@ self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), galaxy.queue_worker.control_message_to_task) + self.control_worker.daemon = True self.control_worker.start() def shutdown( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Daemonize threads so that SIGINT (Ctrl-C) works again.
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6b1ea3a6a9e/ Changeset: d6b1ea3a6a9e Branch: stable User: natefoo Date: 2014-06-12 15:53:37 Summary: Daemonize threads so that SIGINT (Ctrl-C) works again. Affected #: 1 file diff -r 5a9adea86d411348023b7307b3c935cd99c6dea9 -r d6b1ea3a6a9ed2e7c3fa41518c5a690ed49c1265 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -128,6 +128,7 @@ from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log ) + self.heartbeat.daemon = True self.heartbeat.start() # Enable the memdump signal catcher if configured and available if self.config.use_memdump: @@ -150,6 +151,7 @@ self.control_worker = GalaxyQueueWorker(self, galaxy.queues.control_queue_from_config(self.config), galaxy.queue_worker.control_message_to_task) + self.control_worker.daemon = True self.control_worker.start() def shutdown( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Drop threadframe for heartbeat (its functionality was integrated in sys in Python 2.5...)
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d5ed9cbbf9b/ Changeset: 5d5ed9cbbf9b User: natefoo Date: 2014-06-12 15:51:45 Summary: Drop threadframe for heartbeat (its functionality was integrated in sys in Python 2.5...) Affected #: 2 files diff -r 07df86dff47c924830c2912500af356180778162 -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,6 @@ pysqlite = 2.5.6 python_lzo = 1.08_2.03_static PyYAML = 3.10 -threadframe = 0.2 guppy = 0.1.10 SQLAlchemy = 0.7.9 ; msgpack_python = 0.2.4 diff -r 07df86dff47c924830c2912500af356180778162 -r 5d5ed9cbbf9b6a37dbf0777cf4b88015df9135f4 lib/galaxy/util/heartbeat.py --- a/lib/galaxy/util/heartbeat.py +++ b/lib/galaxy/util/heartbeat.py @@ -1,182 +1,167 @@ +import threading +import time +import traceback +import os +import sys -# Attempt to load threadframe module, and only define Heartbeat class -# if available +def get_current_thread_object_dict(): + """ + Get a dictionary of all 'Thread' objects created via the threading + module keyed by thread_id. Note that not all interpreter threads + have a thread objects, only the main thread and any created via the + 'threading' module. Threads created via the low level 'thread' module + will not be in the returned dictionary. -try: + HACK: This mucks with the internals of the threading module since that + module does not expose any way to match 'Thread' objects with + intepreter thread identifiers (though it should). + """ + rval = dict() + # Acquire the lock and then union the contents of 'active' and 'limbo' + # threads into the return value. + threading._active_limbo_lock.acquire() + rval.update( threading._active ) + rval.update( threading._limbo ) + threading._active_limbo_lock.release() + return rval - import pkg_resources - pkg_resources.require( "threadframe" ) +class Heartbeat( threading.Thread ): + """ + Thread that periodically dumps the state of all threads to a file + """ + def __init__( self, name="Heartbeat Thread", period=20, fname="heartbeat.log" ): + threading.Thread.__init__( self, name=name ) + self.should_stop = False + self.period = period + self.fname = fname + self.file = None + self.fname_nonsleeping = fname + ".nonsleeping" + self.file_nonsleeping = None + self.nonsleeping_heartbeats = { } + # Save process id + self.pid = os.getpid() + # Event to wait on when sleeping, allows us to interrupt for shutdown + self.wait_event = threading.Event() + def run( self ): + self.file = open( self.fname, "a" ) + print >> self.file, "Heartbeat for pid %d thread started at %s" % ( self.pid, time.asctime() ) + print >> self.file + self.file_nonsleeping = open ( self.fname_nonsleeping, "a" ) + print >> self.file_nonsleeping, "Non-Sleeping-threads for pid %d thread started at %s" % ( self.pid, time.asctime() ) + print >> self.file_nonsleeping + try: + while not self.should_stop: + # Print separator with timestamp + print >> self.file, "Traceback dump for all threads at %s:" % time.asctime() + print >> self.file + # Print the thread states + threads = get_current_thread_object_dict() + for thread_id, frame in sys._current_frames().iteritems(): + if thread_id in threads: + object = repr( threads[thread_id] ) + else: + object = "<No Thread object>" + print >> self.file, "Thread %s, %s:" % ( thread_id, object ) + print >> self.file + traceback.print_stack( frame, file=self.file ) + print >> self.file + print >> self.file, "End dump" + print >> self.file + self.file.flush() + self.print_nonsleeping(threads) + # Sleep for a bit + self.wait_event.wait( self.period ) + finally: + print >> self.file, "Heartbeat for pid %d thread stopped at %s" % ( self.pid, time.asctime() ) + print >> self.file + # Cleanup + self.file.close() + self.file_nonsleeping.close() -except: + def shutdown( self ): + self.should_stop = True + self.wait_event.set() + self.join() - import sys - print >> sys.stderr, "No threadframe module, Heartbeat not available" - Heartbeat = None + def thread_is_sleeping ( self, last_stack_frame ): + """ + Returns True if the given stack-frame represents a known + sleeper function (at least in python 2.5) + """ + _filename = last_stack_frame[0] + _line = last_stack_frame[1] + _funcname = last_stack_frame[2] + _text = last_stack_frame[3] + ### Ugly hack to tell if a thread is supposedly sleeping or not + ### These are the most common sleeping functions I've found. + ### Is there a better way? (python interpreter internals?) + ### Tested only with python 2.5 + if _funcname=="wait" and _text=="waiter.acquire()": + return True + if _funcname=="wait" and _text=="_sleep(delay)": + return True + if _funcname=="accept" and _text[-14:]=="_sock.accept()": + return True + if _funcname=="monitor" and _text.startswith("time.sleep( ") and _text.endswith(" )"): + return True + if _funcname=="drain_events" and _text=="sleep(polling_interval)": + return True + #Ugly hack: always skip the heartbeat thread + #TODO: get the current thread-id in python + # skip heartbeat thread by thread-id, not by filename + if _filename.find("/lib/galaxy/util/heartbeat.py")!=-1: + return True + ## By default, assume the thread is not sleeping + return False -else: + def get_interesting_stack_frame ( self, stack_frames ): + """ + Scans a given backtrace stack frames, returns a single + quadraple of [filename, line, function-name, text] of + the single, deepest, most interesting frame. - import threading - import threadframe - import time - import traceback - import os - import sys + Interesting being:: - def get_current_thread_object_dict(): + inside the galaxy source code ("/lib/galaxy"), + prefreably not an egg. """ - Get a dictionary of all 'Thread' objects created via the threading - module keyed by thread_id. Note that not all interpreter threads - have a thread objects, only the main thread and any created via the - 'threading' module. Threads created via the low level 'thread' module - will not be in the returned dictionary. + for _filename, _line, _funcname, _text in reversed(stack_frames): + idx = _filename.find("/lib/galaxy/") + if idx!=-1: + relative_filename = _filename[idx:] + return ( relative_filename, _line, _funcname, _text ) + # no "/lib/galaxy" code found, return the innermost frame + return stack_frames[-1] - HACK: This mucks with the internals of the threading module since that - module does not expose any way to match 'Thread' objects with - intepreter thread identifiers (though it should). - """ - rval = dict() - # Acquire the lock and then union the contents of 'active' and 'limbo' - # threads into the return value. - threading._active_limbo_lock.acquire() - rval.update( threading._active ) - rval.update( threading._limbo ) - threading._active_limbo_lock.release() - return rval + def print_nonsleeping( self, threads_object_dict ): + print >> self.file_nonsleeping, "Non-Sleeping threads at %s:" % time.asctime() + print >> self.file_nonsleeping + all_threads_are_sleeping = True + threads = get_current_thread_object_dict() + for thread_id, frame in sys._current_frames().iteritems(): + if thread_id in threads: + object = repr( threads[thread_id] ) + else: + object = "<No Thread object>" + tb = traceback.extract_stack(frame) + if self.thread_is_sleeping(tb[-1]): + if thread_id in self.nonsleeping_heartbeats: + del self.nonsleeping_heartbeats[thread_id] + continue - class Heartbeat( threading.Thread ): - """ - Thread that periodically dumps the state of all threads to a file using - the `threadframe` extension - """ - def __init__( self, name="Heartbeat Thread", period=20, fname="heartbeat.log" ): - threading.Thread.__init__( self, name=name ) - self.should_stop = False - self.period = period - self.fname = fname - self.file = None - self.fname_nonsleeping = fname + ".nonsleeping" - self.file_nonsleeping = None - self.nonsleeping_heartbeats = { } - # Save process id - self.pid = os.getpid() - # Event to wait on when sleeping, allows us to interrupt for shutdown - self.wait_event = threading.Event() - def run( self ): - self.file = open( self.fname, "a" ) - print >> self.file, "Heartbeat for pid %d thread started at %s" % ( self.pid, time.asctime() ) - print >> self.file - self.file_nonsleeping = open ( self.fname_nonsleeping, "a" ) - print >> self.file_nonsleeping, "Non-Sleeping-threads for pid %d thread started at %s" % ( self.pid, time.asctime() ) - print >> self.file_nonsleeping - try: - while not self.should_stop: - # Print separator with timestamp - print >> self.file, "Traceback dump for all threads at %s:" % time.asctime() - print >> self.file - # Print the thread states - threads = get_current_thread_object_dict() - for thread_id, frame in threadframe.dict().iteritems(): - if thread_id in threads: - object = repr( threads[thread_id] ) - else: - object = "<No Thread object>" - print >> self.file, "Thread %s, %s:" % ( thread_id, object ) - print >> self.file - traceback.print_stack( frame, file=self.file ) - print >> self.file - print >> self.file, "End dump" - print >> self.file - self.file.flush() - self.print_nonsleeping(threads) - # Sleep for a bit - self.wait_event.wait( self.period ) - finally: - print >> self.file, "Heartbeat for pid %d thread stopped at %s" % ( self.pid, time.asctime() ) - print >> self.file - # Cleanup - self.file.close() - self.file_nonsleeping.close() + # Count non-sleeping thread heartbeats + if thread_id in self.nonsleeping_heartbeats: + self.nonsleeping_heartbeats[thread_id] += 1 + else: + self.nonsleeping_heartbeats[thread_id]=1 - def shutdown( self ): - self.should_stop = True - self.wait_event.set() - self.join() + good_frame = self.get_interesting_stack_frame(tb) + print >> self.file_nonsleeping, "Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s" % \ + ( thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3] ) + all_threads_are_sleeping = False - def thread_is_sleeping ( self, last_stack_frame ): - """ - Returns True if the given stack-frame represents a known - sleeper function (at least in python 2.5) - """ - _filename = last_stack_frame[0] - _line = last_stack_frame[1] - _funcname = last_stack_frame[2] - _text = last_stack_frame[3] - ### Ugly hack to tell if a thread is supposedly sleeping or not - ### These are the most common sleeping functions I've found. - ### Is there a better way? (python interpreter internals?) - ### Tested only with python 2.5 - if _funcname=="wait" and _text=="waiter.acquire()": - return True - if _funcname=="wait" and _text=="_sleep(delay)": - return True - if _funcname=="accept" and _text[-14:]=="_sock.accept()": - return True - #Ugly hack: always skip the heartbeat thread - #TODO: get the current thread-id in python - # skip heartbeat thread by thread-id, not by filename - if _filename.find("/lib/galaxy/util/heartbeat.py")!=-1: - return True - ## By default, assume the thread is not sleeping - return False + if all_threads_are_sleeping: + print >> self.file_nonsleeping, "All threads are sleeping." + print >> self.file_nonsleeping + self.file_nonsleeping.flush() - def get_interesting_stack_frame ( self, stack_frames ): - """ - Scans a given backtrace stack frames, returns a single - quadraple of [filename, line, function-name, text] of - the single, deepest, most interesting frame. - - Interesting being:: - - inside the galaxy source code ("/lib/galaxy"), - prefreably not an egg. - """ - for _filename, _line, _funcname, _text in reversed(stack_frames): - idx = _filename.find("/lib/galaxy/") - if idx!=-1: - relative_filename = _filename[idx:] - return ( relative_filename, _line, _funcname, _text ) - # no "/lib/galaxy" code found, return the innermost frame - return stack_frames[-1] - - def print_nonsleeping( self, threads_object_dict ): - print >> self.file_nonsleeping, "Non-Sleeping threads at %s:" % time.asctime() - print >> self.file_nonsleeping - all_threads_are_sleeping = True - threads = get_current_thread_object_dict() - for thread_id, frame in threadframe.dict().iteritems(): - if thread_id in threads: - object = repr( threads[thread_id] ) - else: - object = "<No Thread object>" - tb = traceback.extract_stack(frame) - if self.thread_is_sleeping(tb[-1]): - if thread_id in self.nonsleeping_heartbeats: - del self.nonsleeping_heartbeats[thread_id] - continue - - # Count non-sleeping thread heartbeats - if thread_id in self.nonsleeping_heartbeats: - self.nonsleeping_heartbeats[thread_id] += 1 - else: - self.nonsleeping_heartbeats[thread_id]=1 - - good_frame = self.get_interesting_stack_frame(tb) - print >> self.file_nonsleeping, "Thread %s\t%s\tnon-sleeping for %d heartbeat(s)\n File %s:%d\n Function \"%s\"\n %s" % \ - ( thread_id, object, self.nonsleeping_heartbeats[thread_id], good_frame[0], good_frame[1], good_frame[2], good_frame[3] ) - all_threads_are_sleeping = False - - if all_threads_are_sleeping: - print >> self.file_nonsleeping, "All threads are sleeping." - print >> self.file_nonsleeping - self.file_nonsleeping.flush() - Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415)
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a9adea86d41/ Changeset: 5a9adea86d41 Branch: stable User: natefoo Date: 2014-06-12 14:50:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415) [stable] API bug fixes for stable Affected #: 2 files diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 12 Jun '14

12 Jun '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddddb19cb1bf/ Changeset: ddddb19cb1bf Branch: stable User: jmchilton Date: 2014-06-11 19:37:24 Summary: Modify url_for in history_contents.py. No clue why - but this randomly fails on main. Will keep looking into it - but it wasn't really giving the pretty URL I wanted anyway (though it was working and this still works due to backward compatbility on this route). Affected #: 1 file diff -r 0af48b3c8f33fbe0f05e775f98a14761804c7ac5 -r ddddb19cb1bf2c12aa4d6f824b7a850d4c858e2c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): https://bitbucket.org/galaxy/galaxy-central/commits/f7be4e7782c1/ Changeset: f7be4e7782c1 Branch: stable User: dannon Date: 2014-06-11 17:39:21 Summary: Correct tools handling of tool.handle_input -- this doesn't always return a successful job. Affected #: 1 file diff -r ddddb19cb1bf2c12aa4d6f824b7a850d4c858e2c -r f7be4e7782c1368a3c4a868c7c63989e11c151fd lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): https://bitbucket.org/galaxy/galaxy-central/commits/5a9adea86d41/ Changeset: 5a9adea86d41 Branch: stable User: natefoo Date: 2014-06-12 14:50:00 Summary: Merged in jmchilton/galaxy-central-fork-1/stable (pull request #415) [stable] API bug fixes for stable Affected #: 2 files diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -143,7 +143,7 @@ 'purged': hda.purged, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, - 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id, type="dataset" ), + 'url' : url_for( 'history_content', history_id=encoded_history_id, id=encoded_id ), } def __collection_dict( self, trans, dataset_collection_instance, view="collection" ): diff -r ca53bc55bdc5f8c0d8089da2f42cf9d81f0a15d4 -r 5a9adea86d411348023b7307b3c935cd99c6dea9 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -156,7 +156,7 @@ output_dict[ 'output_name' ] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) - for job in vars[ 'jobs' ]: + for job in vars.get('jobs', []): rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) ) for output_name, collection_instance in vars.get( 'implicit_collections', {} ).iteritems(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Pack scripts
