Index

_

__abstractmethods__ (fastr.core.dimension.ForwardsDimensions attribute) (fastr.core.dimension.HasDimensions attribute) (fastr.core.interface.Interface attribute) (fastr.core.ioplugin.IOPlugin attribute) (fastr.core.samples.ContainsSamples attribute) (fastr.core.samples.HasSamples attribute) (fastr.core.samples.SampleCollection attribute) (fastr.core.samples.SampleValue attribute) (fastr.core.target.ProcessUsageCollection attribute) (fastr.core.target.SubprocessBasedTarget attribute) (fastr.core.target.Target attribute) (fastr.datatypes.AnyFile attribute) (fastr.datatypes.AnyType attribute) (fastr.datatypes.BaseDataType attribute) (fastr.datatypes.DataType attribute) (fastr.datatypes.DataTypeManager attribute) (fastr.datatypes.Deferred attribute) (fastr.datatypes.EnumType attribute) (fastr.datatypes.TypeGroup attribute) (fastr.datatypes.URLType attribute) (fastr.datatypes.ValueType attribute) (fastr.execution.basenoderun.BaseNodeRun attribute) (fastr.execution.flownoderun.AdvancedFlowNodeRun attribute) (fastr.execution.flownoderun.FlowNodeRun attribute) (fastr.execution.inputoutputrun.AdvancedFlowOutputRun attribute) (fastr.execution.inputoutputrun.BaseInputRun attribute) (fastr.execution.inputoutputrun.InputRun attribute) (fastr.execution.inputoutputrun.MacroOutputRun attribute) (fastr.execution.inputoutputrun.NamedSubinputRun attribute) (fastr.execution.inputoutputrun.OutputRun attribute) (fastr.execution.inputoutputrun.SourceOutputRun attribute) (fastr.execution.inputoutputrun.SubInputRun attribute) (fastr.execution.inputoutputrun.SubOutputRun attribute) (fastr.execution.linkrun.LinkRun attribute) (fastr.execution.macronoderun.MacroNodeRun attribute) (fastr.execution.noderun.NodeRun attribute) (fastr.execution.sinknoderun.SinkNodeRun attribute) (fastr.execution.sourcenoderun.ConstantNodeRun attribute) (fastr.execution.sourcenoderun.SourceNodeRun attribute) (fastr.planning.inputgroup.InputGroup attribute) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner attribute) (fastr.planning.inputgroupcombiner.DefaultInputGroupCombiner attribute) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner attribute) (fastr.planning.inputoutput.AdvancedFlowOutput attribute) (fastr.planning.inputoutput.BaseInput attribute) (fastr.planning.inputoutput.BaseInputOutput attribute) (fastr.planning.inputoutput.BaseOutput attribute) (fastr.planning.inputoutput.Input attribute) (fastr.planning.inputoutput.MacroInput attribute) (fastr.planning.inputoutput.MacroOutput attribute) (fastr.planning.inputoutput.NamedSubInput attribute) (fastr.planning.inputoutput.Output attribute) (fastr.planning.inputoutput.SourceOutput attribute) (fastr.planning.inputoutput.SubInput attribute) (fastr.planning.inputoutput.SubOutput attribute) (fastr.planning.link.Link attribute) (fastr.planning.node.AdvancedFlowNode attribute) (fastr.planning.node.BaseNode attribute) (fastr.planning.node.ConstantNode attribute) (fastr.planning.node.FlowNode attribute) (fastr.planning.node.MacroNode attribute) (fastr.planning.node.Node attribute) (fastr.planning.node.SinkNode attribute) (fastr.planning.node.SourceNode attribute) (fastr.plugins.BlockingExecution attribute) (fastr.plugins.CommaSeperatedValueFile attribute) (fastr.plugins.CrossValidation attribute) (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.DockerTarget attribute) (fastr.plugins.ElasticsearchReporter attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FileSystem attribute) (fastr.plugins.FlowInterface attribute) (fastr.plugins.HTTPPlugin attribute) (fastr.plugins.LinearExecution attribute) (fastr.plugins.LocalBinaryTarget attribute) (fastr.plugins.MacroTarget attribute) (fastr.plugins.NipypeInterface attribute) (fastr.plugins.Null attribute) (fastr.plugins.PimReporter attribute) (fastr.plugins.ProcessPoolExecution attribute) (fastr.plugins.RQExecution attribute) (fastr.plugins.Reference attribute) (fastr.plugins.S3Filesystem attribute) (fastr.plugins.SimpleReport attribute) (fastr.plugins.SingularityTarget attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.StrongrExecution attribute) (fastr.plugins.VirtualFileSystem attribute) (fastr.plugins.VirtualFileSystemRegularExpression attribute) (fastr.plugins.VirtualFileSystemValueList attribute) (fastr.plugins.XNATStorage attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) (fastr.plugins.managers.executionpluginmanager.ExecutionPluginManager attribute) (fastr.plugins.managers.interfacemanager.InterfacePluginManager attribute) (fastr.plugins.managers.iopluginmanager.IOPluginManager attribute) (fastr.plugins.managers.networkmanager.NetworkManager attribute) (fastr.plugins.managers.objectmanager.ObjectManager attribute) (fastr.plugins.managers.pluginmanager.PluginManager attribute) (fastr.plugins.managers.pluginmanager.PluginSubManager attribute) (fastr.plugins.managers.pluginmanager.PluginsView attribute) (fastr.plugins.managers.targetmanager.TargetManager attribute) (fastr.plugins.managers.toolmanager.ToolManager attribute) (fastr.plugins.reportingplugin.ReportingPlugin attribute) __add__() (fastr.core.samples.SampleBaseId method) (fastr.core.samples.SampleItemBase method) (fastr.core.samples.SamplePayload method) (fastr.core.samples.SampleValue method) (fastr.helpers.configmanager.EmptyDefault method) __bool__() (fastr.execution.networkrun.NetworkRun method) __contains__() (fastr.core.samples.HasSamples method) (fastr.core.samples.SampleCollection method) (fastr.plugins.managers.objectmanager.ObjectManager method) __dataschemafile__ (fastr.core.tool.Tool attribute) (fastr.execution.linkrun.LinkRun attribute) (fastr.execution.noderun.NodeRun attribute) (fastr.execution.sinknoderun.SinkNodeRun attribute) (fastr.execution.sourcenoderun.ConstantNodeRun attribute) (fastr.execution.sourcenoderun.SourceNodeRun attribute) (fastr.planning.link.Link attribute) (fastr.planning.network.Network attribute) (fastr.planning.node.ConstantNode attribute) (fastr.planning.node.Node attribute) (fastr.planning.node.SinkNode attribute) (fastr.planning.node.SourceNode attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FlowInterface attribute) __del__() (fastr.helpers.lockfile.DirectoryLock method) (fastr.plugins.executionplugin.ExecutionPlugin method) __delitem__() (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.helpers.configmanager.EmptyDefault method) (fastr.plugins.managers.pluginmanager.PluginsView method) __dict__ (fastr.core.cardinality.CardinalitySpec attribute) (fastr.core.dimension.HasDimensions attribute) (fastr.core.interface.InputSpec attribute) (fastr.core.interface.InterfaceResult attribute) (fastr.core.interface.OutputSpec attribute) (fastr.core.provenance.Provenance attribute) (fastr.core.samples.SampleBaseId attribute) (fastr.core.samples.SampleCollection attribute) (fastr.core.samples.SampleItemBase attribute) (fastr.core.samples.SampleValue attribute) (fastr.core.target.ProcessUsageCollection attribute) (fastr.core.target.TargetResult attribute) (fastr.core.version.Version attribute) (fastr.core.vfs.VirtualFileSystem attribute) (fastr.execution.environmentmodules.EnvironmentModules attribute) (fastr.execution.networkanalyzer.NetworkAnalyzer attribute) (fastr.execution.networkchunker.NetworkChunker attribute) (fastr.helpers.classproperty.ClassPropertyDescriptor attribute) (fastr.helpers.configmanager.Config attribute) (fastr.helpers.configmanager.EmptyDefault attribute) (fastr.helpers.filesynchelper.FileSyncHelper attribute) (fastr.helpers.lockfile.DirectoryLock attribute) (fastr.helpers.schematotable.SchemaPrinter attribute) (fastr.plugins.managers.pluginmanager.PluginsView attribute) (fastr.utils.cmd.upgrade.dummy_container attribute) (fastr.web.api.Run attribute) __dir__() (in module fastr.__init__) __enter__() (fastr.core.target.Target method) (fastr.helpers.lockfile.DirectoryLock method) (fastr.plugins.DockerTarget method) (fastr.plugins.LocalBinaryTarget method) (fastr.plugins.SingularityTarget method) (fastr.plugins.executionplugin.ExecutionPlugin method) __eq__() (fastr.api.ResourceLimit method) (fastr.core.cardinality.AnyCardinalitySpec method) (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.ChoiceCardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) (fastr.core.cardinality.MaxCardinalitySpec method) (fastr.core.cardinality.MinCardinalitySpec method) (fastr.core.cardinality.RangeCardinalitySpec method) (fastr.core.cardinality.ValueCardinalitySpec method) (fastr.core.dimension.Dimension method) (fastr.core.resourcelimit.ResourceLimit method) (fastr.core.tool.Tool method) (fastr.datatypes.BaseDataType method) (fastr.datatypes.URLType method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) (fastr.plugins.FastrInterface method) (fastr.plugins.FlowInterface method) (fastr.plugins.NipypeInterface method) __exit__() (fastr.core.target.Target method) (fastr.helpers.lockfile.DirectoryLock method) (fastr.plugins.DockerTarget method) (fastr.plugins.LocalBinaryTarget method) (fastr.plugins.SingularityTarget method) (fastr.plugins.executionplugin.ExecutionPlugin method) __format__() (in module fastr.__init__) __get__() (fastr.helpers.classproperty.ClassPropertyDescriptor method) __getattr__() (fastr.helpers.lazy_module.LazyModule method) __getitem__() (fastr.api.Output method) (fastr.core.samples.ContainsSamples method) (fastr.core.samples.HasSamples method) (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.core.target.ProcessUsageCollection method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.NamedSubinputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SourceOutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.helpers.configmanager.EmptyDefault method) (fastr.planning.inputgroup.InputGroup method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.NamedSubInput method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.network.Network method) (fastr.plugins.managers.objectmanager.ObjectManager method) (fastr.plugins.managers.pluginmanager.PluginsView method) (fastr.utils.cmd.upgrade.dummy_container method) __getnewargs__() (fastr.core.samples.SampleItemBase method) (fastr.core.target.SystemUsageInfo method) (fastr.utils.cmd.upgrade.FastrNamespaceType method) __getstate__() (fastr.api.ResourceLimit method) (fastr.core.interface.Interface method) (fastr.core.resourcelimit.ResourceLimit method) (fastr.core.samples.SampleValue method) (fastr.core.tool.Tool method) (fastr.datatypes.BaseDataType method) (fastr.datatypes.Deferred method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.job.Job method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.macronoderun.MacroNodeRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.ConstantNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.ConstantNode method) (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) (fastr.planning.node.SinkNode method) (fastr.planning.node.SourceNode method) (fastr.plugins.FastrInterface method) (fastr.plugins.FlowInterface method) (fastr.plugins.NipypeInterface method) __hash__ (fastr.api.ResourceLimit attribute) (fastr.core.cardinality.AnyCardinalitySpec attribute) (fastr.core.cardinality.AsCardinalitySpec attribute) (fastr.core.cardinality.CardinalitySpec attribute) (fastr.core.cardinality.ChoiceCardinalitySpec attribute) (fastr.core.cardinality.IntCardinalitySpec attribute) (fastr.core.cardinality.MaxCardinalitySpec attribute) (fastr.core.cardinality.MinCardinalitySpec attribute) (fastr.core.cardinality.RangeCardinalitySpec attribute) (fastr.core.cardinality.ValueCardinalitySpec attribute) (fastr.core.dimension.Dimension attribute) (fastr.core.resourcelimit.ResourceLimit attribute) (fastr.core.tool.Tool attribute) (fastr.datatypes.BaseDataType attribute) (fastr.datatypes.URLType attribute) (fastr.execution.linkrun.LinkRun attribute) (fastr.execution.networkrun.NetworkRun attribute) (fastr.execution.noderun.NodeRun attribute) (fastr.execution.sourcenoderun.SourceNodeRun attribute) (fastr.planning.inputoutput.Input attribute) (fastr.planning.inputoutput.Output attribute) (fastr.planning.inputoutput.SubInput attribute) (fastr.planning.inputoutput.SubOutput attribute) (fastr.planning.link.Link attribute) (fastr.planning.network.Network attribute) (fastr.planning.node.MacroNode attribute) (fastr.planning.node.Node attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FlowInterface attribute) (fastr.plugins.NipypeInterface attribute) __iadd__() (fastr.helpers.configmanager.EmptyDefault method) __init__() (fastr.api.ResourceLimit method) (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.ChoiceCardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) (fastr.core.cardinality.MaxCardinalitySpec method) (fastr.core.cardinality.MinCardinalitySpec method) (fastr.core.cardinality.RangeCardinalitySpec method) (fastr.core.cardinality.ValueCardinalitySpec method) (fastr.core.dimension.Dimension method) (fastr.core.interface.InterfaceResult method) (fastr.core.ioplugin.IOPlugin method) (fastr.core.provenance.Provenance method) (fastr.core.resourcelimit.ResourceLimit method) (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.core.target.ProcessUsageCollection method) (fastr.core.target.TargetResult method) (fastr.core.tool.Tool method) (fastr.core.vfs.VirtualFileSystem method) (fastr.datatypes.BaseDataType method) (fastr.datatypes.DataType method) (fastr.datatypes.DataTypeManager method) (fastr.datatypes.Deferred method) (fastr.datatypes.EnumType method) (fastr.datatypes.TypeGroup method) (fastr.datatypes.URLType method) (fastr.datatypes.ValueType method) (fastr.exceptions.FastrError method) (fastr.exceptions.FastrExecutableNotFoundError method) (fastr.exceptions.FastrFileNotFound method) (fastr.exceptions.FastrLockNotAcquired method) (fastr.exceptions.FastrScriptNotFoundError method) (fastr.exceptions.FastrSerializationError method) (fastr.execution.environmentmodules.EnvironmentModules method) (fastr.execution.inputoutputrun.BaseInputRun method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.NamedSubinputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SourceOutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.job.InlineJob method) (fastr.execution.job.Job method) (fastr.execution.job.JobState method) (fastr.execution.job.SinkJob method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.macronoderun.MacroNodeRun method) (fastr.execution.networkchunker.DefaultNetworkChunker method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.ConstantNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.helpers.classproperty.ClassPropertyDescriptor method) (fastr.helpers.configmanager.Config method) (fastr.helpers.configmanager.EmptyDefault method) (fastr.helpers.filesynchelper.FileSyncHelper method) (fastr.helpers.jsonschemaparser.FastrRefResolver method) (fastr.helpers.lazy_module.LazyModule method) (fastr.helpers.lockfile.DirectoryLock method) (fastr.helpers.schematotable.SchemaPrinter method) (fastr.planning.inputgroup.InputGroup method) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner method) (fastr.planning.inputoutput.BaseInput method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.inputoutput.BaseOutput method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.NamedSubInput method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SourceOutput method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.ConstantNode method) (fastr.planning.node.FlowNode method) (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) (fastr.planning.node.SinkNode method) (fastr.planning.node.SourceNode method) (fastr.plugins.BlockingExecution method) (fastr.plugins.CommaSeperatedValueFile method) (fastr.plugins.DRMAAExecution method) (fastr.plugins.DockerTarget method) (fastr.plugins.ElasticsearchReporter method) (fastr.plugins.FastrInterface method) (fastr.plugins.FileSystem method) (fastr.plugins.FlowInterface method) (fastr.plugins.HTTPPlugin method) (fastr.plugins.LinearExecution method) (fastr.plugins.LocalBinaryTarget method) (fastr.plugins.MacroTarget method) (fastr.plugins.NipypeInterface method) (fastr.plugins.Null method) (fastr.plugins.PimReporter method) (fastr.plugins.ProcessPoolExecution method) (fastr.plugins.RQExecution method) (fastr.plugins.Reference method) (fastr.plugins.S3Filesystem method) (fastr.plugins.SingularityTarget method) (fastr.plugins.SlurmExecution method) (fastr.plugins.StrongrExecution method) (fastr.plugins.VirtualFileSystemRegularExpression method) (fastr.plugins.VirtualFileSystemValueList method) (fastr.plugins.XNATStorage method) (fastr.plugins.executionplugin.ExecutionPlugin method) (fastr.plugins.managers.executionpluginmanager.ExecutionPluginManager method) (fastr.plugins.managers.interfacemanager.InterfacePluginManager method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) (fastr.plugins.managers.objectmanager.ObjectManager method) (fastr.plugins.managers.pluginmanager.PluginManager method) (fastr.plugins.managers.pluginmanager.PluginSubManager method) (fastr.plugins.managers.pluginmanager.PluginsView method) (fastr.plugins.managers.targetmanager.TargetManager method) (fastr.web.api.ObjectUrl method) (fastr.web.api.Run method) (fastr.web.api.SubUrl method) __init_subclass__() (fastr.execution.basenoderun.BaseNodeRun class method) (fastr.planning.node.BaseNode class method) (in module fastr.__init__)

