@nfdi4plants/arctrl 3.2.3 → 3.3.0

package/dist/ts/ts/CWLRunResolver.d.ts

@@ -4,9 +4,10 @@ import { CWLProcessingUnit_$union } from './CWL/CWLProcessingUnit.ts';
 import { MutableArray, IEquatable } from '@fable-org/fable-library-ts/Util.ts';
 import { TypeInfo } from '@fable-org/fable-library-ts/Reflection.ts';
 import { CWLWorkflowDescription } from './CWL/WorkflowDescription.ts';
-import { WorkflowStepRun_$union } from './CWL/WorkflowSteps.ts';
-import { FSharpSet } from '@fable-org/fable-library-ts/Set.ts';
 import { Option } from '@fable-org/fable-library-ts/Option.ts';
+import { WorkflowStep, WorkflowStepRun_$union } from './CWL/WorkflowSteps.ts';
+import { FSharpList } from '@fable-org/fable-library-ts/List.ts';
+import { FSharpSet } from '@fable-org/fable-library-ts/Set.ts';
 /**
  * Normalizes a file path for use as a lookup key.
  */
@@ -20,26 +21,43 @@ export declare function RunResolutionState_$reflection(): TypeInfo;
  * Generates candidate lookup paths for a .cwl run reference relative to a workflow file.
  */
 export declare function getRunNodeCandidates(workflowFilePath: string, runPath: string): MutableArray<string>;
-export declare function cacheResolvedProcessingUnit(state: RunResolutionState, candidateKeys: MutableArray<string>, processingUnit: CWLProcessingUnit_$union): void;
-export declare function runFromProcessingUnit(processingUnit: CWLProcessingUnit_$union): WorkflowStepRun_$union;
 /**
- * Iterates all steps in a workflow and resolves each step's run field recursively.
+ * Keeps the process that a reference resolved to, so that every later reference to the same file finds the same object.
+ */
+export declare function cacheResolvedProcessingUnit(state: RunResolutionState, key: string, processingUnit: CWLProcessingUnit_$union): void;
+/**
+ * The run of a step that stands for the process. A process whose class is a directive has none, because the file that
+ * decides its class is not read, so a reference to it stays unresolved.
+ */
+export declare function tryRunFromProcessingUnit(processingUnit: CWLProcessingUnit_$union): Option<WorkflowStepRun_$union>;
+/**
+ * Resolves the run reference of each step of a workflow and of each workflow nested inline in it. A step keeps its
+ * run as it is written and receives the process in its ResolvedRun. A step that holds a process already keeps it,
+ * because the lookup hands out one object for each file and the first resolution of that object decided its steps.
+ * The active workflows are the workflows whose steps are being resolved, outermost last. An inline workflow that is
+ * one of them holds itself, so the walk does not enter it again.
  */
-export declare function resolveWorkflowRunsRecursiveWithResolver(workflowFilePath: string, activePathKeys: FSharpSet<string>, state: RunResolutionState, workflow: CWLWorkflowDescription, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): void;
+export declare function resolveWorkflowRunsRecursiveWithResolver(workflowFilePath: string, activePathKeys: FSharpSet<string>, activeWorkflows: FSharpList<CWLProcessingUnit_$union>, state: RunResolutionState, workflow: CWLWorkflowDescription, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): void;
 /**
- * Resolves a single WorkflowStepRun, trying each candidate path against the resolver for RunString values.
+ * Tries each candidate path of a run reference against the resolver and returns the run of the first process that it
+ * finds. A candidate that leads back to a file that is being resolved is skipped, and so is a process that is one of the
+ * active workflows or reaches one, because the step of the innermost one would then hold a process that holds the step.
+ * The cache holds a process under the path it was found at, because the same relative path in the directory of another
+ * workflow is another file.
  */
-export declare function resolveWorkflowStepRunRecursiveWithResolver(workflowFilePath: string, activePathKeys: FSharpSet<string>, state: RunResolutionState, run: WorkflowStepRun_$union, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): WorkflowStepRun_$union;
+export declare function resolveRunReferenceWithResolver(workflowFilePath: string, activePathKeys: FSharpSet<string>, activeWorkflows: FSharpList<CWLProcessingUnit_$union>, state: RunResolutionState, runPath: string, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): Option<WorkflowStepRun_$union>;
 /**
  * Resolves all CWL WorkflowStep run references for a processing unit by looking up
  * run path strings in the provided resolver function. For Workflow processing units,
- * this recursively resolves all nested step run references in-place.
+ * this recursively resolves all nested step run references in-place: each step keeps its run
+ * reference and holds the process in its ResolvedRun.
  * CommandLineTool and ExpressionTool processing units are returned unchanged.
  */
 export declare function resolveRunReferencesFromLookup(workflowFilePath: string, processingUnit: CWLProcessingUnit_$union, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): CWLProcessingUnit_$union;
 /**
- * Resolves a single workflow step run value by looking up the run path string
- * in the provided resolver function. Returns the resolved run value.
+ * Resolves the run reference of a single workflow step by looking up the run path string in the provided resolver
+ * function. The step keeps its run and receives the process in its ResolvedRun. The workflow that holds the step is not
+ * known here, so a process whose steps lead back to the step stays out of the ResolvedRun.
  */
-export declare function resolveWorkflowStepRunFromLookup(workflowFilePath: string, run: WorkflowStepRun_$union, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): WorkflowStepRun_$union;
+export declare function resolveWorkflowStepFromLookup(workflowFilePath: string, step: WorkflowStep, tryResolveRunPath: ((arg0: string) => Option<CWLProcessingUnit_$union>)): void;
 //# sourceMappingURL=CWLRunResolver.d.ts.map