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/07df86dff47c/ Changeset: 07df86dff47c User: guerler Date: 2014-06-12 00:55:14 Summary: Charts: Pack scripts Affected #: 3 files diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var 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e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","mvc/ui/ui-modal"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="ui-button-menu '+e.cls+'">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n){var r=this;e.groups?this._get_dataset(e.id,function(){r._get(e,t)}):this._get_dataset(e.id,t,n)},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");var t=e.start,n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("FAILED - Datasets::_fill_from_cache() - Invalid range.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e,t,i){e.find("svg").length>0?r(e,t,i):n(e)}function n(e){e.find("#canvas").jqplotSaveImage({})}function r(e,t,n){var r=new XMLSerializer,o="",u=this,a=0,f=0;return e.find("svg").each(function(){var e=$(this);i(e),a=parseInt(e.css("height")),f=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:f,height:a}),e.find(".highcharts-button").hide(),o+=r.serializeToString(this),e.find(".highcharts-button").show()}),s(e,t,{filename:n||"chart",type:"application/pdf",height:a,width:f,scale:2,svg:o}),o}function i(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function s(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","plugin/library/screenshot","utils/utils"],function(e,t,n,r){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=r.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var n=this;this.chart.on("redraw",function(){n._draw(n.chart)}),this.chart.on("set:state",function(){var e=n.$el.find("#info"),t=n.$el.find(".charts-viewport-container"),r=e.find("#icon");r.removeClass(),e.show(),e.find("#text").html(n.chart.get("state_info"));var i=n.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":r.addClass("icon fa fa-warning"),t.hide();break;default:r.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=this.chart_definition.use_panels||e.settings.get("use_panels")==="true",s=1;i&&(s=e.groups.length),this._createContainer(this.chart_definition.tag,s),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=r.merge({index:e.get(o)},u)}t.groups.push({key:++n+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"SVGs are converted to PDF via "+o.app.config.get("screenshot_url")+" and CANVAS-based charts to PNG-files.",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create(o.viewport_view.$el,o.app.config.get("screenshot_url"),o.chart.get("title"))})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)})},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=[],f=n[e];o&&a.push({label:"Column: Row Number",value:"auto"});var l=t.metadata_column_types;for(var c in l){var h=!1;l[c]=="int"||l[c]=="float"?h=u:h=s,h&&a.push({label:"Column: "+(parseInt(c)+1)+" ["+l[c]+"]",value:c})}f.update(a);if(!f.exists(this.group.get(e))){var p=f.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+p+'".'),this.group.set(e,p)}f.value(this.group.get(e)),f.setOnChange(function(t){i.group.set(e,t),i.chart.set("modified",!0)}),f.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<1k)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var 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r=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),a=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="ui-button-menu '+e.cls+'">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:i,Button:s,Icon:o,ButtonIcon:u,Input:h,Anchor:a,Message:f,Searchbox:l,Select:t,ButtonMenu:c,Modal:n,Textarea:p,Image:r,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];if(o.index=="auto")for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}else{var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){var i=new r(t.app,{canvas_list:t.canvas_list});t.chart_definition.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error(r)}}function r(e){var t=e.$el,n=e.url,r=e.name,o=new XMLSerializer,u="",a=this,f=0,l=0;return t.find("svg").each(function(){var e=$(this);i(e),f=parseInt(e.css("height")),l=parseInt(e.css("width")),e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:l,height:f}),e.find(".highcharts-button").hide(),u+=o.serializeToString(this),e.find(".highcharts-button").show()}),s(t,n,{filename:r||"chart",type:"application/pdf",height:f,width:l,scale:2,svg:u}),u}function i(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function s(e,t,n){var r=e.find("#viewport-form");r.length===0&&(r=$("<form>",{id:"viewport-form",method:"post",action:t,display:"none"}),e.append(r)),r.empty();for(name in n){var i=$("<input/>",{type:"hidden",name:name,value:n[name]});r.append(i)}try{r.submit()}catch(s){console.log(s)}}return{create:t}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button:new t.ButtonIcon({icon:"fa-camera",tooltip:"SVGs are converted to PDF via "+o.app.config.get("screenshot_url")+" and CANVAS-based charts to PNG-files.",title:"Screenshot",onclick:function(){o._wait(o.chart,function(){s.create({$el:o.viewport_view.