__iter__() (fastr.core.samples.HasSamples method) (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) (fastr.plugins.managers.pluginmanager.PluginsView method) __keytransform__() (fastr.datatypes.DataTypeManager method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) (fastr.plugins.managers.objectmanager.ObjectManager method) __len__() (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.core.target.ProcessUsageCollection method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.planning.inputoutput.SubOutput method) (fastr.plugins.managers.pluginmanager.PluginsView method) __lshift__() (fastr.api.Input method) (fastr.planning.inputoutput.BaseInput method) __module__ (fastr.api.ResourceLimit attribute) (fastr.core.cardinality.AnyCardinalitySpec attribute) (fastr.core.cardinality.AsCardinalitySpec attribute) (fastr.core.cardinality.CardinalitySpec attribute) (fastr.core.cardinality.ChoiceCardinalitySpec attribute) (fastr.core.cardinality.IntCardinalitySpec attribute) (fastr.core.cardinality.MaxCardinalitySpec attribute) (fastr.core.cardinality.MinCardinalitySpec attribute) (fastr.core.cardinality.RangeCardinalitySpec attribute) (fastr.core.cardinality.ValueCardinalitySpec attribute) (fastr.core.dimension.Dimension attribute) (fastr.core.dimension.ForwardsDimensions attribute) (fastr.core.dimension.HasDimensions attribute) (fastr.core.interface.InputSpec attribute) (fastr.core.interface.Interface attribute) (fastr.core.interface.InterfaceResult attribute) (fastr.core.interface.OutputSpec attribute) (fastr.core.ioplugin.IOPlugin attribute) (fastr.core.provenance.Provenance attribute) (fastr.core.resourcelimit.ResourceLimit attribute) (fastr.core.samples.ContainsSamples attribute) (fastr.core.samples.HasSamples attribute) (fastr.core.samples.SampleBaseId attribute) (fastr.core.samples.SampleCollection attribute) (fastr.core.samples.SampleId attribute) (fastr.core.samples.SampleIndex attribute) (fastr.core.samples.SampleItem attribute) (fastr.core.samples.SampleItemBase attribute) (fastr.core.samples.SamplePayload attribute) (fastr.core.samples.SampleValue attribute) (fastr.core.target.ProcessUsageCollection attribute) (fastr.core.target.SubprocessBasedTarget attribute) (fastr.core.target.SystemUsageInfo attribute) (fastr.core.target.Target attribute) (fastr.core.target.TargetResult attribute) (fastr.core.tool.Tool attribute) (fastr.core.version.Version attribute) (fastr.core.vfs.VirtualFileSystem attribute) (fastr.datatypes.AnyFile attribute) (fastr.datatypes.AnyType attribute) (fastr.datatypes.BaseDataType attribute) (fastr.datatypes.DataType attribute) (fastr.datatypes.DataTypeManager attribute) (fastr.datatypes.Deferred attribute) (fastr.datatypes.EnumType attribute) (fastr.datatypes.TypeGroup attribute) (fastr.datatypes.URLType attribute) (fastr.datatypes.ValueType attribute) (fastr.exceptions.FastrAttributeError attribute) (fastr.exceptions.FastrCannotChangeAttributeError attribute) (fastr.exceptions.FastrCardinalityError attribute) (fastr.exceptions.FastrCollectorError attribute) (fastr.exceptions.FastrDataTypeFileNotReadable attribute) (fastr.exceptions.FastrDataTypeMismatchError attribute) (fastr.exceptions.FastrDataTypeNotAvailableError attribute) (fastr.exceptions.FastrDataTypeNotInstantiableError attribute) (fastr.exceptions.FastrDataTypeValueError attribute) (fastr.exceptions.FastrError attribute) (fastr.exceptions.FastrErrorInSubprocess attribute) (fastr.exceptions.FastrExecutableNotFoundError attribute) (fastr.exceptions.FastrExecutionError attribute) (fastr.exceptions.FastrFileNotFound attribute) (fastr.exceptions.FastrIOError attribute) (fastr.exceptions.FastrImportError attribute) (fastr.exceptions.FastrIndexError attribute) (fastr.exceptions.FastrIndexNonexistent attribute) (fastr.exceptions.FastrKeyError attribute) (fastr.exceptions.FastrLockNotAcquired attribute) (fastr.exceptions.FastrLookupError attribute) (fastr.exceptions.FastrMountUnknownError attribute) (fastr.exceptions.FastrNetworkMismatchError attribute) (fastr.exceptions.FastrNetworkUnknownError attribute) (fastr.exceptions.FastrNoValidTargetError attribute) (fastr.exceptions.FastrNodeAreadyPreparedError attribute) (fastr.exceptions.FastrNodeNotPreparedError attribute) (fastr.exceptions.FastrNodeNotValidError attribute) (fastr.exceptions.FastrNotExecutableError attribute) (fastr.exceptions.FastrNotImplementedError attribute) (fastr.exceptions.FastrOSError attribute) (fastr.exceptions.FastrObjectUnknownError attribute) (fastr.exceptions.FastrOptionalModuleNotAvailableError attribute) (fastr.exceptions.FastrOutputValidationError attribute) (fastr.exceptions.FastrParentMismatchError attribute) (fastr.exceptions.FastrPluginCapabilityNotImplemented attribute) (fastr.exceptions.FastrPluginNotAvailable attribute) (fastr.exceptions.FastrPluginNotLoaded attribute) (fastr.exceptions.FastrResultFileNotFound attribute) (fastr.exceptions.FastrScriptNotFoundError attribute) (fastr.exceptions.FastrSerializationError attribute) (fastr.exceptions.FastrSerializationIgnoreDefaultError attribute) (fastr.exceptions.FastrSerializationInvalidDataError attribute) (fastr.exceptions.FastrSerializationMethodError attribute) (fastr.exceptions.FastrSinkDataUnavailableError attribute) (fastr.exceptions.FastrSizeInvalidError attribute) (fastr.exceptions.FastrSizeMismatchError attribute) (fastr.exceptions.FastrSizeUnknownError attribute) (fastr.exceptions.FastrSourceDataUnavailableError attribute) (fastr.exceptions.FastrStateError attribute) (fastr.exceptions.FastrSubprocessNotFinished attribute) (fastr.exceptions.FastrToolNotAvailableError attribute) (fastr.exceptions.FastrToolTargetNotFound attribute) (fastr.exceptions.FastrToolUnknownError attribute) (fastr.exceptions.FastrToolVersionError attribute) (fastr.exceptions.FastrTypeError attribute) (fastr.exceptions.FastrUnknownURLSchemeError attribute) (fastr.exceptions.FastrValueError attribute) (fastr.exceptions.FastrVersionInvalidError attribute) (fastr.exceptions.FastrVersionMismatchError attribute) (fastr.execution.basenoderun.BaseNodeRun attribute) (fastr.execution.environmentmodules.EnvironmentModules attribute) (fastr.execution.environmentmodules.ModuleSystem attribute) (fastr.execution.flownoderun.AdvancedFlowNodeRun attribute) (fastr.execution.flownoderun.FlowNodeRun attribute) (fastr.execution.inputoutputrun.AdvancedFlowOutputRun attribute) (fastr.execution.inputoutputrun.BaseInputRun attribute) (fastr.execution.inputoutputrun.InputRun attribute) (fastr.execution.inputoutputrun.MacroOutputRun attribute) (fastr.execution.inputoutputrun.NamedSubinputRun attribute) (fastr.execution.inputoutputrun.OutputRun attribute) (fastr.execution.inputoutputrun.SourceOutputRun attribute) (fastr.execution.inputoutputrun.SubInputRun attribute) (fastr.execution.inputoutputrun.SubOutputRun attribute) (fastr.execution.job.InlineJob attribute) (fastr.execution.job.Job attribute) (fastr.execution.job.JobCleanupLevel attribute) (fastr.execution.job.JobState attribute) (fastr.execution.job.SinkJob attribute) (fastr.execution.job.SourceJob attribute) (fastr.execution.linkrun.LinkRun attribute) (fastr.execution.macronoderun.MacroNodeRun attribute) (fastr.execution.networkanalyzer.DefaultNetworkAnalyzer attribute) (fastr.execution.networkanalyzer.NetworkAnalyzer attribute) (fastr.execution.networkchunker.DefaultNetworkChunker attribute) (fastr.execution.networkchunker.NetworkChunker attribute) (fastr.execution.networkrun.NetworkRun attribute) (fastr.execution.noderun.NodeRun attribute) (fastr.execution.sinknoderun.SinkNodeRun attribute) (fastr.execution.sourcenoderun.ConstantNodeRun attribute) (fastr.execution.sourcenoderun.SourceNodeRun attribute) (fastr.helpers.classproperty.ClassPropertyDescriptor attribute) (fastr.helpers.configmanager.Config attribute) (fastr.helpers.configmanager.EmptyDefault attribute) (fastr.helpers.events.EventType attribute) (fastr.helpers.events.FastrLogEventHandler attribute) (fastr.helpers.filesynchelper.FileSyncHelper attribute) (fastr.helpers.jsonschemaparser.FastrRefResolver attribute) (fastr.helpers.lazy_module.LazyModule attribute) (fastr.helpers.lockfile.DirectoryLock attribute) (fastr.helpers.schematotable.SchemaPrinter attribute) (fastr.planning.inputgroup.InputGroup attribute) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner attribute) (fastr.planning.inputgroupcombiner.DefaultInputGroupCombiner attribute) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner attribute) (fastr.planning.inputoutput.AdvancedFlowOutput attribute) (fastr.planning.inputoutput.BaseInput attribute) (fastr.planning.inputoutput.BaseInputOutput attribute) (fastr.planning.inputoutput.BaseOutput attribute) (fastr.planning.inputoutput.Input attribute) (fastr.planning.inputoutput.MacroInput attribute) (fastr.planning.inputoutput.MacroOutput attribute) (fastr.planning.inputoutput.NamedSubInput attribute) (fastr.planning.inputoutput.Output attribute) (fastr.planning.inputoutput.SourceOutput attribute) (fastr.planning.inputoutput.SubInput attribute) (fastr.planning.inputoutput.SubOutput attribute) (fastr.planning.link.Link attribute) (fastr.planning.network.Network attribute) (fastr.planning.node.AdvancedFlowNode attribute) (fastr.planning.node.BaseNode attribute) (fastr.planning.node.ConstantNode attribute) (fastr.planning.node.FlowNode attribute) (fastr.planning.node.InputDict attribute) (fastr.planning.node.MacroNode attribute) (fastr.planning.node.Node attribute) (fastr.planning.node.OutputDict attribute) (fastr.planning.node.SinkNode attribute) (fastr.planning.node.SourceNode attribute) (fastr.plugins.BlockingExecution attribute) (fastr.plugins.CommaSeperatedValueFile attribute) (fastr.plugins.CrossValidation attribute) (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.DockerTarget attribute) (fastr.plugins.ElasticsearchReporter attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FileSystem attribute) (fastr.plugins.FlowInterface attribute) (fastr.plugins.HTTPPlugin attribute) (fastr.plugins.LinearExecution attribute) (fastr.plugins.LocalBinaryTarget attribute) (fastr.plugins.MacroTarget attribute) (fastr.plugins.NipypeInterface attribute) (fastr.plugins.Null attribute) (fastr.plugins.PimReporter attribute) (fastr.plugins.ProcessPoolExecution attribute) (fastr.plugins.RQExecution attribute) (fastr.plugins.Reference attribute) (fastr.plugins.S3Filesystem attribute) (fastr.plugins.SimpleReport attribute) (fastr.plugins.SingularityTarget attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.StrongrExecution attribute) (fastr.plugins.VirtualFileSystem attribute) (fastr.plugins.VirtualFileSystemRegularExpression attribute) (fastr.plugins.VirtualFileSystemValueList attribute) (fastr.plugins.XNATStorage attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) (fastr.plugins.executionplugin.JobAction attribute) (fastr.plugins.managers.executionpluginmanager.ExecutionPluginManager attribute) (fastr.plugins.managers.interfacemanager.InterfacePluginManager attribute) (fastr.plugins.managers.iopluginmanager.IOPluginManager attribute) (fastr.plugins.managers.networkmanager.NetworkManager attribute) (fastr.plugins.managers.objectmanager.ObjectManager attribute) (fastr.plugins.managers.pluginmanager.PluginManager attribute) (fastr.plugins.managers.pluginmanager.PluginSubManager attribute) (fastr.plugins.managers.pluginmanager.PluginsView attribute) (fastr.plugins.managers.targetmanager.TargetManager attribute) (fastr.plugins.managers.toolmanager.ToolManager attribute) (fastr.plugins.reportingplugin.ReportingPlugin attribute) (fastr.utils.cmd.upgrade.FastrNamespaceType attribute) (fastr.utils.cmd.upgrade.dummy_container attribute) (fastr.web.api.NetworkApi attribute) (fastr.web.api.NetworkListApi attribute) (fastr.web.api.ObjectUrl attribute) (fastr.web.api.Run attribute) (fastr.web.api.RunApi attribute) (fastr.web.api.RunListApi attribute) (fastr.web.api.StatusApi attribute) (fastr.web.api.SubUrl attribute) (fastr.web.api.ToolApi attribute) (fastr.web.api.ToolListApi attribute) __ne__() (fastr.api.ResourceLimit method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.dimension.Dimension method) (fastr.core.resourcelimit.ResourceLimit method) (fastr.datatypes.BaseDataType method) (fastr.execution.networkrun.NetworkRun method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.network.Network method) (fastr.planning.node.Node method) __new__() (fastr.core.interface.InputSpec static method) (fastr.core.interface.OutputSpec static method) (fastr.core.samples.SampleBaseId static method) (fastr.core.samples.SampleItem static method) (fastr.core.samples.SampleItemBase static method) (fastr.core.samples.SamplePayload static method) (fastr.core.target.SystemUsageInfo static method) (fastr.core.version.Version static method) (fastr.datatypes.TypeGroup static method) (fastr.utils.cmd.upgrade.FastrNamespaceType static method) (in module fastr.__init__) __radd__() (fastr.core.samples.SampleBaseId method) (fastr.core.samples.SampleValue method) (fastr.helpers.configmanager.EmptyDefault method) __reduce__() (in module fastr.__init__) __reduce_ex__() (fastr.datatypes.BaseDataType method) (fastr.datatypes.EnumType method) (in module fastr.__init__) __repr__() (fastr.core.cardinality.CardinalitySpec method) (fastr.core.dimension.Dimension method) (fastr.core.samples.SampleBaseId method) (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleIndex method) (fastr.core.samples.SampleItemBase method) (fastr.core.samples.SampleValue method) (fastr.core.target.SystemUsageInfo method) (fastr.core.tool.Tool method) (fastr.core.version.Version method) (fastr.datatypes.BaseDataType method) (fastr.datatypes.Deferred method) (fastr.exceptions.FastrError method) (fastr.exceptions.FastrSerializationError method) (fastr.execution.environmentmodules.EnvironmentModules method) (fastr.execution.job.Job method) (fastr.execution.job.SinkJob method) (fastr.execution.job.SourceJob method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.helpers.configmanager.Config method) (fastr.helpers.lazy_module.LazyModule method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.Node method) (fastr.utils.cmd.upgrade.FastrNamespaceType method) __rrshift__() (fastr.api.Input method) (fastr.planning.inputoutput.BaseInput method) __schema_type__ (fastr.web.api.ObjectUrl attribute) (fastr.web.api.SubUrl attribute) __setitem__() (fastr.core.samples.ContainsSamples method) (fastr.core.samples.SampleCollection method) (fastr.core.samples.SampleValue method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SourceOutputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.helpers.configmanager.EmptyDefault method) (fastr.planning.inputgroup.InputGroup method) (fastr.planning.inputoutput.Input method) (fastr.planning.node.InputDict method) (fastr.planning.node.OutputDict method) (fastr.plugins.managers.pluginmanager.PluginManager method) (fastr.plugins.managers.pluginmanager.PluginsView method) __setstate__() (fastr.api.ResourceLimit method) (fastr.core.interface.Interface method) (fastr.core.resourcelimit.ResourceLimit method) (fastr.core.samples.SampleValue method) (fastr.core.tool.Tool method) (fastr.datatypes.BaseDataType method) (fastr.datatypes.Deferred method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.job.Job method) (fastr.execution.linkrun.LinkRun method) (fastr.execution.macronoderun.MacroNodeRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.ConstantNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.ConstantNode method) (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) (fastr.planning.node.SinkNode method) (fastr.planning.node.SourceNode method) (fastr.plugins.FastrInterface method) (fastr.plugins.FlowInterface method) (fastr.plugins.NipypeInterface method) __sizeof__() (in module fastr.__init__) __slotnames__ (fastr.web.api.ObjectUrl attribute) __slots__ (fastr.api.ResourceLimit attribute) (fastr.core.dimension.Dimension attribute) (fastr.core.resourcelimit.ResourceLimit attribute) (fastr.core.target.SystemUsageInfo attribute) (fastr.utils.cmd.upgrade.FastrNamespaceType attribute) __str__() (fastr.core.cardinality.AnyCardinalitySpec method) (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.ChoiceCardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) (fastr.core.cardinality.MaxCardinalitySpec method) (fastr.core.cardinality.MinCardinalitySpec method) (fastr.core.cardinality.RangeCardinalitySpec method) (fastr.core.cardinality.ValueCardinalitySpec method) (fastr.core.samples.SampleBaseId method) (fastr.core.samples.SampleIndex method) (fastr.core.tool.Tool method) (fastr.core.version.Version method) (fastr.datatypes.BaseDataType method) (fastr.exceptions.FastrError method) (fastr.exceptions.FastrExecutableNotFoundError method) (fastr.exceptions.FastrScriptNotFoundError method) (fastr.exceptions.FastrSerializationError method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.NamedSubinputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.noderun.NodeRun method) (fastr.helpers.schematotable.SchemaPrinter method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.NamedSubInput method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.node.Node method) __subclasshook__() (in module fastr.__init__) __updatefunc__() (fastr.planning.inputgroup.InputGroup method) __updatetriggers__ (fastr.planning.inputgroup.InputGroup attribute) __weakref__ (fastr.core.cardinality.CardinalitySpec attribute) (fastr.core.dimension.HasDimensions attribute) (fastr.core.interface.InterfaceResult attribute) (fastr.core.provenance.Provenance attribute) (fastr.core.samples.SampleCollection attribute) (fastr.core.samples.SampleValue attribute) (fastr.core.target.ProcessUsageCollection attribute) (fastr.core.target.TargetResult attribute) (fastr.core.vfs.VirtualFileSystem attribute) (fastr.exceptions.FastrError attribute) (fastr.exceptions.FastrIOError attribute) (fastr.exceptions.FastrImportError attribute) (fastr.exceptions.FastrOSError attribute) (fastr.execution.environmentmodules.EnvironmentModules attribute) (fastr.execution.networkanalyzer.NetworkAnalyzer attribute) (fastr.execution.networkchunker.NetworkChunker attribute) (fastr.helpers.classproperty.ClassPropertyDescriptor attribute) (fastr.helpers.configmanager.Config attribute) (fastr.helpers.configmanager.EmptyDefault attribute) (fastr.helpers.filesynchelper.FileSyncHelper attribute) (fastr.helpers.lockfile.DirectoryLock attribute) (fastr.helpers.schematotable.SchemaPrinter attribute) (fastr.plugins.managers.pluginmanager.PluginsView attribute) (fastr.utils.cmd.upgrade.dummy_container attribute) (fastr.web.api.Run attribute)

