Index

Symbols

--computing-environment easylink-run command line option --input-data easylink-generate-dag command line option easylink-run command line option --no-timestamp easylink-generate-dag command line option easylink-run command line option --output-dir easylink-generate-dag command line option easylink-run command line option --pipeline-specification easylink-generate-dag command line option easylink-run command line option

-e easylink-run command line option -i easylink-generate-dag command line option easylink-run command line option -o easylink-generate-dag command line option easylink-run command line option -p easylink-generate-dag command line option easylink-run command line option

_

_abc_impl (easylink.graph_components.InputSlotMapping attribute) (easylink.graph_components.OutputSlotMapping attribute) (easylink.graph_components.SlotMapping attribute) (easylink.rule.AggregationRule attribute) (easylink.rule.CheckpointRule attribute) (easylink.rule.ImplementedRule attribute) (easylink.rule.InputValidationRule attribute) (easylink.rule.Rule attribute) (easylink.rule.TargetRule attribute) (easylink.step.AggregatorStep attribute) (easylink.step.CloneableStep attribute) (easylink.step.ConfigurationState attribute) (easylink.step.InputStep attribute) (easylink.step.IOStep attribute) (easylink.step.LeafConfigurationState attribute) (easylink.step.LoopStep attribute) (easylink.step.NonLeafConfigurationState attribute) (easylink.step.OutputStep attribute) (easylink.step.SplitterStep attribute) (easylink.step.StandaloneStep attribute) (easylink.step.TemplatedStep attribute) _add_logging_sink() (in module easylink.utilities.general_utils) _build_input() (easylink.rule.ImplementedRule method) _build_io() (easylink.rule.ImplementedRule method) _build_resources() (easylink.rule.ImplementedRule method) _build_shell_cmd() (easylink.rule.ImplementedRule method) _check_edges_are_valid() (easylink.step.HierarchicalStep method) _check_slot_mappings_are_valid() (easylink.step.HierarchicalStep method) _check_validators_are_consistent() (easylink.step.HierarchicalStep method) _configuration_state (easylink.step.Step attribute) _configure_subgraph_steps() (easylink.step.NonLeafConfigurationState method) _deduplicate_input_slots() (easylink.pipeline_graph.PipelineGraph static method) _deduplicate_output_slots() (easylink.pipeline_graph.PipelineGraph static method) _define_aggregator_rule() (easylink.rule.AggregationRule method) _define_input_function() (easylink.rule.AggregationRule method) _download_and_validate_image() (easylink.implementation.Implementation method) _duplicate_template_step() (easylink.step.TemplatedStep method) _filter_snakemake_output() (in module easylink.runner) _get_checkpoint_filepaths() (easylink.pipeline.Pipeline method) _get_combined_slots_and_edges() (easylink.pipeline_graph.PipelineGraph method) _get_config() (easylink.step.TemplatedStep method) _get_duplicate_slots() (easylink.pipeline_graph.PipelineGraph static method) _get_edges_by_slot() (easylink.pipeline_graph.PipelineGraph method) _get_env_vars() (easylink.implementation.Implementation method) _get_environment_args() (in module easylink.runner) _get_input_slots_to_split() (easylink.pipeline.Pipeline static method)