$el,url:o.app.config.get("screenshot_url"),title:o.chart.get("title"),error:function(e){o.message.update({message:"Please reduce your chart to a single panel and try again.",status:"danger"})}})})}})}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0});this.table.add(u.title,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var f=this.chart.deferred.register(),l={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(f)}};this.app.datasets.request(l)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=[],l=n[e];o&&f.push({label:"Column: Row Number",value:"auto"});var c=t.metadata_column_types;for(var h in c){var p=!1;c[h]=="int"||c[h]=="float"?p=u:p=s,p&&f.push({label:"Column: "+(parseInt(h)+1)+" ["+c[h]+"]",value:h})}l.update(f);if(!l.exists(this.group.get(e))){var d=l.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+d+'".'),this.group.set(e,d)}a?l.value(this.chart.groups.first().get(e)):l.value(this.group.get(e)),this.group.on("change:"+e,function(){l.value(i.group.get(e))}),l.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),l.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s){for(var o in s.show){var u=s.show[o];i.table.get(u).show()}for(var o in s.hide){var u=s.hide[o];i.table.get(u).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r];o.append(e.wrap(this._template_item({id:r,title:i.title+" ("+i.library+")",url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new 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e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the 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h=D.yScale().invert(i.mouseY),p=Math.abs(D.yScale().domain()[0]-D.yScale().domain()[1]),d=.03*p,m=e.nearestValueIndex(c.map(function(e){return e.value}),h,d);m!==null&&(c[m].highlight=!0)}var g=n.tickFormat()(D.x()(s,f),f);o.tooltip.position({left:l+u.left,top:i.mouseY+u.top}).chartContainer(A.parentNode).enabled(v).valueFormatter(function(e,t){return r.tickFormat()(e)}).data({value:g,series:c})(),o.renderGuideLine(l)}),o.dispatch.on("elementMouseout",function(e){k.tooltipHide(),t.clearHighlights()}),k.on("tooltipShow",function(e){v&&_(e,A.parentNode)}),k.on("changeState",function(e){typeof e.disabled!="undefined"&&(b.forEach(function(t,n){t.disabled=e.disabled[n]}),x.disabled=e.disabled),typeof e.index!="undefined"&&(M.i=e.index,M.x=O(M.i),x.index=e.index,tt.data([M])),typeof e.rescaleY!="undefined"&&(y=e.rescaleY),D.update()})}),D}function P(e,n){return n.map(function(n,r){if(!n.values)return n;var i=n.values[e];if(i==null)return n;var s=t.y()(i,e);return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],k.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){k.tooltipHide(e)}),k.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),D.dispatch=k,D.lines=t,D.legend=i,D.xAxis=n,D.yAxis=r,D.interactiveLayer=o,d3.rebind(D,t,"defined","isArea","x","y","xScale","yScale","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id"),D.options=e.utils.optionsFunc.bind(D),D.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,D):u},D.width=function(e){return arguments.length?(f=e,D):f},D.height=function(e){return arguments.length?(l=e,D):l},D.color=function(t){return 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e.y},f=[0],l=e.utils.defaultColor(),c=!1,h=d3.format(",.2f"),p,d,v,m,g=d3.dispatch("chartClick","elementClick","elementDblClick","elementMouseover","elementMouseout"),y="discreteBar",b,w;return E.dispatch=g,E.options=e.utils.optionsFunc.bind(E),E.x=function(e){return arguments.length?(u=e,E):u},E.y=function(e){return arguments.length?(a=e,E):a},E.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,E):t},E.width=function(e){return arguments.length?(n=e,E):n},E.height=function(e){return arguments.length?(r=e,E):r},E.xScale=function(e){return arguments.length?(s=e,E):s},E.yScale=function(e){return arguments.length?(o=e,E):o},E.xDomain=function(e){return arguments.length?(p=e,E):p},E.yDomain=function(e){return arguments.length?(d=e,E):d},E.xRange=function(e){return arguments.length?(v=e,E):v},E.yRange=function(e){return arguments.length?(m=e,E):m},E.forceY=function(e){return arguments.length?(f=e,E):f},E.color=function(t){return arguments.length?(l=e.utils.getColor(t),E):l},E.id=function(e){return arguments.length?(i=e,E):i},E.showValues=function(e){return arguments.length?(c=e,E):c},E.valueFormat=function(e){return arguments.length?(h=e,E):h},E.rectClass=function(e){return arguments.length?(y=e,E):y},E},e.models.discreteBarChart=function(){function w(e){return e.each(function(e){var u=d3.select(this),p=this,y=(s||parseInt(u.style("width"))||960)-i.left-i.right,E=(o||parseInt(u.style("height"))||400)-i.top-i.bottom;w.update=function(){g.beforeUpdate(),u.call(w)},w.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var S=u.selectAll(".nv-noData").data([m]);return S.enter().append("text").attr("class","nvd3 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})}); \ No newline at end of file diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 config/plugins/visualizations/charts/static/library/screenshot.js --- a/config/plugins/visualizations/charts/static/library/screenshot.js +++ b/config/plugins/visualizations/charts/static/library/screenshot.js @@ -1,26 +1,40 @@ -/** - * Screenshot creator -*/ - // dependencies define(["libs/underscore"], function(_) { // screenshot - function create ($el, screenshot_url, name) { - if ($el.find('svg').length > 0) { - _fromSVG ($el, screenshot_url, name); + function create (options) { + if (options.