A

abort() (fastr.execution.networkrun.NetworkRun method) (fastr.web.api.Run method) abstract (fastr.core.vfs.VirtualFileSystem attribute) acquire() (fastr.helpers.lockfile.DirectoryLock method) action() (fastr.datatypes.DataType method) activate() (fastr.plugins.ElasticsearchReporter method) (fastr.plugins.PimReporter method) (fastr.plugins.reportingplugin.ReportingPlugin method) activity() (fastr.core.provenance.Provenance method) add_link() (fastr.planning.network.Network method) add_node() (fastr.planning.network.Network method) add_parser_doc_link() (in module fastr.utils.cmd) add_stepid() (fastr.planning.network.Network method) AdvancedFlowNode (class in fastr.planning.node) AdvancedFlowNodeRun (class in fastr.execution.flownoderun) AdvancedFlowOutput (class in fastr.planning.inputoutput) AdvancedFlowOutputRun (class in fastr.execution.inputoutputrun) agent() (fastr.core.provenance.Provenance method) aggregate() (fastr.core.target.ProcessUsageCollection method) all (fastr.execution.job.JobCleanupLevel attribute)

analyze_network() (fastr.execution.networkanalyzer.DefaultNetworkAnalyzer method) (fastr.execution.networkanalyzer.NetworkAnalyzer method) any_of_draft4() (in module fastr.helpers.jsonschemaparser) AnyCardinalitySpec (class in fastr.core.cardinality) AnyFile (class in fastr.datatypes) AnyType (class in fastr.datatypes) append() (fastr.api.Input method) (fastr.core.target.ProcessUsageCollection method) (fastr.helpers.configmanager.EmptyDefault method) (fastr.planning.inputoutput.Input method) as_dict() (fastr.core.target.TargetResult method) AsCardinalitySpec (class in fastr.core.cardinality) asdict() (fastr.core.interface.InputSpec method) (fastr.core.interface.OutputSpec method) (fastr.helpers.configmanager.EmptyDefault method) aslist() (fastr.helpers.configmanager.EmptyDefault method) authors (fastr.core.tool.Tool attribute) automatic() (fastr.execution.inputoutputrun.OutputRun property) (fastr.planning.inputoutput.BaseOutput property) avail() (fastr.execution.environmentmodules.EnvironmentModules method) avail_modules() (fastr.execution.environmentmodules.EnvironmentModules property)

B

BaseDataType (class in fastr.datatypes) BaseInput (class in fastr.planning.inputoutput) BaseInputGroupCombiner (class in fastr.planning.inputgroupcombiner) BaseInputOutput (class in fastr.planning.inputoutput) BaseInputRun (class in fastr.execution.inputoutputrun) basename() (in module fastr.data.url) BaseNode (class in fastr.planning.node) BaseNodeRun (class in fastr.execution.basenoderun)

