From 4bb47f08d402884f351cab0f95059eb11552fb3a Mon Sep 17 00:00:00 2001 From: Brandon Duane Walker Date: Mon, 3 Jun 2024 13:00:03 -0400 Subject: [PATCH] refactor config-tag-mdp --- .../tests/test_config_tag_mdp.py | 35 - .../config-tag-mdp-tool}/.bumpversion.cfg | 0 .../config-tag-mdp-tool}/.dockerignore | 0 .../config-tag-mdp-tool}/.gitignore | 0 .../config-tag-mdp-tool}/CHANGELOG.md | 0 .../config-tag-mdp-tool}/README.md | 0 .../config-tag-mdp-tool}/VERSION | 0 .../autogenerated/config_tag_mdp_workflow.cwl | 53 ++ .../config_tag_mdp_0@1@0.cwl | 50 ++ .../config_tag_mdp_0@1@0_inputs.yml | 3 + .../config_tag_mdp_workflow_inputs.yml | 12 + .../4cc56456b99cd83771068ac7c958a576.status | 1 + .../config_tag_mdp_0@1@0.cwl} | 4 +- .../config-tag-mdp-tool}/ict.yml | 6 +- .../output_config_tag_mdp_workflow.json | 3 + .../config_tag_mdp_workflow/bag-info.txt | 6 + .../config_tag_mdp_workflow/bagit.txt | 2 + .../dc0dbba18d47b040109f16862d39de918039856d | 1 + .../config_tag_mdp_workflow/manifest-sha1.txt | 1 + ...e.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt | 13 + .../metadata/manifest.json | 271 ++++++++ .../metadata/provenance/primary.cwlprov.json | 280 ++++++++ .../provenance/primary.cwlprov.jsonld | 623 ++++++++++++++++++ .../metadata/provenance/primary.cwlprov.nt | 124 ++++ .../metadata/provenance/primary.cwlprov.provn | 53 ++ .../metadata/provenance/primary.cwlprov.ttl | 131 ++++ .../metadata/provenance/primary.cwlprov.xml | 164 +++++ .../snapshot/config_tag_mdp_workflow.cwl | 53 ++ .../tagmanifest-sha1.txt | 13 + .../tagmanifest-sha256.txt | 13 + .../tagmanifest-sha512.txt | 13 + .../workflow/packed.cwl | 155 +++++ .../workflow/primary-job.json | 7 + .../workflow/primary-output.json | 3 + .../config-tag-mdp-tool}/pyproject.toml | 3 +- .../config-tag-mdp-tool}/tests/__init__.py | 0 .../tests/test_config_tag_mdp.py | 41 ++ 37 files changed, 2095 insertions(+), 42 deletions(-) delete mode 100644 utils/config-tag-mdp-plugin/tests/test_config_tag_mdp.py rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/.bumpversion.cfg (100%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/.dockerignore (100%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/.gitignore (100%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/CHANGELOG.md (100%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/README.md (100%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/VERSION (100%) create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0_inputs.yml create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow_inputs.yml create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status rename utils/{config-tag-mdp-plugin/config_tag_mdp.cwl => molecular-dynamics/config-tag-mdp-tool/config_tag_mdp_0@1@0.cwl} (99%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/ict.yml (91%) create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/output_config_tag_mdp_workflow.json create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bag-info.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bagit.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/data/dc/dc0dbba18d47b040109f16862d39de918039856d create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/manifest.json create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.json create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.jsonld create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.nt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.provn create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.ttl create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.xml create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/snapshot/config_tag_mdp_workflow.cwl create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha1.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha256.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha512.txt create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/packed.cwl create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-job.json create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-output.json rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/pyproject.toml (92%) rename utils/{config-tag-mdp-plugin => molecular-dynamics/config-tag-mdp-tool}/tests/__init__.py (100%) create mode 100644 utils/molecular-dynamics/config-tag-mdp-tool/tests/test_config_tag_mdp.py diff --git a/utils/config-tag-mdp-plugin/tests/test_config_tag_mdp.py b/utils/config-tag-mdp-plugin/tests/test_config_tag_mdp.py deleted file mode 100644 index bfd6637e..00000000 --- a/utils/config-tag-mdp-plugin/tests/test_config_tag_mdp.py +++ /dev/null @@ -1,35 +0,0 @@ -"""Tests for config_tag_mdp.""" -import sys -from pathlib import Path - -current_dir = Path(__file__).resolve().parent -target_dir = current_dir.parent.parent.parent / "cwl_utils" -sys.path.append(str(target_dir)) - -from cwl_utilities import call_cwltool # noqa: E402 -from cwl_utilities import create_input_yaml # noqa: E402 -from cwl_utilities import parse_cwl_arguments # noqa: E402 - - -def test_config_tag_mdp() -> None: - """Test config_tag_mdp.""" - cwl_file_str = "config_tag_mdp.cwl" - cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str) - input_to_props = parse_cwl_arguments(cwl_file) - input_to_props["nsteps"] = 10000 - input_to_props["dt"] = 0.02 - input_to_props["ref-t"] = 298.0 - input_to_props["ref-p"] = 1.0 - input_to_props[ - "config" - ] = '{"mdp": {"integrator": "md", "rvdw": 1.0, "rcoulomb": 1.0, "coulombtype": \ - "PME", "tc-grps": "system", "tau-t": 2, "constraints": "h-bonds", "nstxout": \ - 1000, "nstenergy": 1000, "pcoupl": "Parrinello-Rahman", "tau-p": 1,\ - "compressibility": 4.5e-5, "comm-mode": "Linear", "comm-grps": "system"}}' - - input_yaml_path = Path("config_tag_mdp.yml") - create_input_yaml(input_to_props, input_yaml_path) - - stdout, stderr = call_cwltool(cwl_file, input_yaml_path) - - assert "output_config_string" in stdout diff --git a/utils/config-tag-mdp-plugin/.bumpversion.cfg b/utils/molecular-dynamics/config-tag-mdp-tool/.bumpversion.cfg similarity index 100% rename from utils/config-tag-mdp-plugin/.bumpversion.cfg rename to utils/molecular-dynamics/config-tag-mdp-tool/.bumpversion.cfg diff --git a/utils/config-tag-mdp-plugin/.dockerignore b/utils/molecular-dynamics/config-tag-mdp-tool/.dockerignore similarity index 100% rename from utils/config-tag-mdp-plugin/.dockerignore rename to utils/molecular-dynamics/config-tag-mdp-tool/.dockerignore diff --git a/utils/config-tag-mdp-plugin/.gitignore b/utils/molecular-dynamics/config-tag-mdp-tool/.gitignore similarity index 100% rename from utils/config-tag-mdp-plugin/.gitignore rename to utils/molecular-dynamics/config-tag-mdp-tool/.gitignore diff --git a/utils/config-tag-mdp-plugin/CHANGELOG.md b/utils/molecular-dynamics/config-tag-mdp-tool/CHANGELOG.md similarity index 100% rename from utils/config-tag-mdp-plugin/CHANGELOG.md rename to utils/molecular-dynamics/config-tag-mdp-tool/CHANGELOG.md diff --git a/utils/config-tag-mdp-plugin/README.md b/utils/molecular-dynamics/config-tag-mdp-tool/README.md similarity index 100% rename from utils/config-tag-mdp-plugin/README.md rename to utils/molecular-dynamics/config-tag-mdp-tool/README.md diff --git a/utils/config-tag-mdp-plugin/VERSION b/utils/molecular-dynamics/config-tag-mdp-tool/VERSION similarity index 100% rename from utils/config-tag-mdp-plugin/VERSION rename to utils/molecular-dynamics/config-tag-mdp-tool/VERSION diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl new file mode 100644 index 00000000..b9465865 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl @@ -0,0 +1,53 @@ +#!