$el.find('svg').length > 0) { + _fromSVG (options); } else { - _fromCanvas ($el); + _fromCanvas (options); } }; // from jqplot - function _fromCanvas ($el) { - $el.find('.charts-viewport-canvas').jqplotSaveImage({}); + function _fromCanvas (options) { + try { + var $canvas = options.$el.find('.jqplot-target'); + var imgData = $canvas.jqplotToImageStr({}); + if (imgData) { + window.location.href = imgData.replace('image/png', 'image/octet-stream'); + } + } catch (err) { + console.debug('FAILED - Screenshot::_fromCanvas() - ' + err); + if (options.error) { + options.error(err); + } + } }; // from svg - function _fromSVG ($el, screenshot_url, name) { + function _fromSVG (options) { + + // get parameters + var $el = options.$el; + var screenshot_url = options.url; + var name = options.name; + + // serialize svg var serializer = new XMLSerializer(); var xmlString = ''; var self = this; diff -r 7ac55136509c9c43964dc0d3a773d85e680a93ea -r 07df86dff47c924830c2912500af356180778162 config/plugins/visualizations/charts/static/views/viewer.js --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -48,7 +48,14 @@ onclick : function() { // attempt to load chart editor self._wait (self.chart, function() { - Screenshot.create(self.viewport_view.$el, self.app.config.get('screenshot_url'), self.chart.get('title')); + Screenshot.create({ + $el : self.viewport_view.$el, + url : self.app.config.get('screenshot_url'), + title : self.chart.get('title'), + error : function(err) { + self.message.update({ message: 'Please reduce your chart to a single panel and try again.', status: 'danger' }); + } + }); }); } }) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Finalize box plots, add axes labels, series labels, grid options
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ac55136509c/ Changeset: 7ac55136509c User: guerler Date: 2014-06-11 23:40:40 Summary: Charts: Finalize box plots, add axes labels, series labels, grid options Affected #: 12 files diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -17,7 +17,7 @@ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config){ + makeConfig : function(groups, plot_config){ $.extend(true, plot_config, { seriesDefaults: { renderer : $.jqplot.BarRenderer diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js @@ -6,7 +6,7 @@ library : 'jqPlot', tag : 'div', execute : 'boxplot', - keywords : 'default large', + keywords : 'small medium large', columns : { y : { title : 'Observations', @@ -14,123 +14,8 @@ } }, settings : { - separator_label : { - title : 'X axis', - type : 'separator' - }, - x_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'X-axis', - placeholder : 'Axis label' - }, - separator_tick : { - title : 'Y axis', - type : 'separator' - }, - y_axis_label : { - title : 'Axis label', - info : 'Provide a label for the axis.', - type : 'text', - init : 'Y-axis', - placeholder : 'Axis label' - }, - y_axis_type : { - title : 'Axis value type', - info : 'Select the value type of the axis.', - type : 'select', - init : 'auto', - data : [ - { - label : '-- Do not show values --', - value : 'hide', - hide : ['y_axis_tick'] - }, - { - label : 'Auto', - value : 'auto', - hide : ['y_axis_tick'] - }, - { - label : 'Float', - value : 'f', - show : ['y_axis_tick'] - }, - { - label : 'Exponent', - value : 'e', - show : ['y_axis_tick'] - }, - { - label : 'Integer', - value : 'd', - hide : ['y_axis_tick'] - }, - { - label : 'Percentage', - value : 'p', - show : ['y_axis_tick'] - }, - { - label : 'Rounded', - value : 'r', - show : ['y_axis_tick'] - }, - { - label : 'SI-prefix', - value : 's', - show : ['y_axis_tick'] - } - ] - }, - y_axis_tick : { - title : 'Axis tick format', - info : 'Select the tick format for the axis.', - type : 'select', - init : '.1', - data : [ - { - label : '0.00001', - value : '.5' - }, - { - label : '0.0001', - value : '.4' - }, - { - label : '0.001', - value : '.3' - }, - { - label : '0.01', - value : '.2' - }, - { - label : '0.1', - value : '.1' - }, - { - label : '1', - value : '1' - } - ] - }, - y_axis_grid : { - title : 'Axis grid', - info : 'Would you like to show grid lines for this axis?', - type : 'radiobutton', - init : '1', - data : [ - { - label : 'On', - value : '1' - }, - { - label : 'Off', - value : '0' - } - ] + show_legend : { + init : 'false' } } }); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -19,17 +19,16 @@ group.columns = null; group.columns = { x: { - index : index++ + index: index++ } } } - var plot = new Plot(this.app, this.options); plot.draw({ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config, groups){ + makeConfig : function(groups, plot_config){ var boundary = Tools.getDomains(groups, 'x'); $.extend(true, plot_config, { seriesDefaults: { @@ -42,7 +41,8 @@ }, axes : { xaxis: { - pad: 1.2 + min: -1, + max: groups.length + 0.01 }, yaxis: { min: boundary.x.min, @@ -51,7 +51,29 @@ } }); }, - makeSeries : function (groups) { + makeCategories: function(groups) { + // define custom category labels + var x_labels = []; + for (var group_index in groups) { + x_labels.push(groups[group_index].key); + } + + // use default mapping + Tools.mapCategories (groups, x_labels); + + // return labels array for x axis + return { + array: { + x : x_labels + } + } + }, + makeSeriesLabels : function (groups, plot_config) { + return [{ + label: 'Boxplot values' + }]; + }, + makeSeries: function (groups) { /* example data var catOHLC = [ [0, 138.7, 139.68, 135.18, 135.4], @@ -72,14 +94,14 @@ } // loop through data groups - for (var