_get_schema() (easylink.configuration.Config method) _get_singularity_args() (in module easylink.runner) _get_step_graph() (easylink.step.HierarchicalStep method) _get_timestamp() (in module easylink.utilities.data_utils) _get_validations() (easylink.pipeline.Pipeline static method) _handle_conflicting_checksums() (easylink.implementation.Implementation static method) _load_computing_environment() (in module easylink.configuration) _load_input_data_paths() (in module easylink.configuration) _load_metadata() (easylink.implementation.Implementation method) _merge_combined_implementations() (easylink.pipeline_graph.PipelineGraph method) _name (easylink.step.Step attribute) _pass_shared_options() (in module easylink.cli) _pass_verbose_with_debugger_options() (in module easylink.cli) _read_file() (in module easylink.utilities.validation_utils) _run_snakemake_with_filtered_output() (in module easylink.runner) _save_dag_image() (in module easylink.runner) _step (easylink.step.ConfigurationState attribute) _update_slot_filepaths() (easylink.pipeline_graph.PipelineGraph method) _update_slot_mappings() (easylink.step.AutoParallelStep method) (easylink.step.CloneableStep method) (easylink.step.LoopStep method) (easylink.step.TemplatedStep method) _update_step_graph() (easylink.step.AutoParallelStep method) (easylink.step.CloneableStep method) (easylink.step.LoopStep method) (easylink.step.TemplatedStep method) _validate() (easylink.configuration.Config method) (easylink.pipeline.Pipeline method) (easylink.step.AutoParallelStep method) _validate_combined_implementation_topology() (easylink.pipeline_graph.PipelineGraph method) _validate_environment() (easylink.configuration.Config method) _validate_expected_steps() (easylink.implementation.Implementation method) _validate_implementations() (easylink.pipeline.Pipeline method) _validate_input_data() (easylink.configuration.Config method) _validate_pairs() (in module easylink.utilities.validation_utils) _validate_required_columns() (in module easylink.utilities.validation_utils) _validate_step_graph() (easylink.step.HierarchicalStep method) _validate_unique_column() (in module easylink.utilities.validation_utils) _validate_unique_column_set() (in module easylink.utilities.validation_utils) _write_aggregation_rule() (easylink.pipeline.Pipeline method) _write_checkpoint_rule() (easylink.pipeline.Pipeline method) _write_implementation_rules() (easylink.pipeline.Pipeline method) _write_imports() (easylink.pipeline.Pipeline method) _write_spark_config() (easylink.pipeline.Pipeline method) _write_spark_module() (easylink.pipeline.Pipeline method) _write_target_rules() (easylink.pipeline.Pipeline method) _write_wildcard_constraints() (easylink.pipeline.Pipeline method)

A

add_edge_from_params() (easylink.graph_components.ImplementationGraph method) (easylink.graph_components.StepGraph method) add_edges_to_implementation_graph() (easylink.step.ConfigurationState method) (easylink.step.LeafConfigurationState method) (easylink.step.NonLeafConfigurationState method) (easylink.step.StandaloneStep method) (easylink.step.Step method) add_node_from_implementation() (easylink.graph_components.ImplementationGraph method) add_node_from_step() (easylink.graph_components.StepGraph method) add_nodes_to_implementation_graph() (easylink.step.AggregatorStep method) (easylink.step.ConfigurationState method) (easylink.step.IOStep method) (easylink.step.LeafConfigurationState method) (easylink.step.NonLeafConfigurationState method) (easylink.step.SplitterStep method) (easylink.step.StandaloneStep method) (easylink.step.Step method)

aggregated_output_file (easylink.rule.AggregationRule attribute) AggregationRule (class in easylink.rule) aggregator_func_name (easylink.implementation.NullAggregatorImplementation attribute) (easylink.rule.AggregationRule attribute) (easylink.step.AggregatorStep attribute) aggregator_nodes (easylink.graph_components.ImplementationGraph property) AggregatorStep (class in easylink.step) any_auto_parallel (easylink.pipeline.Pipeline attribute) (easylink.pipeline_graph.PipelineGraph property) AutoParallelStep (class in easylink.step)

B

build_rule() (easylink.rule.AggregationRule method) (easylink.rule.CheckpointRule method) (easylink.rule.ImplementedRule method) (easylink.rule.InputValidationRule method) (easylink.rule.Rule method) (easylink.rule.TargetRule method)

build_snakefile() (easylink.pipeline.Pipeline method)

C

calculate_md5_checksum() (in module easylink.utilities.data_utils) checkpoint_filepath (easylink.rule.AggregationRule attribute) (easylink.rule.CheckpointRule attribute) checkpoint_rule_name (easylink.rule.AggregationRule attribute) CheckpointRule (class in easylink.rule) child_node (easylink.graph_components.SlotMapping attribute) child_slot (easylink.graph_components.SlotMapping attribute) choices (easylink.step.ChoiceStep attribute) ChoiceStep (class in easylink.step) CloneableStep (class in easylink.step) combined_implementations (easylink.step.ConfigurationState attribute) combined_name (easylink.implementation.NullImplementation attribute) (easylink.implementation.PartialImplementation attribute) command (easylink.configuration.Config attribute)