/usr/bin/env cwl-runner +# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown +# https://github.com/PolusAI/workflow-inference-compiler +steps: +- id: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0 + in: + config: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config + dt: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt + nsteps: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps + ref_p: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p + ref_t: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t + out: + - output_config_string + run: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl +cwlVersion: v1.2 +class: Workflow +$namespaces: + edam: https://edamontology.org/ +$schemas: +- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl +inputs: + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config: + type: string + format: edam:format_2330 + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt: + type: float + label: The length of each timestep + doc: The length of each timestep + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps: + type: int + label: The number of timesteps + doc: The number of timesteps + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p: + type: float + label: The nominal pressure + doc: The nominal pressure + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t: + type: float + label: The nominal temperature + doc: The nominal temperature +outputs: + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string: + type: string + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + outputSource: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl new file mode 100644 index 00000000..46bb93ec --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl @@ -0,0 +1,50 @@ +#!/usr/bin/env cwl-runner +# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown +# https://github.com/PolusAI/workflow-inference-compiler +class: CommandLineTool +cwlVersion: v1.0 +label: Returns a dictionary of the given arguments as a JSON-encoded string. +doc: Returns a dictionary of the given arguments as a JSON-encoded string. +baseCommand: echo +requirements: + InlineJavascriptRequirement: {} +inputs: + config: + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + type: string + format: edam:format_2330 + default: '{}' + nsteps: + label: The number of timesteps + doc: The number of timesteps + type: int + dt: + label: The length of each timestep + doc: The length of each timestep + type: float + ref_t: + label: The nominal temperature + doc: The nominal temperature + type: float + ref_p: + label: The nominal pressure + doc: The nominal pressure + type: float +outputs: + output_config_string: + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + type: string + outputBinding: + outputEval: "${\n var config = JSON.parse(inputs.config);\n if ((\"mdp\" in\ + \ config) === false) {\n config[\"mdp\"] = {}; // Initialize it\n }\n\ + \ // TODO: Check for duplicate keys, i.e.\n // \"Pressure coupling incorrect\ + \ number of values (I need exactly 1)\"\n config[\"mdp\"][\"nsteps\"] = inputs.nsteps;\n\ + \ config[\"mdp\"][\"dt\"] = inputs.dt;\n config[\"mdp\"][\"ref-t\"] = inputs[\"\ + ref-t\"]; //Javascript interprets dash as subtract...\n config[\"mdp\"][\"\ + ref-p\"] = inputs[\"ref-p\"];\n return JSON.stringify(config);\n}\n" +$namespaces: + edam: https://edamontology.org/ +$schemas: +- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0_inputs.yml b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0_inputs.yml new file mode 100644 index 00000000..6cb028a2 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0_inputs.yml @@ -0,0 +1,3 @@ +# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown +# https://github.com/PolusAI/workflow-inference-compiler +{} diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow_inputs.yml b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow_inputs.yml new file mode 100644 index 00000000..8012671b --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow_inputs.yml @@ -0,0 +1,12 @@ +# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown +# https://github.com/PolusAI/workflow-inference-compiler +config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config: '"{\"mdp\": {\"integrator\": + \"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\", + \"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\", + \"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\", + \"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\", + \"comm-grps\": \"system\"}}"' +config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt: 0.02 +config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps: 10000 +config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p: 1.0 +config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t: 298.0 diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status b/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status new file mode 100644 index 00000000..55314794 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status @@ -0,0 +1 @@ +permanentFail diff --git a/utils/config-tag-mdp-plugin/config_tag_mdp.cwl b/utils/molecular-dynamics/config-tag-mdp-tool/config_tag_mdp_0@1@0.cwl similarity index 99% rename from utils/config-tag-mdp-plugin/config_tag_mdp.cwl rename to utils/molecular-dynamics/config-tag-mdp-tool/config_tag_mdp_0@1@0.cwl index 6189a1e6..31ed0974 100644 --- a/utils/config-tag-mdp-plugin/config_tag_mdp.cwl +++ b/utils/molecular-dynamics/config-tag-mdp-tool/config_tag_mdp_0@1@0.cwl @@ -33,13 +33,13 @@ inputs: The length of each timestep type: float - ref-t: + ref_t: label: The nominal temperature doc: |- The nominal temperature type: float - ref-p: + ref_p: label: The nominal pressure doc: |- The nominal pressure diff --git a/utils/config-tag-mdp-plugin/ict.yml b/utils/molecular-dynamics/config-tag-mdp-tool/ict.yml similarity index 91% rename from utils/config-tag-mdp-plugin/ict.yml rename to utils/molecular-dynamics/config-tag-mdp-tool/ict.yml index feaa4a37..30d59adb 100644 --- a/utils/config-tag-mdp-plugin/ict.yml +++ b/utils/molecular-dynamics/config-tag-mdp-tool/ict.yml @@ -1,12 +1,12 @@ specVersion: "0.1.0" name: config_tag_mdp version: 0.1.0 -container: config-tag-mdp-plugin +container: config-tag-mdp-tool entrypoint: title: config_tag_mdp description: Returns a dictionary of the given arguments as a JSON-encoded string. -author: Data Scientist -contact: data.scientist@labshare.org +author: Brandon Walker, Nazanin Donyapour +contact: brandon.walker@axleinfo.com, nazanin.donyapour@axleinfo.com repository: documentation: citation: diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/output_config_tag_mdp_workflow.json b/utils/molecular-dynamics/config-tag-mdp-tool/output_config_tag_mdp_workflow.json new file mode 100644 index 00000000..956ac8bb --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/output_config_tag_mdp_workflow.json @@ -0,0 +1,3 @@ +{ + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string": null +} diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bag-info.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bag-info.txt new file mode 100644 index 00000000..8db242b2 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bag-info.txt @@ -0,0 +1,6 @@ +Bag-Software-Agent: cwltool 3.1.20240404144621 +BagIt-Profile-Identifier: https://w3id.org/ro/bagit/profile +Bagging-Date: 2024-07-30 +External-Description: Research Object of CWL workflow run +External-Identifier: arcp://uuid,9a41dad8-a1b5-4a5d-825b-437da47258d6/ +Payload-Oxum: 510.1 diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bagit.