group_index in request_dictionary.groups) { + var indeces = [2, 4, 0, 1]; + for (var group_index in groups) { // get group - var group = request_dictionary.groups[group_index]; + var group = groups[group_index]; // format chart data var point = []; point.push(parseInt(group_index)); - var indeces = [2, 4, 0, 1]; for (var key in indeces) { point.push(group.values[indeces[key]].x); } @@ -88,6 +110,14 @@ plot_data.push (point); } + // HACK: the boxplot renderer has an issue with single elements + var point = []; + point[0] = plot_data.length; + for (var key in indeces) { + point.push(0); + } + plot_data.push (point); + // return return [plot_data]; } diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js @@ -100,6 +100,22 @@ ] }, + x_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for this axis?', + type : 'radiobutton', + init : 'false', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, separator_tick : { title : 'Y axis', type : 'separator' @@ -192,6 +208,22 @@ ] }, + y_axis_grid : { + title : 'Axis grid', + info : 'Would you like to show grid lines for this axis?', + type : 'radiobutton', + init : 'true', + data : [ + { + label : 'On', + value : 'true' + }, + { + label : 'Off', + value : 'false' + } + ] + }, separator_legend : { title : 'Others', type : 'separator' diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js @@ -57,11 +57,6 @@ } }, - // Custom labels for the series are specified with the "label" - // option on the series option. Here a series option object - // is specified for each series. - series: [], - axesDefaults: { labelRenderer : $.jqplot.CanvasAxisLabelRenderer, labelOptions: { @@ -76,25 +71,22 @@ }, axes: { - // Use a category axis on the x axis and use our custom ticks. xaxis: { label : chart.settings.get('x_axis_label'), tickRenderer : $.jqplot.CanvasAxisTickRenderer, tickOptions: { - angle : -30 + angle : chart.settings.get('use_panels') === 'true' ? 0 : -30, + showGridline : chart.settings.get('x_axis_grid') === 'true' }, tickInterval : 1, pad : 0 }, - // Pad the y axis just a little so bars can get close to, but - // not touch, the grid boundaries. 1.2 is the default padding. yaxis: { label : chart.settings.get('y_axis_label'), - tickOptions : {}, + tickOptions : { + showGridline : chart.settings.get('y_axis_grid') === 'true' + }, pad : 0 - //tickOptions : {formatString: '$%d'}, - //padding : 1.2, - //autoscale:true } }, @@ -110,17 +102,17 @@ showTooltip : false, style : 'pointer' }, + highlighter: { show : true, showMarker : false, tooltipAxes : 'xy' - } + }, + + series: [] }; - // Show the legend and put it outside the grid, but inside the - // plot container, shrinking the grid to accomodate the legend. - // A value of "outside" would not shrink the grid and allow - // the legend to overflow the container. + // Show the legend and put it outside the grid if (chart.settings.get('show_legend') == 'true') { plot_config.legend = { renderer : $.jqplot.EnhancedLegendRenderer, diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -38,10 +38,11 @@ // draw all data into a single canvas render: function(canvas_id, groups) { // get parameters - var chart = this.options.chart; - var makeCategories = this.options.makeCategories; - var makeSeries = this.options.makeSeries; - var makeConfig = this.options.makeConfig; + var chart = this.options.chart; + var makeCategories = this.options.makeCategories; + var makeSeries = this.options.makeSeries; + var makeSeriesLabels = this.options.makeSeriesLabels; + var makeConfig = this.options.makeConfig; // create configuration var plot_config = configmaker(chart); @@ -50,18 +51,25 @@ // draw plot try { // make custom categories call - this._makeAxes(plot_config, groups, chart.settings); + this._makeAxes(groups, plot_config, chart.settings); // make custom series call if (makeSeries) { - plot_data = makeSeries(groups); + plot_config.series = makeSeriesLabels(groups, plot_config); + } else { + plot_config.series = this._makeSeriesLabels(groups); + } + + // make custom series call + if (makeSeries) { + plot_data = makeSeries(groups, plot_config); } else { plot_data = Tools.makeSeries(groups); } // make custom config call if (makeConfig) { - makeConfig(plot_config, groups); + makeConfig(groups, plot_config); } // check chart state @@ -96,8 +104,19 @@ } }, + // make series labels + _makeSeriesLabels: function(groups, plot_config) { + var series = []; + for (var group_index in groups) { + series.push({ + label: groups[group_index].key + }); + } + return series; + }, + // create axes formatting - _makeAxes: function(plot_config, groups, settings) { + _makeAxes: function(groups, plot_config, settings) { // result var makeCategories = this.options.makeCategories; var categories; diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js @@ -12,6 +12,11 @@ title : 'Values for y-axis', is_numeric : true } + }, + settings : { + x_axis_grid : { + init : 'true' + } } }); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js @@ -17,7 +17,7 @@ process_id : process_id, chart : chart, request_dictionary : request_dictionary, - makeConfig : function(plot_config){ + makeConfig : function(groups, plot_config){ $.extend(true, plot_config, { seriesDefaults: { renderer: $.jqplot.LineRenderer, diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -62,6 +62,11 @@ makeConfig(d3chart); } + // hide controls if in multi-viewer mode + if (chart.settings.get('use_panels') === 'true') { + d3chart.options({showControls: false}); + } + // hide