BaseOutput (class in fastr.planning.inputoutput) blocking() (fastr.execution.flownoderun.FlowNodeRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.inputoutput.BaseOutput property) (fastr.planning.node.FlowNode property) (fastr.planning.node.Node property) BlockingExecution (class in fastr.plugins) build() (fastr.core.version.Version property)

C

calculate_execution_cardinality() (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) (fastr.core.cardinality.ValueCardinalitySpec method) calculate_job_cardinality() (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) (fastr.core.cardinality.ValueCardinalitySpec method) calculate_planning_cardinality() (fastr.core.cardinality.AsCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) (fastr.core.cardinality.IntCardinalitySpec method) call_subprocess() (fastr.core.target.SubprocessBasedTarget method) cancel (fastr.plugins.executionplugin.JobAction attribute) cancel_job() (fastr.plugins.executionplugin.ExecutionPlugin method) cancelled (fastr.execution.job.JobState attribute) CANCELS_DEPENDENCIES (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) cardinality() (fastr.core.samples.SampleItemBase property) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.OutputRun method) (fastr.execution.inputoutputrun.SourceOutputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.inputoutputrun.SubOutputRun method) (fastr.execution.linkrun.LinkRun method) (fastr.planning.inputoutput.BaseInputOutput method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.Output method) (fastr.planning.inputoutput.SourceOutput method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.inputoutput.SubOutput method) (fastr.planning.link.Link method) cardinality_from_nargs() (in module fastr.utils.cmd.extract_argparse) CardinalitySpec (class in fastr.core.cardinality) cast() (fastr.core.samples.SampleValue method) cast_to_type() (fastr.execution.job.Job static method) check_cardinality() (fastr.planning.inputoutput.BaseInput method) (fastr.planning.inputoutput.BaseInputOutput method) check_finished() (fastr.plugins.RQExecution method) (fastr.plugins.StrongrExecution method) check_id() (fastr.execution.networkrun.NetworkRun method) (fastr.planning.network.Network method) check_input_id() (fastr.plugins.FastrInterface method) check_job_requirements() (fastr.plugins.executionplugin.ExecutionPlugin method) check_job_status() (fastr.plugins.executionplugin.ExecutionPlugin method) check_network() (in module fastr.utils.cmd.test) check_networks() (in module fastr.utils.cmd.test) check_output_id() (fastr.plugins.FastrInterface method) check_tool() (in module fastr.utils.cmd.test) check_tools() (in module fastr.utils.cmd.test) checksum() (fastr.datatypes.BaseDataType method) (fastr.datatypes.Deferred method) (fastr.datatypes.URLType method) (in module fastr.helpers.checksum) checksum_directory() (in module fastr.helpers.checksum) ChoiceCardinalitySpec (class in fastr.core.cardinality) chunck_network() (fastr.execution.networkchunker.DefaultNetworkChunker method) (fastr.execution.networkchunker.NetworkChunker method) cite (fastr.core.tool.Tool attribute) classproperty() (in module fastr.helpers.classproperty) ClassPropertyDescriptor (class in fastr.helpers.classproperty) clean() (fastr.execution.job.Job method) clean_free_jobs() (fastr.plugins.executionplugin.ExecutionPlugin method) cleanup() (fastr.core.ioplugin.IOPlugin method) (fastr.plugins.BlockingExecution method) (fastr.plugins.DRMAAExecution method) (fastr.plugins.LinearExecution method) (fastr.plugins.ProcessPoolExecution method) (fastr.plugins.RQExecution method) (fastr.plugins.S3Filesystem method) (fastr.plugins.SlurmExecution method) (fastr.plugins.StrongrExecution method) (fastr.plugins.XNATStorage method) (fastr.plugins.executionplugin.ExecutionPlugin method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) clear() (fastr.execution.environmentmodules.EnvironmentModules method) (fastr.planning.inputoutput.Input method) clear_version() (in module fastr.version) collapse() (fastr.api.Link property) (fastr.execution.linkrun.LinkRun property) (fastr.planning.link.Link property) collapse_indexes() (fastr.execution.linkrun.LinkRun property) (fastr.planning.link.Link property) collect_errors() (fastr.plugins.FastrInterface static method) collect_input_argument_provenance() (fastr.core.provenance.Provenance method) collect_jobs() (fastr.plugins.DRMAAExecution method) collect_provenance() (fastr.core.provenance.Provenance method) (fastr.execution.job.InlineJob method) (fastr.execution.job.Job method) (fastr.execution.job.SourceJob method)

collect_results() (fastr.plugins.FastrInterface method) collector_plugin_type (fastr.plugins.FastrInterface attribute) collectors (fastr.plugins.FastrInterface attribute) combine() (fastr.core.samples.SampleItemBase static method) combine_dimensions() (fastr.core.dimension.ForwardsDimensions method) command (fastr.core.tool.Tool attribute) COMMAND_DUMP (fastr.execution.job.Job attribute) command_version() (fastr.core.tool.Tool property) commandfile() (fastr.execution.job.Job property) commandurl() (fastr.execution.job.Job property) CommaSeperatedValueFile (class in fastr.plugins) compare_execution_dir() (in module fastr.utils.compare) compare_job_dirs() (in module fastr.utils.compare) compare_job_output_data() (in module fastr.utils.compare) compare_output_data() (fastr.core.tool.Tool static method) compare_set() (in module fastr.utils.compare) compare_value_dict_item() (in module fastr.utils.compare) compare_value_list() (in module fastr.utils.compare) Config (class in fastr.helpers.configmanager) config (in module fastr.helpers) configuration_fields (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.ElasticsearchReporter attribute) (fastr.plugins.PimReporter attribute) (fastr.plugins.ProcessPoolExecution attribute) (fastr.plugins.RQExecution attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.StrongrExecution attribute) connect() (fastr.plugins.XNATStorage method) constant_id() (fastr.planning.inputoutput.BaseInput method) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.NamedSubInput property) (fastr.planning.inputoutput.SubInput property) constantlist() (fastr.execution.networkrun.NetworkRun property) ConstantNode (class in fastr.planning.node) ConstantNodeRun (class in fastr.execution.sourcenoderun) container() (fastr.plugins.DockerTarget property) ContainsSamples (class in fastr.core.samples) content() (fastr.datatypes.URLType class method) copy() (fastr.api.ResourceLimit method) (fastr.core.dimension.Dimension method) (fastr.core.resourcelimit.ResourceLimit method) copy_file_dir() (fastr.core.vfs.VirtualFileSystem static method) cores() (fastr.api.ResourceLimit property) (fastr.core.resourcelimit.ResourceLimit property) cpu_percent() (fastr.core.target.SystemUsageInfo property) create_cardinality() (in module fastr.core.cardinality) create_constant() (fastr.api.Network method) (fastr.planning.network.Network method) create_enumtype() (fastr.datatypes.DataTypeManager method) create_ioplugin_tool() (fastr.plugins.managers.iopluginmanager.IOPluginManager static method) create_job() (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) create_link() (fastr.api.Network method) (fastr.planning.network.Network method) create_link_from() (fastr.planning.inputoutput.BaseInput method) create_macro() (fastr.api.Network method) (fastr.planning.network.Network method) create_native_spec() (fastr.plugins.DRMAAExecution method) create_network() (fastr.api method) (in module fastr.api) create_network_copy() (fastr.api method) (in module fastr.api) create_network_parser() (in module fastr.utils.cmd.run) create_node() (fastr.api.Network method) (fastr.planning.network.Network method) create_payload() (fastr.execution.job.Job method) (fastr.execution.job.SinkJob method) create_reference() (fastr.core.tool.Tool method) (fastr.planning.network.Network method) create_rest_table() (in module fastr.helpers.rest_generation) create_sink() (fastr.api.Network method) (fastr.planning.network.Network method) create_source() (fastr.api.Network method) (fastr.planning.network.Network method) create_vfs_url() (in module fastr.data.url) create_zip() (in module fastr.utils.cmd.dump) created (fastr.execution.job.JobState attribute) createobj() (fastr.execution.linkrun.LinkRun class method) (fastr.execution.noderun.NodeRun class method) (fastr.planning.link.Link class method) (fastr.planning.node.Node class method) CrossValidation (class in fastr.plugins) current_jobs() (fastr.plugins.DRMAAExecution property)

D

data() (fastr.core.samples.SampleItemBase property) (fastr.execution.sourcenoderun.ConstantNodeRun property) (fastr.planning.node.ConstantNode property) (fastr.plugins.managers.pluginmanager.PluginSubManager property) data_uri() (fastr.core.provenance.Provenance static method) DataType (class in fastr.datatypes) datatype() (fastr.execution.inputoutputrun.InputRun property) (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.execution.sinknoderun.SinkNodeRun property) (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.inputoutput.BaseInputOutput property) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubOutput property) (fastr.planning.node.SinkNode property) (fastr.planning.node.SourceNode property) datatype_from_type() (in module fastr.utils.cmd.extract_argparse) DataTypeManager (class in fastr.datatypes) date_version_matcher (fastr.core.version.Version attribute) deactivate() (fastr.plugins.reportingplugin.ReportingPlugin method) debug() (fastr.helpers.configmanager.Config property) DEFAULT_FIELDS (fastr.helpers.configmanager.Config attribute) DEFAULT_TARGET_CLASS (fastr.core.tool.Tool attribute) DefaultInputGroupCombiner (class in fastr.planning.inputgroupcombiner) DefaultNetworkAnalyzer (class in fastr.execution.networkanalyzer) DefaultNetworkChunker (class in fastr.execution.networkchunker) Deferred (class in fastr.datatypes) delete() (fastr.web.api.RunApi method) descend() (fastr.helpers.schematotable.SchemaPrinter method) description (fastr.core.tool.Tool attribute) (fastr.datatypes.AnyFile attribute) (fastr.datatypes.AnyType attribute) (fastr.datatypes.BaseDataType attribute) (fastr.datatypes.EnumType attribute) description() (fastr.execution.inputoutputrun.SubInputRun property) (fastr.planning.inputoutput.BaseInputOutput property) (fastr.planning.inputoutput.SubInput property) description_type (fastr.planning.inputoutput.BaseInput attribute) (fastr.planning.inputoutput.BaseInputOutput attribute) (fastr.planning.inputoutput.BaseOutput attribute) destroy() (fastr.execution.linkrun.LinkRun method) (fastr.planning.link.Link method) dicteq() (in module fastr.utils.dicteq) diffdict() (in module fastr.utils.dicteq) diffobj() (in module fastr.utils.dicteq) diffobj_str() (in module fastr.utils.dicteq) Dimension (class in fastr.core.dimension) dimensionality() (fastr.core.samples.SampleItemBase property) dimensions() (fastr.core.dimension.ForwardsDimensions property) (fastr.core.dimension.HasDimensions property) (fastr.core.samples.ContainsSamples property) (fastr.core.samples.SampleCollection property) (fastr.execution.inputoutputrun.InputRun property) (fastr.execution.inputoutputrun.MacroOutputRun property) (fastr.execution.inputoutputrun.SourceOutputRun property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.execution.linkrun.LinkRun property) (fastr.planning.inputgroup.InputGroup property) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner property) (fastr.planning.inputoutput.AdvancedFlowOutput property) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.MacroOutput property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubInput property) (fastr.planning.link.Link property) (fastr.planning.node.FlowNode property) (fastr.planning.node.Node property) (fastr.planning.node.SourceNode property)

dimnames() (fastr.core.dimension.HasDimensions property) (fastr.execution.flownoderun.FlowNodeRun property) (fastr.execution.noderun.NodeRun property) (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.node.Node property) dir_list() (in module fastr.helpers.clear_pycs) directory() (in module fastr.utils.cmd.test) DirectoryLock (class in fastr.helpers.lockfile) dirname() (in module fastr.data.url) dirurl() (in module fastr.data.url) dispatch_callbacks() (fastr.plugins.DRMAAExecution method) doc() (in module fastr.web.views) DockerTarget (class in fastr.plugins) done() (fastr.execution.job.JobState property) dot_extension (fastr.datatypes.BaseDataType attribute) draw() (fastr.api.Network method) (fastr.planning.link.Link method) (fastr.planning.network.Network method) (fastr.planning.node.ConstantNode method) (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) (fastr.planning.node.SinkNode method) (fastr.planning.node.SourceNode method) draw_id() (fastr.planning.node.Node method) draw_link_target() (fastr.planning.node.MacroNode method) (fastr.planning.node.Node method) draw_network() (fastr.planning.network.Network method) DRMAAExecution (class in fastr.plugins) dummy_container (class in fastr.utils.cmd.upgrade) dump() (in module fastr.helpers.xmltodict) dumps() (in module fastr.helpers.xmltodict) DYNAMIC_LIBRARY_PATH_DICT (fastr.plugins.LocalBinaryTarget attribute)