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bagit.txt new file mode 100644 index 00000000..c4aebb43 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/bagit.txt @@ -0,0 +1,2 @@ +BagIt-Version: 0.97 +Tag-File-Character-Encoding: UTF-8 diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/data/dc/dc0dbba18d47b040109f16862d39de918039856d b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/data/dc/dc0dbba18d47b040109f16862d39de918039856d new file mode 100644 index 00000000..9378310b --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/data/dc/dc0dbba18d47b040109f16862d39de918039856d @@ -0,0 +1 @@ +"{\"mdp\": {\"integrator\": \"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\", \"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\", \"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\", \"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\", \"comm-grps\": \"system\"}}" diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt new file mode 100644 index 00000000..6c62dcef --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt @@ -0,0 +1 @@ +dc0dbba18d47b040109f16862d39de918039856d data/dc/dc0dbba18d47b040109f16862d39de918039856d diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt new file mode 100644 index 00000000..20dd72c0 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt @@ -0,0 +1,13 @@ +[2024-07-30T18:16:05,559.492588Z] [cwltool] /home/walkerbd/miniconda3/envs/wic_github_actions/bin/cwltool_filterlog --disable-pull --cachedir cachedir --provenance provenance/config_tag_mdp_workflow --write-summary output_config_tag_mdp_workflow.json --skip-schemas --relax-path-checks --leave-outputs autogenerated/config_tag_mdp_workflow.cwl autogenerated/config_tag_mdp_workflow_inputs.yml +[2024-07-30T18:16:07,64.969540Z] [workflow ] start +[2024-07-30T18:16:07,65.366507Z] [workflow ] starting step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0 +[2024-07-30T18:16:07,65.612078Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] start +[2024-07-30T18:16:07,66.546917Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Output of job will be cached in /home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576 +[2024-07-30T18:16:07,67.748308Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] /home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576$ echo +[2024-07-30T18:16:07,308.171272Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Job error: +('Error collecting output for parameter \'output_config_string\': autogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: Expression evaluation error:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: Expecting value: line 1 column 1 (char 0)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: script was:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 01 "use strict";\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 02 var inputs = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 03 "config": "\\"{\\\\\\"mdp\\\\\\": {\\\\\\"integrator\\\\\\": \\\\\\"md\\\\\\", \\\\\\"rvdw\\\\\\": 1.0, \\\\\\"rcoulomb\\\\\\": 1.0, \\\\\\"coulombtype\\\\\\": \\\\\\"PME\\\\\\", \\\\\\"tc-grps\\\\\\": \\\\\\"system\\\\\\", \\\\\\"tau-t\\\\\\": 2, \\\\\\"constraints\\\\\\": \\\\\\"h-bonds\\\\\\", \\\\\\"nstxout\\\\\\": 1000, \\\\\\"nstenergy\\\\\\": 1000, \\\\\\"pcoupl\\\\\\": \\\\\\"Parrinello-Rahman\\\\\\", \\\\\\"tau-p\\\\\\": 1, \\\\\\"compressibility\\\\\\": 4.5e-5, \\\\\\"comm-mode\\\\\\": \\\\\\"Linear\\\\\\", \\\\\\"comm-grps\\\\\\": \\\\\\"system\\\\\\"}}\\"",\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 04 "dt": 0.02,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 05 "nsteps": 10000,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 06 "ref_p": 1.0,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 07 "ref_t": 298.0\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 08 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 09 var self = [];\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 10 var runtime = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 11 "cores": 1,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 12 "ram": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 13 "tmpdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 14 "outdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 15 "tmpdir": "/tmp/belht484",\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 16 "outdir": "/home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576"\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 17 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 18 (function(){\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 19 var config = JSON.parse(inputs.config);\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 20 if (("mdp" in config) === false) {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 21 config["mdp"] = {}; // Initialize it\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 22 }\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 23 // TODO: Check for duplicate keys, i.e.\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 24 // "Pressure coupling incorrect number of values (I need exactly 1)"\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 25 config["mdp"]["nsteps"] = inputs.nsteps;\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 26 config["mdp"]["dt"] = inputs.dt;\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 27 config["mdp"]["ref-t"] = inputs["ref-t"]; //Javascript interprets dash as subtract...\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 28 config["mdp"]["ref-p"] = inputs["ref-p"];\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 29 return JSON.stringify(config);\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: 30 })()\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: stdout was: \'\'\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: stderr was: \'evalmachine.:20\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: if (("mdp" in config) === false) {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: ^\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: \nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: TypeError: Cannot use \'in\' operator to search for \'mdp\' in {"mdp": {"integrator": "md", "rvdw": 1.0, "rcoulomb": 1.0, "coulombtype": "PME", "tc-grps": "system", "tau-t": 2, "constraints": "h-bonds", "nstxout": 1000, "nstenergy": 1000, "pcoupl": "Parrinello-Rahman", "tau-p": 1, "compressibility": 4.5e-5, "comm-mode": "Linear", "comm-grps": "system"}}\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at evalmachine.:20:14\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at evalmachine.:30:3\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Script.runInContext (node:vm:148:12)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Script.runInNewContext (node:vm:153:17)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Object.runInNewContext (node:vm:309:38)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Socket. ([eval]:11:57)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Socket.emit (node:events:520:28)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at addChunk (node:internal/streams/readable:559:12)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at