computing_environment (easylink.configuration.Config property) concatenate_datasets() (in module easylink.utilities.aggregator_utils) Config (class in easylink.configuration) config (easylink.pipeline.Pipeline attribute) config_key (easylink.step.CloneableStep property) (easylink.step.HierarchicalStep property) (easylink.step.LoopStep property) (easylink.step.Step property) configuration_state (easylink.step.Step property) ConfigurationState (class in easylink.step) configure_logging_to_terminal() (in module easylink.utilities.general_utils) configure_pipeline() (easylink.pipeline_schema.PipelineSchema method) copy_configuration_files_to_results_directory() (in module easylink.utilities.data_utils) create_results_directory() (in module easylink.utilities.data_utils) create_results_intermediates() (in module easylink.utilities.data_utils)

D

DEFAULT_ENVIRONMENT (in module easylink.configuration) DEFAULT_IMAGES_DIR (in module easylink.utilities.paths) default_implementation (easylink.step.Step attribute) DEV_IMAGES_DIR (in module easylink.utilities.paths)

diagnostics_dir (easylink.rule.ImplementedRule attribute) directly_implemented (easylink.step.HierarchicalStep attribute) dont_validate() (in module easylink.utilities.validation_utils) download_image() (in module easylink.utilities.data_utils)

E

easylink module easylink-generate-dag command line option --input-data --no-timestamp --output-dir --pipeline-specification -i -o -p easylink-run command line option --computing-environment --input-data --no-timestamp --output-dir --pipeline-specification -e -i -o -p easylink.cli module easylink.configuration module easylink.graph_components module easylink.implementation module easylink.pipeline module easylink.pipeline_graph module easylink.pipeline_schema module easylink.pipeline_schema_constants module

easylink.pipeline_schema_constants.development module easylink.pipeline_schema_constants.main module easylink.pipeline_schema_constants.testing module easylink.rule module easylink.runner module easylink.step module easylink.utilities module easylink.utilities.aggregator_utils module easylink.utilities.data_utils module easylink.utilities.general_utils module easylink.utilities.paths module easylink.utilities.splitter_utils module easylink.utilities.validation_utils module EASYLINK_TEMP (in module easylink.utilities.paths) EdgeParams (class in easylink.graph_components) edges (easylink.step.HierarchicalStep attribute) env_var (easylink.graph_components.InputSlot attribute) environment (easylink.configuration.Config attribute) environment_variables (easylink.implementation.Implementation attribute) envvars (easylink.rule.ImplementedRule attribute) exit_with_validation_error() (in module easylink.utilities.general_utils)

F

filepaths (easylink.graph_components.EdgeParams attribute)

from_graph_edge() (easylink.graph_components.EdgeParams class method)

G

get_implementation_edges() (easylink.step.ConfigurationState method) (easylink.step.LeafConfigurationState method) (easylink.step.NonLeafConfigurationState method) (easylink.step.Step method) get_implementation_graph() (easylink.pipeline_schema.PipelineSchema method)

get_implementation_slot_mappings() (easylink.step.Step method) get_io_filepaths() (easylink.pipeline_graph.PipelineGraph method) get_io_slot_attributes() (easylink.pipeline_graph.PipelineGraph method) get_results_directory() (in module easylink.utilities.data_utils) get_schema() (easylink.pipeline_schema.PipelineSchema class method) get_whether_auto_parallel() (easylink.pipeline_graph.PipelineGraph method)

H

handle_exceptions() (in module easylink.utilities.general_utils)

HierarchicalStep (class in easylink.step)

I

image_path (easylink.rule.ImplementedRule attribute) images_dir (easylink.configuration.Config attribute) Implementation (class in easylink.implementation) implementation_config (easylink.step.LeafConfigurationState property) IMPLEMENTATION_METADATA (in module easylink.utilities.paths) implementation_name (easylink.rule.ImplementedRule attribute) implementation_node_name (easylink.step.StandaloneStep property) (easylink.step.Step property) implementation_nodes (easylink.graph_components.ImplementationGraph property) ImplementationGraph (class in easylink.graph_components) implementations (easylink.graph_components.ImplementationGraph property) ImplementedRule (class in easylink.rule) input (easylink.rule.InputValidationRule attribute) input_data (easylink.configuration.Config attribute) input_data_config (easylink.step.ConfigurationState attribute) input_files (easylink.rule.AggregationRule attribute) (easylink.rule.CheckpointRule attribute)