E

elasticsearch_update_status() (fastr.plugins.ElasticsearchReporter method) ElasticsearchReporter (class in fastr.plugins) emit() (fastr.helpers.events.FastrLogEventHandler method) emit_event() (in module fastr.helpers.events) empty() (fastr.planning.inputgroup.InputGroup property) EmptyDefault (class in fastr.helpers.configmanager) endpoint (fastr.web.api.NetworkApi attribute) (fastr.web.api.NetworkListApi attribute) (fastr.web.api.RunApi attribute) (fastr.web.api.RunListApi attribute) (fastr.web.api.StatusApi attribute) (fastr.web.api.ToolApi attribute) (fastr.web.api.ToolListApi attribute) ensure_tmp_dir() (fastr.execution.job.Job method) entity() (fastr.core.provenance.Provenance method) EnumType (class in fastr.datatypes) EnvironmentModules (class in fastr.execution.environmentmodules) envmod (fastr.execution.environmentmodules.ModuleSystem attribute) EventType (class in fastr.helpers.events) examplesdir() (fastr.helpers.configmanager.Config property) excerpt() (fastr.exceptions.FastrError method) exec_worker() (fastr.plugins.LinearExecution method) execute() (fastr.api.Network method) (fastr.core.interface.Interface method) (fastr.core.tool.Tool method) (fastr.execution.flownoderun.AdvancedFlowNodeRun method) (fastr.execution.job.Job method) (fastr.execution.macronoderun.MacroNodeRun method) (fastr.execution.networkrun.NetworkRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.ConstantNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.planning.network.Network method) (fastr.plugins.CrossValidation static method) (fastr.plugins.FastrInterface method) (fastr.plugins.FlowInterface method) (fastr.plugins.NipypeInterface method)

execute_job() (in module fastr.execution.executionscript) execution_done (fastr.execution.job.JobState attribute) execution_failed (fastr.execution.job.JobState attribute) execution_finished() (fastr.execution.networkrun.NetworkRun method) execution_plugin() (fastr.helpers.configmanager.Config property) ExecutionPlugin (class in fastr.plugins.executionplugin) ExecutionPluginManager (class in fastr.plugins.managers.executionpluginmanager) executionscript() (fastr.helpers.configmanager.Config property) expand() (fastr.api.Link property) (fastr.core.samples.SampleIndex method) (fastr.execution.linkrun.LinkRun property) (fastr.planning.link.Link property) expand_url() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.CommaSeperatedValueFile method) (fastr.plugins.S3Filesystem method) (fastr.plugins.VirtualFileSystemRegularExpression method) (fastr.plugins.VirtualFileSystemValueList method) (fastr.plugins.XNATStorage method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) expanding() (fastr.core.interface.Interface property) (fastr.plugins.FastrInterface property) (fastr.plugins.FlowInterface property) (fastr.plugins.NipypeInterface property) extend() (fastr.helpers.configmanager.EmptyDefault method) (in module fastr.helpers.jsonschemaparser) extension (fastr.datatypes.BaseDataType attribute) extra() (fastr.core.version.Version property) extra_string() (fastr.core.version.Version property) extract_argparser() (in module fastr.utils.cmd.extract_argparse) extrainfofile() (fastr.execution.job.Job property) extrainfourl() (fastr.execution.job.Job property)

F

failed (fastr.execution.job.JobState attribute) failed_annotations() (fastr.core.samples.SampleItemBase property) fastr.__init__ (module) fastr.api (module) fastr.core (module) fastr.core.cardinality (module) fastr.core.dimension (module) fastr.core.interface (module) fastr.core.ioplugin (module) fastr.core.provenance (module) fastr.core.resourcelimit (module) fastr.core.samples (module) fastr.core.target (module) fastr.core.test (module) fastr.core.tool (module) fastr.core.version (module) fastr.core.vfs (module) fastr.data (module) fastr.data.url (module) fastr.datatypes (module) fastr.exceptions (module) fastr.execution (module) fastr.execution.basenoderun (module) fastr.execution.environmentmodules (module) fastr.execution.executionscript (module) fastr.execution.flownoderun (module) fastr.execution.inputoutputrun (module) fastr.execution.job (module) fastr.execution.linkrun (module) fastr.execution.macronoderun (module) fastr.execution.networkanalyzer (module) fastr.execution.networkchunker (module) fastr.execution.networkrun (module) fastr.execution.noderun (module) fastr.execution.sinknoderun (module) fastr.execution.sourcenoderun (module) fastr.helpers (module) fastr.helpers.checksum (module) fastr.helpers.classproperty (module) fastr.helpers.clear_pycs (module) fastr.helpers.configmanager (module) fastr.helpers.events (module) fastr.helpers.filesynchelper (module) fastr.helpers.iohelpers (module) fastr.helpers.jsonschemaparser (module) fastr.helpers.lazy_module (module) fastr.helpers.lockfile (module) fastr.helpers.procutils (module) fastr.helpers.report (module) fastr.helpers.rest_generation (module) fastr.helpers.schematotable (module) fastr.helpers.shellescape (module) fastr.helpers.sysinfo (module) fastr.helpers.xmltodict (module) fastr.planning (module) fastr.planning.inputgroup (module) fastr.planning.inputgroupcombiner (module) fastr.planning.inputoutput (module) fastr.planning.link (module) fastr.planning.network (module) fastr.planning.node (module) fastr.plugins (module) fastr.plugins.executionplugin (module) fastr.plugins.managers (module) fastr.plugins.managers.executionpluginmanager (module) fastr.plugins.managers.interfacemanager (module) fastr.plugins.managers.iopluginmanager (module) fastr.plugins.managers.networkmanager (module) fastr.plugins.managers.objectmanager (module) fastr.plugins.managers.pluginmanager (module) fastr.plugins.managers.targetmanager (module) fastr.plugins.managers.toolmanager (module) fastr.plugins.reportingplugin (module) fastr.test (module) fastr.utils (module) fastr.utils.cmd (module) fastr.utils.cmd.cat (module) fastr.utils.cmd.dump (module) fastr.utils.cmd.execute (module) fastr.utils.cmd.extract_argparse (module) fastr.utils.cmd.provenance (module) fastr.utils.cmd.pylint (module) fastr.utils.cmd.report (module) fastr.utils.cmd.run (module) fastr.utils.cmd.sink (module) fastr.utils.cmd.source (module) fastr.utils.cmd.test (module) fastr.utils.cmd.trace (module) fastr.utils.cmd.upgrade (module) fastr.utils.cmd.verify (module) fastr.utils.cmd.webapp (module) fastr.utils.compare (module) fastr.utils.dicteq (module) fastr.utils.gettools (module) fastr.utils.multiprocesswrapper (module) fastr.utils.verify (module) fastr.version (module) fastr.web (module) fastr.web.api (module) fastr.web.run (module) fastr.web.views (module) fastr_cat() (in module fastr.utils.cmd.cat) fastr_isinstance() (in module fastr.datatypes) FastrAttributeError FastrCannotChangeAttributeError FastrCardinalityError FastrCollectorError FastrDataTypeFileNotReadable FastrDataTypeMismatchError FastrDataTypeNotAvailableError FastrDataTypeNotInstantiableError FastrDataTypeValueError FastrError FastrErrorInSubprocess FastrExecutableNotFoundError FastrExecutionError FastrFileNotFound FastrImportError FastrIndexError FastrIndexNonexistent FastrInterface (class in fastr.plugins) FastrIOError FastrKeyError FastrLockNotAcquired FastrLogEventHandler (class in fastr.helpers.events) FastrLookupError FastrMountUnknownError

FastrNamespaceType (class in fastr.utils.cmd.upgrade) FastrNetworkMismatchError FastrNetworkUnknownError FastrNodeAreadyPreparedError FastrNodeNotPreparedError FastrNodeNotValidError FastrNotExecutableError FastrNotImplementedError FastrNoValidTargetError FastrObjectUnknownError FastrOptionalModuleNotAvailableError FastrOSError FastrOutputValidationError FastrParentMismatchError FastrPluginCapabilityNotImplemented FastrPluginNotAvailable FastrPluginNotLoaded FastrRefResolver (class in fastr.helpers.jsonschemaparser) FastrResultFileNotFound FastrScriptNotFoundError FastrSerializationError FastrSerializationIgnoreDefaultError FastrSerializationInvalidDataError FastrSerializationMethodError FastrSinkDataUnavailableError FastrSizeInvalidError FastrSizeMismatchError FastrSizeUnknownError FastrSourceDataUnavailableError FastrStateError FastrSubprocessNotFinished FastrToolNotAvailableError FastrToolTargetNotFound FastrToolUnknownError FastrToolVersionError FastrTypeError FastrUnknownURLSchemeError FastrValueError FastrVersionInvalidError FastrVersionMismatchError fetch_url() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) (fastr.plugins.HTTPPlugin method) (fastr.plugins.S3Filesystem method) (fastr.plugins.XNATStorage method) fetch_value() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) (fastr.plugins.S3Filesystem method) filename (fastr.datatypes.BaseDataType attribute) (fastr.plugins.BlockingExecution attribute) (fastr.plugins.CommaSeperatedValueFile attribute) (fastr.plugins.CrossValidation attribute) (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.DockerTarget attribute) (fastr.plugins.ElasticsearchReporter attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FileSystem attribute) (fastr.plugins.FlowInterface attribute) (fastr.plugins.HTTPPlugin attribute) (fastr.plugins.LinearExecution attribute) (fastr.plugins.LocalBinaryTarget attribute) (fastr.plugins.MacroTarget attribute) (fastr.plugins.NipypeInterface attribute) (fastr.plugins.Null attribute) (fastr.plugins.PimReporter attribute) (fastr.plugins.ProcessPoolExecution attribute) (fastr.plugins.RQExecution attribute) (fastr.plugins.Reference attribute) (fastr.plugins.S3Filesystem attribute) (fastr.plugins.SimpleReport attribute) (fastr.plugins.SingularityTarget attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.StrongrExecution attribute) (fastr.plugins.VirtualFileSystem attribute) (fastr.plugins.VirtualFileSystemRegularExpression attribute) (fastr.plugins.VirtualFileSystemValueList attribute) (fastr.plugins.XNATStorage attribute) FileSyncHelper (class in fastr.helpers.filesynchelper) filesynchelper_enabled() (in module fastr.helpers.filesynchelper) filesynchelper_url() (fastr.helpers.configmanager.Config property) FileSystem (class in fastr.plugins) fill_output_argument() (fastr.execution.job.Job class method) filter_plugin() (fastr.plugins.managers.pluginmanager.PluginsView method) find_argparser() (in module fastr.utils.cmd.extract_argparse) find_commands() (in module fastr.utils.cmd) find_source_index() (fastr.execution.noderun.NodeRun method) (fastr.planning.inputgroup.InputGroup method) (fastr.planning.node.Node method) find_tool() (in module fastr.utils.cmd.upgrade) finished (fastr.execution.job.JobState attribute) flow_plugin_type (fastr.plugins.FlowInterface attribute) flow_plugins (fastr.plugins.FlowInterface attribute) FlowInterface (class in fastr.plugins) FlowNode (class in fastr.planning.node) FlowNodeRun (class in fastr.execution.flownoderun) format() (fastr.web.api.ObjectUrl method) (fastr.web.api.SubUrl method) ForwardsDimensions (class in fastr.core.dimension) from_schema() (fastr.helpers.jsonschemaparser.FastrRefResolver class method) full_split() (in module fastr.data.url) fullid (fastr.datatypes.BaseDataType attribute) fullid() (fastr.core.samples.SampleCollection property) (fastr.core.tool.Tool property) (fastr.datatypes.DataTypeManager property) (fastr.execution.inputoutputrun.InputRun property) (fastr.execution.inputoutputrun.NamedSubinputRun property) (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.execution.job.Job property) (fastr.execution.linkrun.LinkRun property) (fastr.execution.networkrun.NetworkRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.inputgroup.InputGroup property) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner property) (fastr.planning.inputoutput.BaseInputOutput property) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.NamedSubInput property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubInput property) (fastr.planning.inputoutput.SubOutput property) (fastr.planning.link.Link property) (fastr.planning.network.Network property) (fastr.planning.node.Node property) function_wrapper() (in module fastr.utils.multiprocesswrapper)