readableAddChunkPushByteMode (node:internal/streams/readable:510:3)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl:40:7: at Readable.push (node:internal/streams/readable:390:5)\'', {}) +[2024-07-30T18:16:07,308.703661Z] [job config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] completed permanentFail +[2024-07-30T18:16:07,308.988571Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] Output is missing expected field file:///home/walkerbd/mm-tools/utils/molecular-dynamics/config-tag-mdp-tool/autogenerated/config_tag_mdp_workflow.cwl#config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string +[2024-07-30T18:16:07,309.092522Z] [step config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0] completed permanentFail +[2024-07-30T18:16:07,309.232473Z] [workflow ] completed permanentFail +[2024-07-30T18:16:07,350.886106Z] Final process status is permanentFail diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/manifest.json b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/manifest.json new file mode 100644 index 00000000..4e274443 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/manifest.json @@ -0,0 +1,271 @@ +{ + "@context": [ + { + "@base": "arcp://uuid,9a41dad8-a1b5-4a5d-825b-437da47258d6/metadata/" + }, + "https://w3id.org/bundle/context" + ], + "id": "/", + "conformsTo": "https://w3id.org/cwl/prov/0.6.0", + "manifest": "manifest.json", + "createdOn": "2024-07-30T14:16:07.353332", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + }, + "authoredBy": null, + "aggregates": [ + { + "uri": "urn:hash::sha1:dc0dbba18d47b040109f16862d39de918039856d", + "bundledAs": { + "uri": "arcp://uuid,9a41dad8-a1b5-4a5d-825b-437da47258d6/data/dc/dc0dbba18d47b040109f16862d39de918039856d", + "folder": "/data/dc/", + "filename": "dc0dbba18d47b040109f16862d39de918039856d" + }, + "mediatype": "text/plain; charset='UTF-8'" + }, + { + "uri": "../metadata/provenance/primary.cwlprov.jsonld", + "mediatype": "application/ld+json", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2024-07-30T14:16:07.353490", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + } + }, + { + "uri": "../metadata/provenance/primary.cwlprov.json", + "mediatype": "application/json", + "conformsTo": [ + "http://www.w3.org/Submission/2013/SUBM-prov-json-20130424/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2024-07-30T14:16:07.353517", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + } + }, + { + "uri": "../metadata/provenance/primary.cwlprov.ttl", + "mediatype": "text/turtle; charset=\"UTF-8\"", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2024-07-30T14:16:07.353541", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + } + }, + { + "uri": "../metadata/provenance/primary.cwlprov.provn", + "mediatype": "text/provenance-notation; charset=\"UTF-8\"", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-n-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2024-07-30T14:16:07.353564", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + } + }, + { + "uri": null, + "mediatype": null, + "conformsTo": null, + "createdOn": "2024-07-30T14:16:03.917919", + "bundledAs": null + }, + { + "uri": "../metadata/provenance/primary.cwlprov.nt", + "mediatype": "application/n-triples", + "conformsTo": [ + "http://www.w3.org/TR/2013/REC-prov-o-20130430/", + "https://w3id.org/cwl/prov/0.6.0" + ], + "createdOn": "2024-07-30T14:16:07.353611", + "createdBy": { + "uri": "urn:uuid:49b7c1d9-09c2-4607-b6de-a68051d1aaca", + "name": "cwltool 3.1.20240404144621" + } + }, + { + "uri": "../workflow/primary-job.json", + "mediatype": "application/json", + "conformsTo": null, + "createdOn": "2024-07-30T14:16:07.353634", + "createdBy": { + "uri": 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of workflow/packed.cwl#main"^^ . + _:N9ff66d6b7e1143078d472c6a00e58ebb . + "1.0"^^ . + . + _:N05d3fb0795804756a73a243e892b5568 . + "0.02"^^ . + _:N92ff8ea496064f12989b4596faab9f7a . +_:Nd90654c9c3884cb3a0a4e89f31618b6b "2024-07-30T14:16:07.064609"^^ . + _:N0a53f9e8682c4b70b50bb472c759d294 . + "Prospective provenance"^^ . +_:N05d3fb0795804756a73a243e892b5568 "2024-07-30T14:16:06.727967"^^ . +_:N87f45fa470324d42b41095e03521bd4b . + _:N87f45fa470324d42b41095e03521bd4b . +_:N233afd53b2e24ba1b230113f09c69963 . + "None"^^ . +_:N025297f46b4546199750012baaf8f9c5 . + . + "1.0"^^ . +_:N091220ee8c904f36bc1165b285e0b7e6 . + . +_:Nc90ab78432e84b25a5b8bb3adbda43c8 . + _:N8797448018fb463684d3a384bdb4f94a . +_:N92683be783e94038954a462d38453240 . + . +_:N025297f46b4546199750012baaf8f9c5 "2024-07-30T14:16:07.309782"^^ . + "\"{\\\"mdp\\\": {\\\"integrator\\\": \\\"md\\\", \\\"rvdw\\\": 1.0, \\\"rcoulomb\\\": 1.0, \\\"coulombtype\\\": \\\"PME\\\", \\\"tc-grps\\\": \\\"system\\\", \\\"tau-t\\\": 2, \\\"constraints\\\": \\\"h-bonds\\\", \\\"nstxout\\\": 1000, \\\"nstenergy\\\": 1000, \\\"pcoupl\\\": \\\"Parrinello-Rahman\\\", \\\"tau-p\\\": 1, \\\"compressibility\\\": 4.5e-5, \\\"comm-mode\\\": \\\"Linear\\\", \\\"comm-grps\\\": \\\"system\\\"}}\""^^ . + . +_:N025297f46b4546199750012baaf8f9c5 . +_:N091220ee8c904f36bc1165b285e0b7e6 . +_:N87f45fa470324d42b41095e03521bd4b "2024-07-30T14:16:07.308537"^^ . +_:Ne1f8e7a9915240b09d80466e4311c0ce . +_:Nc90ab78432e84b25a5b8bb3adbda43c8 . + _:Nc90ab78432e84b25a5b8bb3adbda43c8 . + _:Ncc2b0a63789045bb85e8ddc14d27dd8e . + . +_:N233afd53b2e24ba1b230113f09c69963 "2024-07-30T14:16:07.309888"^^ . +_:N05d3fb0795804756a73a243e892b5568 . +_:N091220ee8c904f36bc1165b285e0b7e6 . +_:Nb7a3e71c368548648128e31a55306be5 . + . + _:Nd90654c9c3884cb3a0a4e89f31618b6b . +_:N92ff8ea496064f12989b4596faab9f7a . + "2024-07-30T14:16:06.727901"^^ . + . +_:N8797448018fb463684d3a384bdb4f94a "2024-07-30T14:16:06.727868"^^ . + . +_:N43d541b2bad44b799bada7ea2656c78d . +_:Ne1f8e7a9915240b09d80466e4311c0ce . +_:N43d541b2bad44b799bada7ea2656c78d . +_:Ncc2b0a63789045bb85e8ddc14d27dd8e . + _:N233afd53b2e24ba1b230113f09c69963 . +_:N091220ee8c904f36bc1165b285e0b7e6 "2024-07-30T14:16:07.068194"^^ . +_:N05d3fb0795804756a73a243e892b5568 . + _:N091220ee8c904f36bc1165b285e0b7e6 . +_:N92683be783e94038954a462d38453240 . +_:Ncc2b0a63789045bb85e8ddc14d27dd8e "2024-07-30T14:16:07.064776"^^ . +_:N0a53f9e8682c4b70b50bb472c759d294 "2024-07-30T14:16:07.068123"^^ . +_:Nef833d1a33e44b7e909c0361495c1804 . + _:Ne10c32a78cf5474189c411d6fd72d9b5 . +_:Ne1f8e7a9915240b09d80466e4311c0ce . + . + . +_:N92683be783e94038954a462d38453240 . +_:Ne1f8e7a9915240b09d80466e4311c0ce "2024-07-30T14:16:07.068324"^^ . +_:Nc90ab78432e84b25a5b8bb3adbda43c8 . +_:N43d541b2bad44b799bada7ea2656c78d . +_:Ncc2b0a63789045bb85e8ddc14d27dd8e . +_:Nd90654c9c3884cb3a0a4e89f31618b6b . +_:Nb7a3e71c368548648128e31a55306be5 . + "10000"^^ . +_:N92ff8ea496064f12989b4596faab9f7a "2024-07-30T14:16:07.064896"^^ . +_:N233afd53b2e24ba1b230113f09c69963 . + . +_:Ncc2b0a63789045bb85e8ddc14d27dd8e . +_:Ne10c32a78cf5474189c411d6fd72d9b5 . + "10000"^^ . + _:Nb7a3e71c368548648128e31a55306be5 . + _:N025297f46b4546199750012baaf8f9c5 . +_:N43d541b2bad44b799bada7ea2656c78d "2024-07-30T14:16:07.068382"^^ . + . +_:N0a53f9e8682c4b70b50bb472c759d294 . + _:N92683be783e94038954a462d38453240 . + . + . + "0.02"^^ . + . + . + . +_:Nb7a3e71c368548648128e31a55306be5 "2024-07-30T14:16:07.064715"^^ . +_:Nd90654c9c3884cb3a0a4e89f31618b6b . +_:N9ff66d6b7e1143078d472c6a00e58ebb . +_:N92ff8ea496064f12989b4596faab9f7a . +_:N92ff8ea496064f12989b4596faab9f7a . + . + _:Ne1f8e7a9915240b09d80466e4311c0ce . +_:N9ff66d6b7e1143078d472c6a00e58ebb . + _:Nef833d1a33e44b7e909c0361495c1804 . +_:N0a53f9e8682c4b70b50bb472c759d294 . + . + "Run of workflow/packed.cwl#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400"^^ . + _:N43d541b2bad44b799bada7ea2656c78d . + . +_:N92683be783e94038954a462d38453240 "2024-07-30T14:16:07.064839"^^ . +_:N025297f46b4546199750012baaf8f9c5 . + . + . + . diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.provn b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.provn new file mode 100644 index 00000000..a3e584ee --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.provn @@ -0,0 +1,53 @@ +document + prefix wfprov + prefix wfdesc + prefix cwlprov + prefix foaf + prefix schema + prefix orcid + prefix id + prefix data + prefix sha256 + prefix researchobject + prefix metadata + prefix provenance + prefix wf + prefix input + + agent(id:b032933c-ac36-47f7-bf12-a700a67617f0) + agent(id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, [prov:type='wfprov:WorkflowEngine', prov:type='prov:SoftwareAgent', prov:label="cwltool 3.1.20240404144621"]) + wasStartedBy(id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, -, id:b032933c-ac36-47f7-bf12-a700a67617f0, 2024-07-30T14:16:06.727868) + activity(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, 2024-07-30T14:16:06.727901, -, [prov:type='wfprov:WorkflowRun', prov:label="Run of workflow/packed.cwl#main"]) + wasAssociatedWith(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, wf:main) + wasStartedBy(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, -, id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, 2024-07-30T14:16:06.727967) + entity(wf:main, [prov:type='prov:Plan', prov:type='wfdesc:Workflow', prov:label="Prospective provenance"]) + entity(wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400, [prov:type='prov:Plan', prov:type='wfdesc:Process']) + entity(wf:main, [wfdesc:hasSubProcess='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400', prov:label="Prospective provenance"]) + entity(data:dc0dbba18d47b040109f16862d39de918039856d, [prov:type='wfprov:Artifact', prov:value="\"{\\"mdp\\": {\\"integrator\\": \\"md\\", \\"rvdw\\": 1.0, \\"rcoulomb\\": 1.0, \\"coulombtype\\": \\"PME\\", \\"tc-grps\\": \\"system\\", \\"tau-t\\": 2, \\"constraints\\": \\"h-bonds\\", \\"nstxout\\": 1000, \\"nstenergy\\": 1000, \\"pcoupl\\": \\"Parrinello-Rahman\\", \\"tau-p\\": 1, \\"compressibility\\": 4.5e-5, \\"comm-mode\\": \\"Linear\\", \\"comm-grps\\": \\"system\\"}}\""]) + used(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, data:dc0dbba18d47b040109f16862d39de918039856d, 2024-07-30T14:16:07.064609, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config']) + entity(id:bd639999-e2b4-40a4-b469-9047cec5249e, [prov:value="0.02" %% xsd:float]) + used(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, id:bd639999-e2b4-40a4-b469-9047cec5249e, 2024-07-30T14:16:07.064715, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt']) + entity(id:4aadde66-443a-42fe-a7de-62bc8b465c89, [prov:value=10000]) + used(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, id:4aadde66-443a-42fe-a7de-62bc8b465c89, 2024-07-30T14:16:07.064776, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps']) + entity(id:3dad8691-b8f9-4b53-bc77-22e0a16f41c7, [prov:value="1" %% xsd:float]) + used(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, id:3dad8691-b8f9-4b53-bc77-22e0a16f41c7, 2024-07-30T14:16:07.064839, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p']) + entity(id:0eeb0e65-6b4e-402a-abcf-5b08cdf5b9db, [prov:value="298" %% xsd:float]) + used(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, id:0eeb0e65-6b4e-402a-abcf-5b08cdf5b9db, 2024-07-30T14:16:07.064896, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t']) + activity(id:c2e2034a-7838-44e9-9479-adefca3550f1, -, -, [prov:type='wfprov:ProcessRun', prov:label="Run of workflow/packed.cwl#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400"]) + wasAssociatedWith(id:c2e2034a-7838-44e9-9479-adefca3550f1, id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400) + wasStartedBy(id:c2e2034a-7838-44e9-9479-adefca3550f1, -, id:9a41dad8-a1b5-4a5d-825b-437da47258d6, 2024-07-30T14:16:07.067550) + entity(data:dc0dbba18d47b040109f16862d39de918039856d, [prov:type='wfprov:Artifact', prov:value="\"{\\"mdp\\": {\\"integrator\\": \\"md\\", \\"rvdw\\": 1.0, \\"rcoulomb\\": 1.0, \\"coulombtype\\": \\"PME\\", \\"tc-grps\\": \\"system\\", \\"tau-t\\": 2, \\"constraints\\": \\"h-bonds\\", \\"nstxout\\": 1000, \\"nstenergy\\": 1000, \\"pcoupl\\": \\"Parrinello-Rahman\\", \\"tau-p\\": 1, \\"compressibility\\": 4.5e-5, \\"comm-mode\\": \\"Linear\\", \\"comm-grps\\": \\"system\\"}}\""]) + used(id:c2e2034a-7838-44e9-9479-adefca3550f1, data:dc0dbba18d47b040109f16862d39de918039856d, 2024-07-30T14:16:07.068123, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config']) + entity(id:4cb14849-a2f9-4113-8712-16ac3be08dbc, [prov:value="0.02" %% xsd:float]) + used(id:c2e2034a-7838-44e9-9479-adefca3550f1, id:4cb14849-a2f9-4113-8712-16ac3be08dbc, 2024-07-30T14:16:07.068194, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/dt']) + entity(id:10fd9e9c-5227-4617-ad0e-65cbcc3eb7a9, [prov:value=10000]) + used(id:c2e2034a-7838-44e9-9479-adefca3550f1, id:10fd9e9c-5227-4617-ad0e-65cbcc3eb7a9, 2024-07-30T14:16:07.068254, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/nsteps']) + entity(id:c7cc3c24-3190-432a-bc96-bdc8c304fcb6, [prov:value="1" %% xsd:float]) + used(id:c2e2034a-7838-44e9-9479-adefca3550f1, id:c7cc3c24-3190-432a-bc96-bdc8c304fcb6, 2024-07-30T14:16:07.068324, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_p']) + entity(id:8b4817d4-1b47-4291-ad9a-1de0e0af2422, [prov:value="298" %% xsd:float]) + used(id:c2e2034a-7838-44e9-9479-adefca3550f1, id:8b4817d4-1b47-4291-ad9a-1de0e0af2422, 2024-07-30T14:16:07.068382, [prov:role='wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_t']) + wasEndedBy(id:c2e2034a-7838-44e9-9479-adefca3550f1, -, id:9a41dad8-a1b5-4a5d-825b-437da47258d6, 2024-07-30T14:16:07.308537) + entity(cwlprov:None, [prov:label="None"]) + wasGeneratedBy(cwlprov:None, id:9a41dad8-a1b5-4a5d-825b-437da47258d6, 2024-07-30T14:16:07.309782, [prov:role='wf:main/primary/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string']) + wasEndedBy(id:9a41dad8-a1b5-4a5d-825b-437da47258d6, -, id:49b7c1d9-09c2-4607-b6de-a68051d1aaca, 2024-07-30T14:16:07.309888) +endDocument diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.ttl b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.ttl new file mode 100644 index 00000000..9bac1f8b --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.ttl @@ -0,0 +1,131 @@ +@prefix cwlprov: . +@prefix data: . +@prefix id: . +@prefix prov: . +@prefix rdfs: . +@prefix wf: . +@prefix wfdesc: . +@prefix wfprov: . +@prefix xsd: . + +cwlprov:None a prov:Entity ; + rdfs:label "None"^^xsd:string ; + prov:qualifiedGeneration [ a prov:Generation ; + prov:activity id:9a41dad8-a1b5-4a5d-825b-437da47258d6 ; + prov:atTime "2024-07-30T14:16:07.309782"^^xsd:dateTime ; + prov:hadRole ] . + +id:c2e2034a-7838-44e9-9479-adefca3550f1 a wfprov:ProcessRun, + prov:Activity ; + rdfs:label "Run of workflow/packed.cwl#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan ] ; + prov:qualifiedEnd [ a prov:End ; + prov:atTime "2024-07-30T14:16:07.308537"^^xsd:dateTime ; + prov:hadActivity id:9a41dad8-a1b5-4a5d-825b-437da47258d6 ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2024-07-30T14:16:07.067550"^^xsd:dateTime ; + prov:hadActivity id:9a41dad8-a1b5-4a5d-825b-437da47258d6 ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.068123"^^xsd:dateTime ; + prov:entity data:dc0dbba18d47b040109f16862d39de918039856d ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.068324"^^xsd:dateTime ; + prov:entity id:c7cc3c24-3190-432a-bc96-bdc8c304fcb6 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.068382"^^xsd:dateTime ; + prov:entity id:8b4817d4-1b47-4291-ad9a-1de0e0af2422 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.068254"^^xsd:dateTime ; + prov:entity id:10fd9e9c-5227-4617-ad0e-65cbcc3eb7a9 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.068194"^^xsd:dateTime ; + prov:entity id:4cb14849-a2f9-4113-8712-16ac3be08dbc ; + prov:hadRole ] ; + prov:wasAssociatedWith id:49b7c1d9-09c2-4607-b6de-a68051d1aaca . + +wf:main a wfdesc:Workflow, + prov:Entity, + prov:Plan ; + rdfs:label "Prospective provenance"^^xsd:string ; + wfdesc:hasSubProcess . + +id:0eeb0e65-6b4e-402a-abcf-5b08cdf5b9db a prov:Entity ; + prov:value 2.98e+02 . + +id:10fd9e9c-5227-4617-ad0e-65cbcc3eb7a9 a prov:Entity ; + prov:value "10000"^^xsd:int . + +id:3dad8691-b8f9-4b53-bc77-22e0a16f41c7 a prov:Entity ; + prov:value 1e+00 . + +id:4aadde66-443a-42fe-a7de-62bc8b465c89 a prov:Entity ; + prov:value "10000"^^xsd:int . + +id:4cb14849-a2f9-4113-8712-16ac3be08dbc a prov:Entity ; + prov:value 2e-02 . + +id:8b4817d4-1b47-4291-ad9a-1de0e0af2422 a prov:Entity ; + prov:value 2.98e+02 . + +id:b032933c-ac36-47f7-bf12-a700a67617f0 a prov:Agent . + +id:bd639999-e2b4-40a4-b469-9047cec5249e a prov:Entity ; + prov:value 2e-02 . + +id:c7cc3c24-3190-432a-bc96-bdc8c304fcb6 a prov:Entity ; + prov:value 1e+00 . + + a wfdesc:Process, + prov:Entity, + prov:Plan . + +data:dc0dbba18d47b040109f16862d39de918039856d a wfprov:Artifact, + prov:Entity ; + prov:value "\"{\\\"mdp\\\": {\\\"integrator\\\": \\\"md\\\", \\\"rvdw\\\": 1.0, \\\"rcoulomb\\\": 1.0, \\\"coulombtype\\\": \\\"PME\\\", \\\"tc-grps\\\": \\\"system\\\", \\\"tau-t\\\": 2, \\\"constraints\\\": \\\"h-bonds\\\", \\\"nstxout\\\": 1000, \\\"nstenergy\\\": 1000, \\\"pcoupl\\\": \\\"Parrinello-Rahman\\\", \\\"tau-p\\\": 1, \\\"compressibility\\\": 4.5e-5, \\\"comm-mode\\\": \\\"Linear\\\", \\\"comm-grps\\\": \\\"system\\\"}}\""^^xsd:string . + +id:9a41dad8-a1b5-4a5d-825b-437da47258d6 a wfprov:WorkflowRun, + prov:Activity ; + rdfs:label "Run of workflow/packed.cwl#main"^^xsd:string ; + prov:qualifiedAssociation [ a prov:Association ; + prov:hadPlan wf:main ] ; + prov:qualifiedEnd [ a prov:End ; + prov:atTime "2024-07-30T14:16:07.309888"^^xsd:dateTime ; + prov:hadActivity id:49b7c1d9-09c2-4607-b6de-a68051d1aaca ] ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2024-07-30T14:16:06.727967"^^xsd:dateTime ; + prov:hadActivity id:49b7c1d9-09c2-4607-b6de-a68051d1aaca ] ; + prov:qualifiedUsage [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.064896"^^xsd:dateTime ; + prov:entity id:0eeb0e65-6b4e-402a-abcf-5b08cdf5b9db ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.064715"^^xsd:dateTime ; + prov:entity id:bd639999-e2b4-40a4-b469-9047cec5249e ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.064609"^^xsd:dateTime ; + prov:entity data:dc0dbba18d47b040109f16862d39de918039856d ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.064776"^^xsd:dateTime ; + prov:entity id:4aadde66-443a-42fe-a7de-62bc8b465c89 ; + prov:hadRole ], + [ a prov:Usage ; + prov:atTime "2024-07-30T14:16:07.064839"^^xsd:dateTime ; + prov:entity id:3dad8691-b8f9-4b53-bc77-22e0a16f41c7 ; + prov:hadRole ] ; + prov:startedAtTime "2024-07-30T14:16:06.727901"^^xsd:dateTime ; + prov:wasAssociatedWith id:49b7c1d9-09c2-4607-b6de-a68051d1aaca . + +id:49b7c1d9-09c2-4607-b6de-a68051d1aaca a wfprov:WorkflowEngine, + prov:Agent, + prov:SoftwareAgent ; + rdfs:label "cwltool 3.1.20240404144621"^^xsd:string ; + prov:qualifiedStart [ a prov:Start ; + prov:atTime "2024-07-30T14:16:06.727868"^^xsd:dateTime ; + prov:hadActivity id:b032933c-ac36-47f7-bf12-a700a67617f0 ] . diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.xml b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.xml new file mode 100644 index 00000000..4ce6f5c3 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/metadata/provenance/primary.cwlprov.xml @@ -0,0 +1,164 @@ + + + + + cwltool 3.1.20240404144621 + wfprov:WorkflowEngine + + + + + 2024-07-30T14:16:06.727868 + + + 2024-07-30T14:16:06.727901 + Run of workflow/packed.cwl#main + wfprov:WorkflowRun + + + + + + + + + + 2024-07-30T14:16:06.727967 + + + Prospective provenance + wfdesc:Workflow + + + wfdesc:Process + + + Prospective provenance + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400 + + + wfprov:Artifact + "{\"mdp\": {\"integrator\": \"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\", \"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\", \"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\", \"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\", \"comm-grps\": \"system\"}}" + + + + + 2024-07-30T14:16:07.064609 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config + + + 0.02 + + + + + 2024-07-30T14:16:07.064715 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt + + + 10000 + + + + + 2024-07-30T14:16:07.064776 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps + + + 1.0 + + + + + 2024-07-30T14:16:07.064839 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p + + + 298.0 + + + + + 2024-07-30T14:16:07.064896 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t + + + Run of workflow/packed.cwl#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0%401%400 + wfprov:ProcessRun + + + + + + + + + + 2024-07-30T14:16:07.067550 + + + wfprov:Artifact + "{\"mdp\": {\"integrator\": \"md\", \"rvdw\": 1.0, \"rcoulomb\": 1.0, \"coulombtype\": \"PME\", \"tc-grps\": \"system\", \"tau-t\": 2, \"constraints\": \"h-bonds\", \"nstxout\": 1000, \"nstenergy\": 1000, \"pcoupl\": \"Parrinello-Rahman\", \"tau-p\": 1, \"compressibility\": 4.5e-5, \"comm-mode\": \"Linear\", \"comm-grps\": \"system\"}}" + + + + + 2024-07-30T14:16:07.068123 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config + + + 0.02 + + + + + 2024-07-30T14:16:07.068194 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/dt + + + 10000 + + + + + 2024-07-30T14:16:07.068254 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/nsteps + + + 1.0 + + + + + 2024-07-30T14:16:07.068324 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_p + + + 298.0 + + + + + 2024-07-30T14:16:07.068382 + wf:main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_t + + + + + 2024-07-30T14:16:07.308537 + + + None + + + + + 2024-07-30T14:16:07.309782 + wf:main/primary/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string + + + + + 2024-07-30T14:16:07.309888 + + diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/snapshot/config_tag_mdp_workflow.cwl b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/snapshot/config_tag_mdp_workflow.cwl new file mode 100644 index 00000000..b9465865 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/snapshot/config_tag_mdp_workflow.cwl @@ -0,0 +1,53 @@ +#!