input_slot (easylink.graph_components.EdgeParams attribute) input_slot_name (easylink.rule.InputValidationRule attribute) input_slots (easylink.implementation.Implementation attribute) (easylink.implementation.NullImplementation attribute) (easylink.implementation.PartialImplementation attribute) (easylink.rule.ImplementedRule attribute) (easylink.step.Step attribute) InputSlot (class in easylink.graph_components) InputSlotMapping (class in easylink.graph_components) InputStep (class in easylink.step) InputValidationRule (class in easylink.rule) IOStep (class in easylink.step) is_auto_parallel (easylink.rule.ImplementedRule attribute) (easylink.step.Step attribute) is_combined (easylink.step.LeafConfigurationState property) is_on_slurm() (in module easylink.utilities.general_utils)

L

LeafConfigurationState (class in easylink.step) load_params_from_specification() (in module easylink.configuration)

load_yaml() (in module easylink.utilities.data_utils) LoopStep (class in easylink.step)

M

main() (in module easylink.runner) metadata_steps (easylink.implementation.Implementation attribute) modify_umask() (in module easylink.utilities.data_utils) module easylink easylink.cli easylink.configuration easylink.graph_components easylink.implementation easylink.pipeline easylink.pipeline_graph easylink.pipeline_schema easylink.pipeline_schema_constants easylink.pipeline_schema_constants.development easylink.pipeline_schema_constants.main easylink.pipeline_schema_constants.testing easylink.rule easylink.runner easylink.step easylink.utilities easylink.utilities.aggregator_utils easylink.utilities.data_utils easylink.utilities.general_utils easylink.utilities.paths easylink.utilities.splitter_utils easylink.utilities.validation_utils

N

name (easylink.graph_components.InputSlot attribute) (easylink.graph_components.OutputSlot attribute) (easylink.implementation.Implementation attribute) (easylink.implementation.NullImplementation attribute) (easylink.rule.AggregationRule attribute) (easylink.rule.CheckpointRule attribute) (easylink.rule.ImplementedRule attribute) (easylink.rule.InputValidationRule attribute) (easylink.step.AutoParallelStep property) (easylink.step.Step property)

node_prefix (easylink.step.CloneableStep property) (easylink.step.LoopStep property) (easylink.step.TemplatedStep property) nodes (easylink.step.HierarchicalStep attribute) NonLeafConfigurationState (class in easylink.step) NullAggregatorImplementation (class in easylink.implementation) NullImplementation (class in easylink.implementation) NullSplitterImplementation (class in easylink.implementation)

O

output (easylink.rule.ImplementedRule attribute) (easylink.rule.InputValidationRule attribute) output_dir (easylink.rule.CheckpointRule attribute) output_slot (easylink.graph_components.EdgeParams attribute) output_slots (easylink.implementation.Implementation attribute) (easylink.implementation.NullImplementation attribute) (easylink.implementation.PartialImplementation attribute) (easylink.step.Step attribute)

outputs (easylink.implementation.Implementation property) OutputSlot (class in easylink.graph_components) OutputSlotMapping (class in easylink.graph_components) OutputStep (class in easylink.step)

P

parent_slot (easylink.graph_components.SlotMapping attribute) parent_step (easylink.step.Step attribute) PartialImplementation (class in easylink.implementation) Pipeline (class in easylink.pipeline)

pipeline (easylink.configuration.Config attribute) pipeline_graph (easylink.pipeline.Pipeline attribute) PipelineGraph (class in easylink.pipeline_graph) PipelineSchema (class in easylink.pipeline_schema)

R

remap_edge() (easylink.graph_components.InputSlotMapping method) (easylink.graph_components.OutputSlotMapping method) (easylink.graph_components.SlotMapping method) requires_spark (easylink.implementation.Implementation attribute) (easylink.rule.ImplementedRule attribute) (easylink.rule.TargetRule attribute)

resources (easylink.rule.ImplementedRule attribute) results_dir (in module easylink.runner) Rule (class in easylink.rule)