G

GE_NATIVE_SPEC (fastr.plugins.DRMAAExecution attribute) generate_jobs() (fastr.execution.networkrun.NetworkRun method) get() (fastr.web.api.NetworkApi method) (fastr.web.api.NetworkListApi method) (fastr.web.api.RunApi method) (fastr.web.api.RunListApi method) (fastr.web.api.StatusApi method) (fastr.web.api.ToolApi method) (fastr.web.api.ToolListApi method) get_arguments() (fastr.plugins.FastrInterface method) get_base_version() (in module fastr.version) get_command() (fastr.plugins.FastrInterface method) get_command_module() (in module fastr.utils.cmd) get_cpu_usage() (in module fastr.helpers.sysinfo) get_deferred() (fastr.execution.job.Job method) get_drmaa_info() (in module fastr.helpers.sysinfo) get_field() (fastr.helpers.configmanager.Config method) get_hg_info() (in module fastr.version) get_hostinfo() (in module fastr.helpers.sysinfo) get_job() (fastr.plugins.executionplugin.ExecutionPlugin method) get_memory_usage() (in module fastr.helpers.sysinfo) get_message() (in module fastr.exceptions) get_mounts() (in module fastr.helpers.sysinfo) get_object_version() (fastr.plugins.managers.networkmanager.NetworkManager method) (fastr.plugins.managers.objectmanager.ObjectManager method) (fastr.plugins.managers.toolmanager.ToolManager method) get_os() (in module fastr.helpers.sysinfo) get_output_datatype() (fastr.execution.job.Job method) (fastr.execution.job.SourceJob method) get_output_info() (fastr.execution.macronoderun.MacroNodeRun method) (fastr.planning.node.MacroNode method) get_parent_provenance() (fastr.core.provenance.Provenance static method) get_parser() (in module fastr.utils.cmd.cat) (in module fastr.utils.cmd.dump) (in module fastr.utils.cmd.execute) (in module fastr.utils.cmd.extract_argparse) (in module fastr.utils.cmd.provenance) (in module fastr.utils.cmd.pylint) (in module fastr.utils.cmd.report) (in module fastr.utils.cmd.run) (in module fastr.utils.cmd.sink) (in module fastr.utils.cmd.source) (in module fastr.utils.cmd.test) (in module fastr.utils.cmd.trace) (in module fastr.utils.cmd.upgrade) (in module fastr.utils.cmd.verify) (in module fastr.utils.cmd.webapp)

get_path_from_url() (in module fastr.data.url) get_processes() (in module fastr.helpers.sysinfo) get_prov_document() (in module fastr.utils.cmd.provenance) get_python() (in module fastr.helpers.sysinfo) get_result() (fastr.execution.job.InlineJob method) (fastr.execution.job.Job method) (fastr.execution.job.SinkJob method) get_saved_version() (in module fastr.version) get_sourced_nodes() (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.execution.noderun.NodeRun method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.node.Node method) get_sourced_outputs() (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.SubInput method) get_specials() (fastr.plugins.FastrInterface method) get_status() (fastr.plugins.executionplugin.ExecutionPlugin method) get_sysinfo() (in module fastr.helpers.sysinfo) get_type() (fastr.datatypes.DataTypeManager method) (fastr.plugins.NipypeInterface method) get_url_scheme() (in module fastr.data.url) get_users() (in module fastr.helpers.sysinfo) get_value() (fastr.execution.job.Job class method) getblueprinter() (in module fastr.helpers.jsonschemaparser) global_id() (fastr.execution.networkrun.NetworkRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.network.Network property) (fastr.planning.node.Node property) guess_type() (fastr.datatypes.DataTypeManager method)

H

has_file_promise() (fastr.helpers.filesynchelper.FileSyncHelper method) has_type() (fastr.datatypes.DataTypeManager method) HasDimensions (class in fastr.core.dimension) hash() (fastr.core.tool.Tool property) hash_inputs() (fastr.execution.job.Job method) (fastr.execution.job.SinkJob method) (fastr.execution.job.SourceJob method)

hash_results() (fastr.execution.job.Job method) hashsum() (in module fastr.helpers.checksum) HasSamples (class in fastr.core.samples) help (fastr.core.tool.Tool attribute) hold (fastr.execution.job.JobState attribute) (fastr.plugins.executionplugin.JobAction attribute) hold_job() (fastr.plugins.executionplugin.ExecutionPlugin method) HTTPPlugin (class in fastr.plugins)

I

id (fastr.datatypes.BaseDataType attribute) id() (fastr.api.Input property) (fastr.api.Link property) (fastr.api.Network property) (fastr.api.Node property) (fastr.api.Output property) (fastr.core.samples.SampleItemBase property) (fastr.core.tool.Tool property) (fastr.execution.job.Job property) (fastr.execution.job.SinkJob property) (fastr.execution.networkrun.NetworkRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.inputoutput.BaseInputOutput property) (fastr.planning.inputoutput.Input property) (fastr.planning.network.Network property) (fastr.planning.node.Node property) idle() (fastr.execution.job.JobState property) ids() (fastr.core.samples.HasSamples method) in_progress() (fastr.execution.job.JobState property) index() (fastr.core.samples.SampleItemBase property) (fastr.execution.inputoutputrun.InputRun method) (fastr.planning.inputoutput.Input method) (in module fastr.web.views) indexes() (fastr.core.samples.HasSamples method) indexrep() (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.planning.inputoutput.SubOutput property) INFO_DUMP (fastr.execution.job.Job attribute) init_provenance() (fastr.core.provenance.Provenance method) InlineJob (class in fastr.execution.job) Input (class in fastr.api) (class in fastr.planning.inputoutput) input() (fastr.api.Node property) (fastr.execution.sinknoderun.SinkNodeRun property) (fastr.planning.node.SinkNode property) input_group() (fastr.api.Input property) (fastr.execution.inputoutputrun.InputRun property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.MacroInput property) (fastr.planning.inputoutput.SubInput property) input_groups() (fastr.execution.noderun.NodeRun property) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner property) (fastr.planning.node.Node property) InputDict (class in fastr.planning.node) InputGroup (class in fastr.planning.inputgroup) InputRun (class in fastr.execution.inputoutputrun) inputs (fastr.planning.node.Node attribute)

inputs() (fastr.api.Node property) (fastr.core.interface.Interface property) (fastr.core.tool.Tool property) (fastr.plugins.FastrInterface property) (fastr.plugins.FlowInterface property) (fastr.plugins.NipypeInterface property) InputSpec (class in fastr.core.interface) InputSpecBase (in module fastr.core.interface) insert() (fastr.execution.inputoutputrun.InputRun method) (fastr.planning.inputoutput.Input method) IntCardinalitySpec (class in fastr.core.cardinality) Interface (class in fastr.core.interface) InterfacePluginManager (class in fastr.plugins.managers.interfacemanager) InterfaceResult (class in fastr.core.interface) IOPlugin (class in fastr.core.ioplugin) IOPluginManager (class in fastr.plugins.managers.iopluginmanager) is_mapping() (fastr.core.samples.SampleValue property) is_sequence() (fastr.core.samples.SampleValue property) is_valid() (fastr.planning.network.Network method) isdatatype() (fastr.datatypes.DataTypeManager static method) isinstance() (fastr.datatypes.BaseDataType class method) (fastr.datatypes.TypeGroup class method) isloaded() (fastr.execution.environmentmodules.EnvironmentModules method) isslice() (fastr.core.samples.SampleIndex property) isurl() (fastr.core.ioplugin.IOPlugin static method) (in module fastr.data.url) item_index() (fastr.execution.inputoutputrun.NamedSubinputRun property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.planning.inputoutput.BaseInput property) (fastr.planning.inputoutput.NamedSubInput property) (fastr.planning.inputoutput.SubInput property) items() (fastr.core.samples.HasSamples method) items_prevalidate() (in module fastr.helpers.jsonschemaparser) iter_input_groups() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputgroupcombiner.DefaultInputGroupCombiner method) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner method) iterconvergingindices() (fastr.execution.inputoutputrun.OutputRun method) iterelements() (fastr.core.samples.SampleValue method) iterinputvalues() (fastr.planning.inputgroup.InputGroup property) iteritems() (fastr.core.samples.HasSamples method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.planning.inputoutput.SubInput method) itersubinputs() (fastr.execution.inputoutputrun.BaseInputRun method) (fastr.execution.inputoutputrun.InputRun method) (fastr.execution.inputoutputrun.SubInputRun method) (fastr.planning.inputoutput.BaseInput method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.SubInput method)

J

Job (class in fastr.execution.job) job() (fastr.datatypes.Deferred property) job_cleanup_level() (fastr.helpers.configmanager.Config property) job_finished() (fastr.execution.networkrun.NetworkRun method) (fastr.helpers.filesynchelper.FileSyncHelper method) (fastr.plugins.executionplugin.ExecutionPlugin method) job_finished_callback() (fastr.plugins.ProcessPoolExecution method) job_regression_check() (fastr.plugins.DRMAAExecution method) job_status_check() (fastr.plugins.SlurmExecution method)

job_updated (fastr.helpers.events.EventType attribute) job_updated() (fastr.plugins.ElasticsearchReporter method) (fastr.plugins.PimReporter method) (fastr.plugins.reportingplugin.ReportingPlugin method) JobAction (class in fastr.plugins.executionplugin) JobCleanupLevel (class in fastr.execution.job) jobs() (fastr.core.samples.SampleItemBase property) JobState (class in fastr.execution.job) join() (in module fastr.data.url) json (in module fastr.plugins)

L

LazyModule (class in fastr.helpers.lazy_module) LinearExecution (class in fastr.plugins) linearized() (fastr.execution.inputoutputrun.SourceOutputRun property) (fastr.planning.inputoutput.SourceOutput property) Link (class in fastr.api) (class in fastr.planning.link) link_or_copy() (in module fastr.helpers.iohelpers) LinkRun (class in fastr.execution.linkrun) listeners() (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubOutput property) (fastr.planning.node.Node property) lmod (fastr.execution.environmentmodules.ModuleSystem attribute) load() (fastr.api.Network class method) (fastr.execution.environmentmodules.EnvironmentModules method) (fastr.helpers.filesynchelper.FileSyncHelper method) (in module fastr.helpers.xmltodict)

load_gpickle() (in module fastr.helpers.iohelpers) load_json() (in module fastr.helpers.iohelpers) loaded_modules() (fastr.execution.environmentmodules.EnvironmentModules property) loads() (in module fastr.helpers.xmltodict) LocalBinaryTarget (class in fastr.plugins) lock_dir() (fastr.helpers.lockfile.DirectoryLock property) lock_dir_name (fastr.helpers.lockfile.DirectoryLock attribute) log_record_emitted (fastr.helpers.events.EventType attribute) log_record_emitted() (fastr.plugins.PimReporter method) (fastr.plugins.reportingplugin.ReportingPlugin method) log_to_file() (fastr.helpers.configmanager.Config property) logdir() (fastr.helpers.configmanager.Config property) logfile() (fastr.execution.job.Job property) logging_config() (fastr.helpers.configmanager.Config property) loglevel() (fastr.helpers.configmanager.Config property) logtype() (fastr.helpers.configmanager.Config property) logurl() (fastr.execution.job.Job property) long_id() (fastr.execution.networkrun.NetworkRun property) lookup() (fastr.datatypes.Deferred class method)

M

MacroInput (class in fastr.planning.inputoutput) MacroNode (class in fastr.planning.node) MacroNodeRun (class in fastr.execution.macronoderun) MacroOutput (class in fastr.planning.inputoutput) MacroOutputRun (class in fastr.execution.inputoutputrun) MacroTarget (class in fastr.plugins) main() (in module fastr.execution.executionscript) (in module fastr.helpers.clear_pycs) (in module fastr.utils.cmd) (in module fastr.utils.cmd.cat) (in module fastr.utils.cmd.dump) (in module fastr.utils.cmd.execute) (in module fastr.utils.cmd.extract_argparse) (in module fastr.utils.cmd.provenance) (in module fastr.utils.cmd.pylint) (in module fastr.utils.cmd.report) (in module fastr.utils.cmd.run) (in module fastr.utils.cmd.sink) (in module fastr.utils.cmd.source) (in module fastr.utils.cmd.test) (in module fastr.utils.cmd.trace) (in module fastr.utils.cmd.upgrade) (in module fastr.utils.cmd.verify) (in module fastr.utils.cmd.webapp) (in module fastr.utils.gettools) (in module fastr.web.run) major() (fastr.core.version.Version property) make_file_promise() (fastr.helpers.filesynchelper.FileSyncHelper method) mapping_part() (fastr.core.samples.SampleValue method) match_types() (fastr.datatypes.DataTypeManager method) match_types_any() (fastr.datatypes.DataTypeManager method) MaxCardinalitySpec (class in fastr.core.cardinality) md5_checksum() (in module fastr.helpers.checksum) mediatypes() (fastr.web.api.NetworkApi method) (fastr.web.api.NetworkListApi method) (fastr.web.api.RunApi method) (fastr.web.api.RunListApi method) (fastr.web.api.StatusApi method) (fastr.web.api.ToolApi method) (fastr.web.api.ToolListApi method) members (fastr.datatypes.TypeGroup attribute) memory() (fastr.api.ResourceLimit property) (fastr.core.resourcelimit.ResourceLimit property) merge() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputgroupcombiner.DefaultInputGroupCombiner method) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner method) merge_default() (fastr.helpers.configmanager.EmptyDefault method) merge_dimensions() (fastr.execution.noderun.NodeRun property) (fastr.planning.node.Node property)

merge_failed_annotations() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) merge_payloads() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) merge_sample_data() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) merge_sample_id() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) merge_sample_index() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) merge_sample_jobs() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) MergingInputGroupCombiner (class in fastr.planning.inputgroupcombiner) methods (fastr.web.api.NetworkApi attribute) (fastr.web.api.NetworkListApi attribute) (fastr.web.api.RunApi attribute) (fastr.web.api.RunListApi attribute) (fastr.web.api.StatusApi attribute) (fastr.web.api.ToolApi attribute) (fastr.web.api.ToolListApi attribute) MinCardinalitySpec (class in fastr.core.cardinality) minor() (fastr.core.version.Version property) module (fastr.plugins.BlockingExecution attribute) (fastr.plugins.CommaSeperatedValueFile attribute) (fastr.plugins.CrossValidation attribute) (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.DockerTarget attribute) (fastr.plugins.ElasticsearchReporter attribute) (fastr.plugins.FastrInterface attribute) (fastr.plugins.FileSystem attribute) (fastr.plugins.FlowInterface attribute) (fastr.plugins.HTTPPlugin attribute) (fastr.plugins.LinearExecution attribute) (fastr.plugins.LocalBinaryTarget attribute) (fastr.plugins.MacroTarget attribute) (fastr.plugins.NipypeInterface attribute) (fastr.plugins.Null attribute) (fastr.plugins.PimReporter attribute) (fastr.plugins.ProcessPoolExecution attribute) (fastr.plugins.RQExecution attribute) (fastr.plugins.Reference attribute) (fastr.plugins.S3Filesystem attribute) (fastr.plugins.SimpleReport attribute) (fastr.plugins.SingularityTarget attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.StrongrExecution attribute) (fastr.plugins.VirtualFileSystem attribute) (fastr.plugins.VirtualFileSystemRegularExpression attribute) (fastr.plugins.VirtualFileSystemValueList attribute) (fastr.plugins.XNATStorage attribute) ModuleSystem (class in fastr.execution.environmentmodules) monitor_docker() (fastr.plugins.DockerTarget method) monitor_process() (fastr.core.target.SubprocessBasedTarget method) mounts() (fastr.helpers.configmanager.Config property)