min/max values d3chart.xAxis.showMaxMin(false); d3chart.yAxis.showMaxMin(chart.definition.showmaxmin); diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/charts/tools.js --- a/config/plugins/visualizations/charts/static/charts/tools.js +++ b/config/plugins/visualizations/charts/static/charts/tools.js @@ -22,7 +22,7 @@ request_dictionary.success = function() { try { // check if this chart has multiple panels - if (chart.definition.use_panels || chart.settings.get('use_panels') === 'true') { + if (chart.settings.get('use_panels') === 'true') { // draw groups in separate panels var valid = true; for (var group_index in request_dictionary.groups) { @@ -131,7 +131,6 @@ // append series plot_data.push(data); } - // return return plot_data; @@ -163,6 +162,17 @@ } // index all values contained in label columns (for all groups) + mapCategories(array, groups); + + // return dictionary + return { + array : array + } +}; + +// apply default mapping +// index all values contained in label columns (for all groups) +function mapCategories(array, groups) { for (var i in groups) { var group = groups[i]; for (var j in group.values) { @@ -172,15 +182,10 @@ } } } - - // return dictionary - return { - array : array - } }; // category make for unique category labels -function makeCategoriesUnique(groups, with_index) { +function makeUniqueCategories(groups, with_index) { // hashkeys, arrays and counter for labeled columns var categories = {}; var array = {}; @@ -247,7 +252,8 @@ panelHelper : panelHelper, makeCategories : makeCategories, makeSeries : makeSeries, - getDomains : getDomains + getDomains : getDomains, + mapCategories : mapCategories } }); \ No newline at end of file diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/library/screenshot.js --- a/config/plugins/visualizations/charts/static/library/screenshot.js +++ b/config/plugins/visualizations/charts/static/library/screenshot.js @@ -16,7 +16,7 @@ // from jqplot function _fromCanvas ($el) { - $el.find('#canvas').jqplotSaveImage({}); + $el.find('.charts-viewport-canvas').jqplotSaveImage({}); }; // from svg diff -r 23b8a52409a41e13a8869b51a7360e4040537579 -r 7ac55136509c9c43964dc0d3a773d85e680a93ea config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -1,6 +1,6 @@ // dependencies -define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'plugin/library/screenshot', 'utils/utils'], - function(Portlet, Ui, Screenshot, Utils) { +define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'], + function(Portlet, Ui, Utils) { // widget return Backbone.View.extend({ @@ -134,12 +134,9 @@ // load chart settings this.chart_definition = chart.definition; - // read settings - var use_panels = this.chart_definition.use_panels || (chart.settings.get('use_panels') === 'true'); - // determine number of svg/div-elements to create var n_panels = 1; - if (use_panels) { + if (chart.settings.get('use_panels') === 'true') { n_panels = chart.groups.length; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: davebgx: Merge stable.
by commits-noreply＠bitbucket.org 11 Jun '14

11 Jun '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/23b8a52409a4/ Changeset: 23b8a52409a4 User: davebgx Date: 2014-06-11 23:00:56 Summary: Merge stable. Affected #: 1 file diff -r 651c1ed8e4d35cc140d20038c17e33eeb4381804 -r 23b8a52409a41e13a8869b51a7360e4040537579 lib/tool_shed/util/import_util.py --- a/lib/tool_shed/util/import_util.py +++ b/lib/tool_shed/util/import_util.py @@ -24,26 +24,27 @@ name, owner = name_owner if not ok: repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - # Do not allow the repository to be automatically installed if population resulted in errors. - tip_changeset_revision = repository.tip( trans.app ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, - trans.security.encode_id( repository.id ), - tip_changeset_revision ) - if repository_metadata: - if repository_metadata.downloadable: - repository_metadata.downloadable = False - trans.sa_session.add( repository_metadata ) - if not flush: - flush = True - # Do not allow dependent repository revisions to be automatically installed if population - # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) - for dependent_downloadable_revision in dependent_downloadable_revisions: - if dependent_downloadable_revision.downloadable: - dependent_downloadable_revision.downloadable = False - trans.sa_session.add( dependent_downloadable_revision ) + if repository is not None: + # Do not allow the repository to be automatically installed if population resulted in errors. + tip_changeset_revision = repository.tip( trans.app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, + trans.security.encode_id( repository.id ), + tip_changeset_revision ) + if repository_metadata: + if repository_metadata.downloadable: + repository_metadata.downloadable = False + trans.sa_session.add( repository_metadata ) if not flush: flush = True + # Do not allow dependent repository revisions to be automatically installed if population + # resulted in errors. + dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata ) + for dependent_downloadable_revision in dependent_downloadable_revisions: + if dependent_downloadable_revision.downloadable: + dependent_downloadable_revision.downloadable = False + trans.sa_session.add( dependent_downloadable_revision ) + if not flush: + flush = True if flush: trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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