refactor config-tag-mdp

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@[email protected]
+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

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

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
+{}

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

utils/molecular-dynamics/config-tag-mdp-tool/cachedir/4cc56456b99cd83771068ac7c958a576.status

@@ -0,0 +1 @@
+permanentFail

utils/config-tag-mdp-plugin/config_tag_mdp.cwl → 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

utils/config-tag-mdp-plugin/ict.yml → 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: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

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
+}

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

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

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\"}}"

utils/molecular-dynamics/config-tag-mdp-tool/provenance/config_tag_mdp_workflow/manifest-sha1.txt

@@ -0,0 +1 @@
+dc0dbba18d47b040109f16862d39de918039856d  data/dc/dc0dbba18d47b040109f16862d39de918039856d

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@[email protected]:40:7: Expression evaluation error:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]:40:7: script was:\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 01 "use strict";\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 02 var inputs = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]:40:7: 04     "dt": 0.02,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 05     "nsteps": 10000,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 06     "ref_p": 1.0,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 07     "ref_t": 298.0\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 08 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 09 var self = [];\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 10 var runtime = {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 11     "cores": 1,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 12     "ram": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 13     "tmpdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 14     "outdirSize": 1024,\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 15     "tmpdir": "/tmp/belht484",\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]:40:7: 17 };\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 18 (function(){\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]: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@[email protected]:40:7: 21     config["mdp"] = {}; // Initialize it\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 22   }\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]:40:7: 29   return JSON.stringify(config);\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: 30 })()\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: stdout was: \'\'\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: stderr was: \'evalmachine.<anonymous>:20\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7:   if (("mdp" in config) === false) {\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7:              ^\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7: \nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]:40:7:     at evalmachine.<anonymous>:20:14\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]:40:7:     at evalmachine.<anonymous>:30:3\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]:40:7:     at Socket.<anonymous> ([eval]:11:57)\nautogenerated/config_tag_mdp_workflow__step__1__config_tag_mdp_0@1@0/config_tag_mdp_0@[email protected]: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@[email protected]: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@[email protected]: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@[email protected]: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