N

name (fastr.core.tool.Tool attribute) (fastr.datatypes.BaseDataType attribute) name() (fastr.core.dimension.Dimension property) (fastr.execution.noderun.NodeRun property) (fastr.planning.node.Node property) NamedSubInput (class in fastr.planning.inputoutput) NamedSubinputRun (class in fastr.execution.inputoutputrun) namedtuple_to_dict() (in module fastr.helpers.sysinfo) namespace (fastr.core.tool.Tool attribute) (fastr.planning.network.Network attribute) NATIVE_SPEC (fastr.plugins.DRMAAExecution attribute) ndims() (fastr.core.dimension.HasDimensions property) (fastr.core.samples.SampleCollection property) (fastr.execution.inputoutputrun.SourceOutputRun property) Network (class in fastr.api) (class in fastr.planning.network) network() (fastr.execution.networkrun.NetworkRun property) (fastr.planning.node.MacroNode property) (in module fastr.web.views) NETWORK_DUMP_FILE_NAME (fastr.execution.networkrun.NetworkRun attribute) (fastr.planning.network.Network attribute) network_lock_thread() (in module fastr.web.api) network_run() (fastr.execution.macronoderun.MacroNodeRun property) network_runner() (in module fastr.web.api) NetworkAnalyzer (class in fastr.execution.networkanalyzer) NetworkApi (class in fastr.web.api) NetworkChunker (class in fastr.execution.networkchunker) NetworkListApi (class in fastr.web.api) NetworkManager (class in fastr.plugins.managers.networkmanager) NetworkRun (class in fastr.execution.networkrun)

networks (fastr attribute) networks() (in module fastr.web.views) networks_path() (fastr.helpers.configmanager.Config property) NipypeInterface (class in fastr.plugins) no_cleanup (fastr.execution.job.JobCleanupLevel attribute) Node (class in fastr.api) (class in fastr.planning.node) node() (fastr.core.cardinality.AsCardinalitySpec property) (fastr.core.cardinality.ValueCardinalitySpec property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.planning.inputoutput.BaseInputOutput property) (fastr.planning.inputoutput.SubInput property) (fastr.planning.inputoutput.SubOutput property) node_class (fastr.core.tool.Tool attribute) NODE_RUN_MAP (fastr.execution.basenoderun.BaseNodeRun attribute) NODE_RUN_TYPES (fastr.execution.basenoderun.BaseNodeRun attribute) NODE_TYPES (fastr.planning.node.BaseNode attribute) nodegroup() (fastr.planning.node.Node property) (fastr.planning.node.SourceNode property) nodegroups() (fastr.execution.networkrun.NetworkRun property) (fastr.planning.network.Network property) NodeRun (class in fastr.execution.noderun) non_failed (fastr.execution.job.JobCleanupLevel attribute) nonexistent (fastr.execution.job.JobState attribute) normurl() (in module fastr.data.url) not_draft4() (in module fastr.helpers.jsonschemaparser) ns_id() (fastr.core.tool.Tool property) (fastr.planning.network.Network property) Null (class in fastr.plugins)

O

object_class() (fastr.plugins.managers.networkmanager.NetworkManager property) (fastr.plugins.managers.objectmanager.ObjectManager property) (fastr.plugins.managers.toolmanager.ToolManager property) ObjectManager (class in fastr.plugins.managers.objectmanager) ObjectUrl (class in fastr.web.api) objectversions() (fastr.plugins.managers.objectmanager.ObjectManager method) one_of_draft4() (in module fastr.helpers.jsonschemaparser) open_url() (in module fastr.utils.cmd.webapp) options (fastr.datatypes.EnumType attribute) Output (class in fastr.api) (class in fastr.planning.inputoutput) output() (fastr.api.Node property) (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.node.SourceNode property) OutputDict (class in fastr.planning.node)

OutputRun (class in fastr.execution.inputoutputrun) outputs (fastr.planning.node.Node attribute) outputs() (fastr.api.Node property) (fastr.core.interface.Interface property) (fastr.core.tool.Tool property) (fastr.plugins.FastrInterface property) (fastr.plugins.FlowInterface property) (fastr.plugins.NipypeInterface property) outputsize() (fastr.execution.flownoderun.FlowNodeRun property) (fastr.execution.noderun.NodeRun property) (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.node.FlowNode property) (fastr.planning.node.Node property) OutputSpec (class in fastr.core.interface) OutputSpecBase (in module fastr.core.interface)

P

parent (fastr.datatypes.BaseDataType attribute) parent() (fastr.core.samples.SampleCollection property) (fastr.execution.linkrun.LinkRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.inputgroup.InputGroup property) (fastr.planning.link.Link property) (fastr.planning.node.Node property) parse() (fastr.helpers.schematotable.SchemaPrinter method) parse_uri() (fastr.plugins.XNATStorage method) parsed_value() (fastr.datatypes.BaseDataType property) (fastr.datatypes.Deferred property) (fastr.datatypes.URLType property) path (in module fastr.plugins) path() (fastr.core.tool.Tool property) path_to_url() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) paths() (fastr.plugins.LocalBinaryTarget property) pattern_properties_prevalid() (in module fastr.helpers.jsonschemaparser) pid_file() (fastr.helpers.lockfile.DirectoryLock property) pid_file_name (fastr.helpers.lockfile.DirectoryLock attribute) pim_batch_size() (fastr.helpers.configmanager.Config property) pim_debug() (fastr.helpers.configmanager.Config property) pim_finished_timeout() (fastr.helpers.configmanager.Config property) pim_host() (fastr.helpers.configmanager.Config property) pim_update_interval() (fastr.helpers.configmanager.Config property) pim_username() (fastr.helpers.configmanager.Config property) PimReporter (class in fastr.plugins) plugin_class() (fastr.datatypes.DataTypeManager property) (fastr.plugins.managers.pluginmanager.PluginManager property) (fastr.plugins.managers.pluginmanager.PluginSubManager property) PluginManager (class in fastr.plugins.managers.pluginmanager) plugins_path() (fastr.helpers.configmanager.Config property) PluginSubManager (class in fastr.plugins.managers.pluginmanager) PluginsView (class in fastr.plugins.managers.pluginmanager) poll_datatype() (fastr.datatypes.DataTypeManager method) populate() (fastr.datatypes.DataTypeManager method) (fastr.plugins.managers.toolmanager.ToolManager method) post() (fastr.web.api.RunListApi method) predefined() (fastr.core.cardinality.AsCardinalitySpec property) (fastr.core.cardinality.CardinalitySpec property) (fastr.core.cardinality.IntCardinalitySpec property) preference (fastr.datatypes.TypeGroup attribute) preferred_types() (fastr.datatypes.DataTypeManager property) (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.helpers.configmanager.Config property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubOutput property)

prepend() (fastr.helpers.configmanager.EmptyDefault method) primary() (fastr.planning.inputgroup.InputGroup property) print_help() (in module fastr.utils.cmd) print_job_result() (in module fastr.helpers.report) print_result() (fastr.core.ioplugin.IOPlugin static method) print_sample_sink() (in module fastr.utils.cmd.trace) print_samples() (in module fastr.utils.cmd.trace) print_sinks() (in module fastr.utils.cmd.trace) print_value() (fastr.planning.node.ConstantNode property) printlines() (fastr.helpers.schematotable.SchemaPrinter method) process_callbacks() (fastr.plugins.executionplugin.ExecutionPlugin method) process_pool_worker_number() (fastr.helpers.configmanager.Config property) processing_callback (fastr.execution.job.JobState attribute) ProcessPoolExecution (class in fastr.plugins) ProcessUsageCollection (class in fastr.core.target) properties_postvalidate() (in module fastr.helpers.jsonschemaparser) properties_prevalidate() (in module fastr.helpers.jsonschemaparser) protected_modules() (fastr.helpers.configmanager.Config property) prov() (in module fastr.web.views) PROV_DUMP (fastr.execution.job.Job attribute) Provenance (class in fastr.core.provenance) provenance() (fastr.datatypes.Deferred property) provfile() (fastr.execution.job.Job property) provurl() (fastr.execution.job.Job property) pull_source_data() (fastr.core.ioplugin.IOPlugin method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) push_sink_data() (fastr.core.ioplugin.IOPlugin method) (fastr.plugins.Reference method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) put_url() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) (fastr.plugins.Null method) (fastr.plugins.S3Filesystem method) (fastr.plugins.XNATStorage method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) put_value() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) (fastr.plugins.Null method) (fastr.plugins.S3Filesystem method) Python Enhancement Proposals PEP 8, [1] PEP 8#class-names PEP 8#global-variable-names PEP 8#method-names-and-instance-variables PEP 8#package-and-module-names PEP 8#prescriptive-naming-conventions

Q

queue (fastr.plugins.executionplugin.JobAction attribute) queue_job() (fastr.plugins.executionplugin.ExecutionPlugin method)

queued (fastr.execution.job.JobState attribute) quote_argument() (in module fastr.helpers.shellescape)

R

RangeCardinalitySpec (class in fastr.core.cardinality) raw_value() (fastr.datatypes.BaseDataType property) read_bytes() (fastr.core.target.SystemUsageInfo property) read_config() (fastr.helpers.configmanager.Config method) read_config_files (fastr.helpers.configmanager.Config attribute) read_config_string() (fastr.helpers.configmanager.Config method) read_sink_data() (in module fastr.utils.cmd.trace) readfastrschema() (fastr.helpers.jsonschemaparser.FastrRefResolver static method) readfile() (fastr.helpers.jsonschemaparser.FastrRefResolver static method) Reference (class in fastr.plugins) references (fastr.core.tool.Tool attribute) register_fields() (fastr.helpers.configmanager.Config method) register_job() (fastr.plugins.executionplugin.ExecutionPlugin method) register_listener() (in module fastr.helpers.events) register_signals() (fastr.execution.networkrun.NetworkRun method) register_url_scheme() (fastr.plugins.managers.iopluginmanager.IOPluginManager static method) (in module fastr.data.url) release() (fastr.helpers.lockfile.DirectoryLock method) release_job() (fastr.plugins.executionplugin.ExecutionPlugin method) reload() (fastr.execution.environmentmodules.EnvironmentModules method) remove() (fastr.execution.inputoutputrun.InputRun method) (fastr.planning.inputoutput.Input method) (fastr.planning.inputoutput.SubInput method) (fastr.planning.network.Network method) remove_listener() (in module fastr.helpers.events) reporting_plugins() (fastr.helpers.configmanager.Config property) ReportingPlugin (class in fastr.plugins.reportingplugin) request_parser (fastr.web.api.RunListApi attribute) required() (fastr.planning.inputoutput.BaseInputOutput property) requirements (fastr.core.tool.Tool attribute) ResourceLimit (class in fastr.api) (class in fastr.core.resourcelimit)

resources() (fastr.execution.job.Job property) (fastr.execution.noderun.NodeRun property) resourcesdir() (fastr.helpers.configmanager.Config property) RESULT_DUMP (fastr.execution.job.Job attribute) resulting_datatype() (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.planning.inputoutput.Output property) (fastr.planning.inputoutput.SubOutput property) rmem() (fastr.core.target.SystemUsageInfo property) RQExecution (class in fastr.plugins) Run (class in fastr.web.api) run_command() (fastr.core.target.Target method) (fastr.plugins.DockerTarget method) (fastr.plugins.LocalBinaryTarget method) (fastr.plugins.MacroTarget method) (fastr.plugins.SingularityTarget method) run_finished (fastr.helpers.events.EventType attribute) run_finished() (fastr.plugins.PimReporter method) (fastr.plugins.SimpleReport method) (fastr.plugins.reportingplugin.ReportingPlugin method) run_job() (fastr.plugins.RQExecution class method) run_network() (fastr.web.api.Run method) run_pylint() (in module fastr.utils.cmd.pylint) run_started (fastr.helpers.events.EventType attribute) run_started() (fastr.plugins.PimReporter method) (fastr.plugins.reportingplugin.ReportingPlugin method) RunApi (class in fastr.web.api) runapp() (in module fastr.web.run) RunListApi (class in fastr.web.api) running (fastr.execution.job.JobState attribute)