/usr/bin/env cwl-runner +# This file was autogenerated using the Workflow Inference Compiler, version 0+unknown +# https://github.com/PolusAI/workflow-inference-compiler +steps: +- id: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0 + in: + config: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config + dt: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt + nsteps: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps + ref_p: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p + ref_t: + source: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t + out: + - output_config_string + run: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@1@0.cwl +cwlVersion: v1.2 +class: Workflow +$namespaces: + edam: https://edamontology.org/ +$schemas: +- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl +inputs: + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config: + type: string + format: edam:format_2330 + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt: + type: float + label: The length of each timestep + doc: The length of each timestep + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps: + type: int + label: The number of timesteps + doc: The number of timesteps + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p: + type: float + label: The nominal pressure + doc: The nominal pressure + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t: + type: float + label: The nominal temperature + doc: The nominal temperature +outputs: + config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string: + type: string + label: A dictionary of the given arguments as a JSON-encoded string. + doc: A dictionary of the given arguments as a JSON-encoded string. + outputSource: config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha1.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha1.txt new file mode 100644 index 00000000..bc63a54f --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha1.txt @@ -0,0 +1,13 @@ +60f5537026eaa43a1e0c5f91f1f18b8dfd6198ed workflow/packed.cwl +9b30d0ad7f679ba6f1444a7cc998b7fc2fc1f4db workflow/primary-job.json +26f42b15a34694af7ec9739d144a7b247404f867 metadata/provenance/primary.cwlprov.xml +2e829ac3e31bbe17449d2da03f0ea97e6afa8676 metadata/provenance/primary.cwlprov.provn +67fb7e88ab61a4e8d160f190a8b265cfa56f180d metadata/provenance/primary.cwlprov.json +0265bbca1a8a7e6e0782b8d701bc38243eaa9329 metadata/provenance/primary.cwlprov.ttl +64bd4b84cabe002760912d575a11d94c2ce1b552 metadata/provenance/primary.cwlprov.nt +8e032b7c56cbc88cea4a2845ed599edf2ca262c7 metadata/provenance/primary.cwlprov.jsonld +4ad34a4d342e89fd2c00069c624aa018a9980a4f workflow/primary-output.json +9d1ce6da0b93213246a38268203c43276728518c snapshot/config_tag_mdp_workflow.cwl +a49eea1705572a3bb88108e2a3333496dfe95616 metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt +07ef0256ab0ee0b00ccb557dd35dfa2203d2d32e metadata/manifest.json +ec1171513d8491bbc08c0bb7542e5feed82da50b bag-info.txt diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha256.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha256.txt new file mode 100644 index 00000000..71798aff --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha256.txt @@ -0,0 +1,13 @@ +7d55523b7f8d0514a3f8a22315139a5fc63b260063db57ce5e8494fc7f7aba8a workflow/packed.cwl +cd50aafe12d1d8929903e5efb1636ed361ef874322670db54e81565c1f88e9df workflow/primary-job.json +d3423fea1943e80aab46efe865af5c6fafa22dc62e344612614e554ea0bf714e metadata/provenance/primary.cwlprov.xml +e1043c410d7331f5fcef94e1ebf985c373c80083e003362d553ba38dc2ac46c1 metadata/provenance/primary.cwlprov.provn +3b17a733e81318fafbfd18e19d3a666b74e136f3440320fbdbaae458d7b620fa metadata/provenance/primary.cwlprov.json +24234247fed3c7eda673b13d7feb83ce373cbc973adc251b08be1dd5d25c53e3 metadata/provenance/primary.cwlprov.ttl +abc4ec1ac1b30ea45dd8975f329162b5c1e66369e3175c6587b053ff2c21e38a metadata/provenance/primary.cwlprov.nt +a9254cced4fb3a5c6c4a5628ba21422d16c4f04dee8ba7b41914774d23038018 metadata/provenance/primary.cwlprov.jsonld +55a621dcd1675c0b3c5c5484d6735bbb1157be5ab52666f57ed961ba6d0c6f52 workflow/primary-output.json +5462b5ded971c8037ea3244bbbfb6803976b64ef956ad6b60271ab0715f282e7 snapshot/config_tag_mdp_workflow.cwl +1bb83d4ca19637d05663ab7c99700c5ef941a9658df43907c8677407b0f4732e metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt +da56a99b513f6ecfede05577482f7268215102527c6e7fd797ef613e3c343327 metadata/manifest.json +56db734fb47026c2f7054fca95450b73b3fb510547c28f164c4a1b8b7a7ed545 bag-info.txt diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha512.txt b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha512.txt new file mode 100644 index 00000000..c5f02d19 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/tagmanifest-sha512.txt @@ -0,0 +1,13 @@ +4577c5e0d6704a1d548c9ff72ca327b7b0378fd04cab17eb415a935341cec87ed729eb8d90152c9948fc4e64376935dcf2f19f68cdefe267872519f64efe04c4 workflow/packed.cwl +cec4815daeb6d410b3428871d86ea43287de9536a0f67e34bf1973b300127b0ad46aacc4b7d381033010b13f36b5ac5e786ae5067e981b6bbca475ddc2bd432f workflow/primary-job.json +89ecc20b583d37c38c939eb5811175c46b613cb059a27f9f5a2151ddd36e7643887fdce7b4212e58b4e51b6d71434f107c61347e3f17bccffebb99667957eab7 metadata/provenance/primary.cwlprov.xml +d17974b4e981d8fc621dade7992e7b35edad79da2c8064522f6b6d91bd38b4277c37d5f4d842fa3b016d94447194287afffed643d5c3dd59fe74ee423ac4df10 metadata/provenance/primary.cwlprov.provn +0d4b75c5a38170c5c82d74e62ae2d1143b59a387b77de26d418018f1bb28c5fd3722cb1bb46e9d69ea8e8060330b28b974fad61e91fea15a1b7cff38907d0686 metadata/provenance/primary.cwlprov.json +beb820e9dbd3d5d88b8ff881ffe72317dea2f4a8cb7bc86efce1bfe288cb649ce7956a24fe70181394954c2d99524f39895fb92080656993529191f6f27f69dc metadata/provenance/primary.cwlprov.ttl +17ac2f8bb335608d5e98b64f6f33ce3f74240a7ae9319c90d107733d37636bc50a2f607a2df9cedb69da24e9eb27a6389736d4f3631cf198254f3cc3e9a416ee metadata/provenance/primary.cwlprov.nt +7457f8ca187166a035b7d95aa8acd205014cf092c2c87957027c27e71ab280673430f788a2144da267fc11db15f679141731b74c097e4e2cb0f4de352989fc01 metadata/provenance/primary.cwlprov.jsonld +72ca2978aaed747e27e52ac37250d70010edb99121c451103841204931ca8d8eb6682619bc63e66342a2923fa3dec4a359f2a6b09d332b943851c7de7d159e85 workflow/primary-output.json +c048a633161fc011cc5a44471d9899d631bb0fa9f85097e7dcf9d74db9dd3a0e4dd8946ea3166677cc87650cc2150d5685f5cbe4212a53cd096921441e654e81 snapshot/config_tag_mdp_workflow.cwl +cf4cd045006735c800a54e57eea235b095608ba686d6dee4c85e01ba1d6227cd228450ea23065369b1401299002c4ba9fbbfedbccd23c3bfa87cf5b99fcc16bd metadata/logs/engine.49b7c1d9-09c2-4607-b6de-a68051d1aaca.txt +366d5b7896622682ed624b0d7b4d9ba27689c101c22a97ba42e205f9d453828f8d83d269e5fe793fccc88c492d95a82a9b57646c734769cf65ae89569055c2b8 metadata/manifest.json +c6f661f4b759e11d7c5934be7ad4b29ccd47108c0dd9acaa461a538d1ace38322c9530a803ddcb0f7a8d13999c6999677a4736212ab9c41e34b9145c06b036d3 bag-info.txt diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/packed.cwl b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/packed.cwl new file mode 100644 index 00000000..48936475 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/packed.cwl @@ -0,0 +1,155 @@ +{ + "$graph": [ + { + "steps": [ + { + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0", + "in": [ + { + "source": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config" + }, + { + "source": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/dt" + }, + { + "source": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/nsteps" + }, + { + "source": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_p" + }, + { + "source": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/ref_t" + } + ], + "out": [ + "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string" + ], + "run": "#config_tag_mdp_0@1@0.cwl" + } + ], + "class": "Workflow", + "inputs": [ + { + "type": "string", + "format": "https://edamontology.org/format_2330", + "label": "A dictionary of the given arguments