S

schema (easylink.configuration.Config attribute) schema_step (easylink.implementation.PartialImplementation attribute) schema_steps (easylink.implementation.Implementation attribute) (easylink.implementation.NullImplementation attribute) script_cmd (easylink.implementation.Implementation property) (easylink.rule.ImplementedRule attribute) self_edges (easylink.step.LoopStep attribute) set_configuration_state() (easylink.step.AutoParallelStep method) (easylink.step.ChoiceStep method) (easylink.step.HierarchicalStep method) (easylink.step.InputStep method) (easylink.step.StandaloneStep method) (easylink.step.Step method) (easylink.step.TemplatedStep method) set_parent_step() (easylink.step.Step method) singularity_image_name (easylink.implementation.Implementation property) slot_aggregator_mapping (easylink.step.AutoParallelStep attribute) slot_mappings (easylink.step.Step attribute) slot_splitter_mapping (easylink.step.AutoParallelStep attribute) SlotMapping (class in easylink.graph_components) slurm (easylink.configuration.Config property) slurm_resources (easylink.configuration.Config property) snakefile (in module easylink.runner) snakefile_path (easylink.pipeline.Pipeline property) source_node (easylink.graph_components.EdgeParams attribute)

spark (easylink.configuration.Config property) SPARK_DEFAULTS (in module easylink.configuration) spark_is_required (easylink.pipeline.Pipeline attribute) (easylink.pipeline_graph.PipelineGraph property) spark_resources (easylink.configuration.Config property) SPARK_SNAKEFILE (in module easylink.utilities.paths) split_data_by_size() (in module easylink.utilities.splitter_utils) split_data_in_two() (in module easylink.utilities.splitter_utils) split_slot_name (easylink.step.AutoParallelStep attribute) splitter_func_name (easylink.implementation.NullSplitterImplementation attribute) (easylink.rule.CheckpointRule attribute) (easylink.step.SplitterStep attribute) splitter_node_name (easylink.implementation.NullAggregatorImplementation attribute) (easylink.step.AggregatorStep attribute) splitter_nodes (easylink.graph_components.ImplementationGraph property) SplitterStep (class in easylink.step) StandaloneStep (class in easylink.step) Step (class in easylink.step) step_config (easylink.step.ConfigurationState attribute) step_graph (easylink.step.HierarchicalStep attribute) (easylink.step.TemplatedStep attribute) step_name (easylink.rule.ImplementedRule attribute) (easylink.step.Step attribute) step_nodes (easylink.graph_components.StepGraph property) StepGraph (class in easylink.graph_components) steps (easylink.graph_components.StepGraph property)

T

target_files (easylink.rule.TargetRule attribute) target_node (easylink.graph_components.EdgeParams attribute)

TargetRule (class in easylink.rule) template_step (easylink.step.TemplatedStep attribute) TemplatedStep (class in easylink.step)

V

validate() (easylink.implementation.Implementation method) validate_blocks() (in module easylink.utilities.validation_utils) validate_clusters() (in module easylink.utilities.validation_utils) validate_dataset() (in module easylink.utilities.validation_utils) validate_dataset_dir() (in module easylink.utilities.validation_utils) validate_datasets_directory() (in module easylink.utilities.validation_utils) validate_dir() (in module easylink.utilities.validation_utils) validate_ids_to_remove() (in module easylink.utilities.validation_utils) validate_input_dataset_or_known_clusters() (in module easylink.utilities.validation_utils) validate_input_file_dummy() (in module easylink.utilities.validation_utils) validate_inputs() (easylink.pipeline_schema.PipelineSchema method) validate_links() (in module easylink.utilities.validation_utils)

validate_records() (in module easylink.utilities.validation_utils) validate_step() (easylink.pipeline_schema.PipelineSchema method) (easylink.step.AutoParallelStep method) (easylink.step.ChoiceStep method) (easylink.step.HierarchicalStep method) (easylink.step.StandaloneStep method) (easylink.step.Step method) (easylink.step.TemplatedStep method) validation (easylink.rule.TargetRule attribute) validations (easylink.rule.ImplementedRule attribute) validator (easylink.graph_components.InputSlot attribute) (easylink.rule.InputValidationRule attribute)

W

write_to_snakefile() (easylink.rule.Rule method)