S

S3Filesystem (class in fastr.plugins) SampleBaseId (class in fastr.core.samples) SampleCollection (class in fastr.core.samples) SampleId (class in fastr.core.samples) SampleIndex (class in fastr.core.samples) SampleItem (class in fastr.core.samples) SampleItemBase (class in fastr.core.samples) SamplePayload (class in fastr.core.samples) samples() (fastr.core.samples.ContainsSamples property) (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.inputoutputrun.SubOutputRun property) (fastr.planning.inputoutput.SubOutput property) SampleValue (class in fastr.core.samples) save() (fastr.api.Network method) save_gpickle() (in module fastr.helpers.iohelpers) save_json() (in module fastr.helpers.iohelpers) save_version() (in module fastr.version) SBATCH (fastr.plugins.SlurmExecution attribute) SCANCEL (fastr.plugins.SlurmExecution attribute) schemadir() (fastr.helpers.configmanager.Config property) SchemaPrinter (class in fastr.helpers.schematotable) scheme (fastr.plugins.CommaSeperatedValueFile attribute) (fastr.plugins.FileSystem attribute) (fastr.plugins.HTTPPlugin attribute) (fastr.plugins.Null attribute) (fastr.plugins.Reference attribute) (fastr.plugins.S3Filesystem attribute) (fastr.plugins.VirtualFileSystem attribute) (fastr.plugins.VirtualFileSystemRegularExpression attribute) (fastr.plugins.VirtualFileSystemValueList attribute) (fastr.plugins.XNATStorage attribute) scheme() (fastr.core.ioplugin.IOPlugin property) (fastr.core.vfs.VirtualFileSystem property) SCONTROL (fastr.plugins.SlurmExecution attribute) send_job() (fastr.plugins.DRMAAExecution method) sequence_part() (fastr.core.samples.SampleValue method) serialize() (fastr.core.provenance.Provenance method) server() (fastr.plugins.XNATStorage property) set_data() (fastr.execution.networkrun.NetworkRun method) (fastr.execution.sinknoderun.SinkNodeRun method) (fastr.execution.sourcenoderun.ConstantNodeRun method) (fastr.execution.sourcenoderun.SourceNodeRun method) (fastr.planning.node.ConstantNode method) (fastr.planning.node.SourceNode method) set_field() (fastr.helpers.configmanager.Config method) set_result() (fastr.execution.flownoderun.AdvancedFlowNodeRun method) (fastr.execution.flownoderun.FlowNodeRun method) (fastr.execution.noderun.NodeRun method) (fastr.execution.sinknoderun.SinkNodeRun method) setup() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) sha1_checksum() (in module fastr.helpers.checksum) show_jobs() (fastr.plugins.executionplugin.ExecutionPlugin method) shutdown() (in module fastr.web.views) shutdown_server() (in module fastr.web.views) signal_dependent_jobs() (fastr.plugins.executionplugin.ExecutionPlugin method) SimpleReport (class in fastr.plugins) SINGULARITY_BIN (fastr.plugins.SingularityTarget attribute) SingularityTarget (class in fastr.plugins) sink() (in module fastr.utils.cmd.sink) SINK_DUMP_FILE_NAME (fastr.execution.networkrun.NetworkRun attribute) (fastr.planning.network.Network attribute) SinkJob (class in fastr.execution.job) sinklist() (fastr.execution.networkrun.NetworkRun property) SinkNode (class in fastr.planning.node) SinkNodeRun (class in fastr.execution.sinknoderun) size() (fastr.core.dimension.Dimension property) (fastr.core.dimension.HasDimensions property) (fastr.execution.inputoutputrun.SourceOutputRun property) (fastr.execution.linkrun.LinkRun property)

slurm_job_check_interval() (fastr.helpers.configmanager.Config property) slurm_partition() (fastr.helpers.configmanager.Config property) SlurmExecution (class in fastr.plugins) solve_broadcast() (fastr.planning.inputgroup.InputGroup class method) source() (fastr.core.dimension.ForwardsDimensions property) (fastr.execution.inputoutputrun.InputRun property) (fastr.execution.inputoutputrun.SubInputRun property) (fastr.execution.linkrun.LinkRun property) (fastr.planning.inputoutput.Input property) (fastr.planning.inputoutput.SubInput property) (fastr.planning.link.Link property) (in module fastr.utils.cmd.source) SOURCE_DUMP_FILE_NAME (fastr.execution.networkrun.NetworkRun attribute) (fastr.planning.network.Network attribute) source_job_limit() (fastr.helpers.configmanager.Config property) source_output() (fastr.execution.inputoutputrun.SubInputRun property) (fastr.planning.inputoutput.SubInput property) sourcegroup() (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.node.SourceNode property) SourceJob (class in fastr.execution.job) sourcelist() (fastr.execution.networkrun.NetworkRun property) SourceNode (class in fastr.planning.node) SourceNodeRun (class in fastr.execution.sourcenoderun) SourceOutput (class in fastr.planning.inputoutput) SourceOutputRun (class in fastr.execution.inputoutputrun) spec_fields() (fastr.plugins.DRMAAExecution property) split() (in module fastr.data.url) SQUEUE (fastr.plugins.SlurmExecution attribute) SQUEUE_FORMAT (fastr.plugins.SlurmExecution attribute) status() (fastr.core.version.Version property) (fastr.execution.job.Job property) (fastr.execution.linkrun.LinkRun property) (fastr.execution.noderun.NodeRun property) (fastr.planning.link.Link property) (fastr.planning.node.Node property) (fastr.web.api.Run method) STATUS_MAPPING (fastr.plugins.SlurmExecution attribute) StatusApi (class in fastr.web.api) STDERR_DUMP (fastr.execution.job.Job attribute) stderrfile() (fastr.execution.job.Job property) stderrurl() (fastr.execution.job.Job property) stdout (in module fastr.plugins) STDOUT_DUMP (fastr.execution.job.Job attribute) stdoutfile() (fastr.execution.job.Job property) stdouturl() (fastr.execution.job.Job property) store() (fastr.helpers.filesynchelper.FileSyncHelper method) StrongrExecution (class in fastr.plugins) SubInput (class in fastr.planning.inputoutput) SubInputRun (class in fastr.execution.inputoutputrun) submit_jobs() (fastr.plugins.DRMAAExecution method) SubOutput (class in fastr.planning.inputoutput) SubOutputRun (class in fastr.execution.inputoutputrun) SubprocessBasedTarget (class in fastr.core.target) substitute() (fastr.execution.job.SinkJob method) SubUrl (class in fastr.web.api) suffix() (fastr.core.version.Version property) SUPPORTED_APIS (fastr.plugins.PimReporter attribute) SUPPORTS_CANCEL (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) SUPPORTS_DEPENDENCY (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) SUPPORTS_HOLD_RELEASE (fastr.plugins.DRMAAExecution attribute) (fastr.plugins.SlurmExecution attribute) (fastr.plugins.executionplugin.ExecutionPlugin attribute) swap() (fastr.execution.environmentmodules.EnvironmentModules method) switch_sample_sink() (in module fastr.utils.cmd.trace) sync() (fastr.execution.environmentmodules.EnvironmentModules method) systemdir() (fastr.helpers.configmanager.Config property) SystemUsageInfo (class in fastr.core.target)

T

tags (fastr.core.tool.Tool attribute) Target (class in fastr.core.target) target() (fastr.core.tool.Tool property) (fastr.datatypes.Deferred property) (fastr.execution.linkrun.LinkRun property) (fastr.planning.link.Link property) TargetManager (class in fastr.plugins.managers.targetmanager) TargetResult (class in fastr.core.target) test() (fastr.core.interface.Interface class method) (fastr.core.target.Target class method) (fastr.core.tool.Tool method) (fastr.datatypes.BaseDataType class method) (fastr.planning.network.Network class method) (fastr.plugins.BlockingExecution class method) (fastr.plugins.DRMAAExecution class method) (fastr.plugins.ElasticsearchReporter class method) (fastr.plugins.LinearExecution class method) (fastr.plugins.MacroTarget class method) (fastr.plugins.NipypeInterface class method) (fastr.plugins.ProcessPoolExecution class method) (fastr.plugins.RQExecution class method) (fastr.plugins.S3Filesystem class method) (fastr.plugins.SingularityTarget class method) (fastr.plugins.SlurmExecution class method) (fastr.plugins.StrongrExecution class method) test_spec (fastr.core.tool.Tool attribute) test_tool() (fastr.core.tool.Tool class method) time() (fastr.api.ResourceLimit property) (fastr.core.resourcelimit.ResourceLimit property)

timestamp() (fastr.core.target.SystemUsageInfo property) tmpurl() (fastr.execution.job.Job property) (fastr.execution.job.SinkJob property) todict() (fastr.plugins.managers.objectmanager.ObjectManager method) Tool (class in fastr.core.tool) tool() (fastr.execution.job.Job property) (fastr.execution.noderun.NodeRun property) (fastr.planning.node.Node property) (in module fastr.utils.cmd.test) (in module fastr.web.views) TOOL_REFERENCE_FILE_NAME (fastr.core.tool.Tool attribute) TOOL_RESULT_FILE_NAME (fastr.core.tool.Tool attribute) ToolApi (class in fastr.web.api) toollist() (fastr.utils.cmd.upgrade.FastrNamespaceType property) ToolListApi (class in fastr.web.api) ToolManager (class in fastr.plugins.managers.toolmanager) tools (fastr attribute) tools_path() (fastr.helpers.configmanager.Config property) toolversions() (fastr.plugins.managers.toolmanager.ToolManager method) TORQUE_NATIVE_SPEC (fastr.plugins.DRMAAExecution attribute) tostring_modvalue() (fastr.execution.environmentmodules.EnvironmentModules static method) totuple_modvalue() (fastr.execution.environmentmodules.EnvironmentModules static method) translate_argument() (fastr.execution.job.Job class method) translate_output_results() (fastr.execution.job.Job static method) translate_results() (fastr.execution.job.Job method) TypeGroup (class in fastr.datatypes) typelist() (fastr.utils.cmd.upgrade.FastrNamespaceType property) types (fastr attribute) types_path() (fastr.helpers.configmanager.Config property)

U

unload() (fastr.execution.environmentmodules.EnvironmentModules method) unmerge() (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputgroupcombiner.DefaultInputGroupCombiner method) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner method) unregister_signals() (fastr.execution.networkrun.NetworkRun method) update() (fastr.helpers.configmanager.EmptyDefault method) (fastr.planning.inputgroupcombiner.BaseInputGroupCombiner method) (fastr.planning.inputgroupcombiner.MergingInputGroupCombiner method) update_input_groups() (fastr.execution.noderun.NodeRun method) (fastr.planning.node.Node method) update_job_result() (in module fastr.web.api) update_size() (fastr.core.dimension.Dimension method)

update_status() (in module fastr.web.api) upgrade_network() (in module fastr.utils.cmd.upgrade) upgrade_tool() (in module fastr.utils.cmd.upgrade) upload() (fastr.plugins.XNATStorage static method) url (fastr.core.tool.Tool attribute) url_to_path() (fastr.core.ioplugin.IOPlugin method) (fastr.core.vfs.VirtualFileSystem method) (fastr.plugins.FileSystem method) (fastr.plugins.managers.iopluginmanager.IOPluginManager method) URLType (class in fastr.datatypes) usage_type (fastr.core.target.ProcessUsageCollection attribute) userdir() (fastr.helpers.configmanager.Config property)

V

valid() (fastr.datatypes.BaseDataType property) (fastr.datatypes.URLType property) (fastr.execution.inputoutputrun.OutputRun property) (fastr.execution.sourcenoderun.SourceNodeRun property) (fastr.planning.inputoutput.Output property) (fastr.planning.node.SourceNode property) validate() (fastr.core.cardinality.AnyCardinalitySpec method) (fastr.core.cardinality.CardinalitySpec method) validate_results() (fastr.execution.job.Job method) (fastr.execution.job.SinkJob method) (fastr.execution.job.SourceJob method) value() (fastr.datatypes.BaseDataType property) (fastr.datatypes.Deferred property) ValueCardinalitySpec (class in fastr.core.cardinality)

ValueType (class in fastr.datatypes) verify_resource_loading() (in module fastr.utils.verify) verify_tool() (in module fastr.utils.verify) Version (class in fastr.core.version) version (fastr.core.tool.Tool attribute) (fastr.datatypes.BaseDataType attribute) (fastr.datatypes.EnumType attribute) version() (fastr.api.Network property) version_matcher (fastr.core.version.Version attribute) VirtualFileSystem (class in fastr.core.vfs) (class in fastr.plugins) VirtualFileSystemRegularExpression (class in fastr.plugins) VirtualFileSystemValueList (class in fastr.plugins) vmem() (fastr.core.target.SystemUsageInfo property)

W

wait_for_file() (fastr.helpers.filesynchelper.FileSyncHelper method) wait_for_job() (fastr.helpers.filesynchelper.FileSyncHelper method) wait_for_pickle() (fastr.helpers.filesynchelper.FileSyncHelper method) wait_for_vfs_url() (fastr.helpers.filesynchelper.FileSyncHelper method) warn_develop() (fastr.helpers.configmanager.Config property) web_hostname() (fastr.helpers.configmanager.Config property)

web_port() (fastr.helpers.configmanager.Config property) web_secret_key() (fastr.helpers.configmanager.Config property) web_url() (fastr.helpers.configmanager.Config method) websocket_client() (in module fastr.web.views) which() (in module fastr.helpers.procutils) write() (fastr.execution.job.Job method) write_bytes() (fastr.core.target.SystemUsageInfo property)

X

xnat() (fastr.plugins.XNATStorage property)

XNATStorage (class in fastr.plugins)