as a JSON-encoded string.", + "doc": "A dictionary of the given arguments as a JSON-encoded string.", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config" + }, + { + "type": "float", + "label": "The length of each timestep", + "doc": "The length of each timestep", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt" + }, + { + "type": "int", + "label": "The number of timesteps", + "doc": "The number of timesteps", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps" + }, + { + "type": "float", + "label": "The nominal pressure", + "doc": "The nominal pressure", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p" + }, + { + "type": "float", + "label": "The nominal temperature", + "doc": "The nominal temperature", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t" + } + ], + "id": "#main", + "outputs": [ + { + "type": "string", + "label": "A dictionary of the given arguments as a JSON-encoded string.", + "doc": "A dictionary of the given arguments as a JSON-encoded string.", + "outputSource": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/output_config_string", + "id": "#main/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string" + } + ] + }, + { + "class": "CommandLineTool", + "label": "Returns a dictionary of the given arguments as a JSON-encoded string.", + "doc": "Returns a dictionary of the given arguments as a JSON-encoded string.", + "baseCommand": "echo", + "requirements": [ + { + "class": "InlineJavascriptRequirement" + } + ], + "inputs": [ + { + "label": "A dictionary of the given arguments as a JSON-encoded string.", + "doc": "A dictionary of the given arguments as a JSON-encoded string.", + "type": "string", + "format": "https://edamontology.org/format_2330", + "default": "{}", + "id": "#config_tag_mdp_0@1@0.cwl/config" + }, + { + "label": "The length of each timestep", + "doc": "The length of each timestep", + "type": "float", + "id": "#config_tag_mdp_0@1@0.cwl/dt" + }, + { + "label": "The number of timesteps", + "doc": "The number of timesteps", + "type": "int", + "id": "#config_tag_mdp_0@1@0.cwl/nsteps" + }, + { + "label": "The nominal pressure", + "doc": "The nominal pressure", + "type": "float", + "id": "#config_tag_mdp_0@1@0.cwl/ref_p" + }, + { + "label": "The nominal temperature", + "doc": "The nominal temperature", + "type": "float", + "id": "#config_tag_mdp_0@1@0.cwl/ref_t" + } + ], + "outputs": [ + { + "label": "A dictionary of the given arguments as a JSON-encoded string.", + "doc": "A dictionary of the given arguments as a JSON-encoded string.", + "type": "string", + "outputBinding": { + "outputEval": "${\n var config = JSON.parse(inputs.config);\n if ((\"mdp\" in config) === false) {\n config[\"mdp\"] = {}; // Initialize it\n }\n // TODO: Check for duplicate keys, i.e.\n // \"Pressure coupling incorrect number of values (I need exactly 1)\"\n config[\"mdp\"][\"nsteps\"] = inputs.nsteps;\n config[\"mdp\"][\"dt\"] = inputs.dt;\n config[\"mdp\"][\"ref-t\"] = inputs[\"ref-t\"]; //Javascript interprets dash as subtract...\n config[\"mdp\"][\"ref-p\"] = inputs[\"ref-p\"];\n return JSON.stringify(config);\n}\n" + }, + "id": "#config_tag_mdp_0@1@0.cwl/output_config_string" + } + ], + "id": "#config_tag_mdp_0@1@0.cwl", + "hints": [ + { + "class": "LoadListingRequirement", + "loadListing": "deep_listing" + }, + { + "class": "NetworkAccess", + "networkAccess": true + } + ] + } + ], + "cwlVersion": "v1.2", + "$schemas": [ + "https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl" + ], + "$namespaces": { + "edam": "https://edamontology.org/" + } +} diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-job.json b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-job.json new file mode 100644 index 00000000..8d659901 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-job.json @@ -0,0 +1,7 @@ +{ + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___config": "\"{\\\"mdp\\\": {\\\"integrator\\\": \\\"md\\\", \\\"rvdw\\\": 1.0, \\\"rcoulomb\\\": 1.0, \\\"coulombtype\\\": \\\"PME\\\", \\\"tc-grps\\\": \\\"system\\\", \\\"tau-t\\\": 2, \\\"constraints\\\": \\\"h-bonds\\\", \\\"nstxout\\\": 1000, \\\"nstenergy\\\": 1000, \\\"pcoupl\\\": \\\"Parrinello-Rahman\\\", \\\"tau-p\\\": 1, \\\"compressibility\\\": 4.5e-5, \\\"comm-mode\\\": \\\"Linear\\\", \\\"comm-grps\\\": \\\"system\\\"}}\"", + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___dt": 0.02, + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___nsteps": 10000, + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_p": 1.0, + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___ref_t": 298.0 +} diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-output.json b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-output.json new file mode 100644 index 00000000..956ac8bb --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/workflow/primary-output.json @@ -0,0 +1,3 @@ +{ + "config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0___output_config_string": null +} diff --git a/utils/config-tag-mdp-plugin/pyproject.toml b/utils/molecular-dynamics/config-tag-mdp-tool/pyproject.toml similarity index 92% rename from utils/config-tag-mdp-plugin/pyproject.toml rename to utils/molecular-dynamics/config-tag-mdp-tool/pyproject.toml index c91517f6..0a0de4f1 100644 --- a/utils/config-tag-mdp-plugin/pyproject.toml +++ b/utils/molecular-dynamics/config-tag-mdp-tool/pyproject.toml @@ -8,8 +8,7 @@ readme = "README.md" [tool.poetry.dependencies] python = ">=3.9,<3.12" typer = "^0.7.0" -cwl-utils = "0.33" -cwltool = "3.1.20240404144621" +sophios = "0.1.1" [tool.poetry.group.dev.dependencies] bump2version = "^1.0.1" diff --git a/utils/config-tag-mdp-plugin/tests/__init__.py b/utils/molecular-dynamics/config-tag-mdp-tool/tests/__init__.py similarity index 100% rename from utils/config-tag-mdp-plugin/tests/__init__.py rename to utils/molecular-dynamics/config-tag-mdp-tool/tests/__init__.py diff --git a/utils/molecular-dynamics/config-tag-mdp-tool/tests/test_config_tag_mdp.py b/utils/molecular-dynamics/config-tag-mdp-tool/tests/test_config_tag_mdp.py new file mode 100644 index 00000000..7de54a04 --- /dev/null +++ b/utils/molecular-dynamics/config-tag-mdp-tool/tests/test_config_tag_mdp.py @@ -0,0 +1,41 @@ +"""Tests for config_tag_mdp.""" +from pathlib import Path + +from sophios.api.pythonapi import Step +from sophios.api.pythonapi import Workflow + + +def test_config_tag_mdp() -> None: + """Test config_tag_mdp.""" + # Define paths and input properties + cwl_file_str = "config_tag_mdp_0@1@0.cwl" + cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str) + input_props = { + "nsteps": 10000, + "dt": 0.02, + "ref-t": 298.0, + "ref-p": 1.0, + "config": '{"mdp": {"integrator": "md", "rvdw": 1.0, \ + "rcoulomb": 1.0, "coulombtype": \ + "PME", "tc-grps": "system", \ + "tau-t": 2, "constraints": \ + "h-bonds", "nstxout": \ + 1000, "nstenergy": 1000, "pcoupl": \ + "Parrinello-Rahman", "tau-p": 1, \ + "compressibility": 4.5e-5, "comm-mode": \ + "Linear", "comm-grps": "system"}}', + } + + # Create the CWL step + config_tag_mdp_step = Step(clt_path=cwl_file) + config_tag_mdp_step.nsteps = input_props["nsteps"] + config_tag_mdp_step.dt = input_props["dt"] + config_tag_mdp_step.ref_t = input_props["ref-t"] + config_tag_mdp_step.ref_p = input_props["ref-p"] + config_tag_mdp_step.config = input_props["config"] + + # Create the workflow and run it + steps = [config_tag_mdp_step] + filename = "config_tag_mdp_workflow" + workflow = Workflow(steps, filename) + workflow.run()