package/dist/ts/ts/CWLRunResolver.d.ts.map

@@ -1 +1 @@
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package/dist/ts/ts/CWLRunResolver.js

@@ -1,15 +1,18 @@
 import { normalizePathKey, normalize, resolvePathFromFile } from './FileSystem/Path.js';
 import { Record } from '../node_modules/@fable-org/fable-library-ts/Types.js';
 import { FSharpMap__Add, FSharpMap__TryFind, empty } from '../node_modules/@fable-org/fable-library-ts/Map.js';
-import { CWLProcessingUnit_$reflection, WorkflowStepRunOps_fromTool, WorkflowStepRunOps_fromOperation, WorkflowStepRunOps_fromExpressionTool, WorkflowStepRunOps_fromWorkflow, CWLProcessingUnit_Workflow, WorkflowStepRunOps_tryGetWorkflow } from './CWL/CWLProcessingUnit.js';
+import { CWLProcessingUnit_$reflection, WorkflowStepRunOps_fromTool, WorkflowStepRunOps_fromOperation, WorkflowStepRunOps_fromExpressionTool, WorkflowStepRunOps_fromWorkflow, CWLProcessingUnit, CWLProcessingUnit_Workflow, WorkflowStepRunOps_tryGetWorkflow } from './CWL/CWLProcessingUnit.js';
 import { stringHash, getEnumerator, disposeSafe, comparePrimitives } from '../node_modules/@fable-org/fable-library-ts/Util.js';
 import { record_type, class_type, string_type } from '../node_modules/@fable-org/fable-library-ts/Reflection.js';
 import { isNullOrWhiteSpace, endsWith } from '../node_modules/@fable-org/fable-library-ts/String.js';
 import { Array_distinct } from '../node_modules/@fable-org/fable-library-ts/Seq2.js';
-import { item, map } from '../node_modules/@fable-org/fable-library-ts/Array.js';
-import { WorkflowStepRun_RunString } from './CWL/WorkflowSteps.js';
-import { FSharpSet__Contains, FSharpSet__Add, empty as empty$1 } from '../node_modules/@fable-org/fable-library-ts/Set.js';
-import { value } from '../node_modules/@fable-org/fable-library-ts/Option.js';
+import { CWLWorkflowDescription } from './CWL/WorkflowDescription.js';
+import { toArray } from '../node_modules/@fable-org/fable-library-ts/Option.js';
+import { ResolvedRun } from './CWL/WorkflowSteps.js';
+import { exists } from '../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { exists as exists$1, choose, ofArray, cons, singleton, empty as empty$1 } from '../node_modules/@fable-org/fable-library-ts/List.js';
+import { FSharpSet__Contains, FSharpSet__Add, ofList, empty as empty$2 } from '../node_modules/@fable-org/fable-library-ts/Set.js';
+import { item } from '../node_modules/@fable-org/fable-library-ts/Array.js';
 
 function pathKey(path) {
   return normalizePathKey(path);
@@ -41,13 +44,10 @@ function getRunNodeCandidates(workflowFilePath, runPath) {
     }
   }
 }
-function cacheResolvedProcessingUnit(state, candidateKeys, processingUnit) {
-  for (let idx = 0; idx <= candidateKeys.length - 1; idx++) {
-    const key = item(idx, candidateKeys);
-    state.Cache = FSharpMap__Add(state.Cache, key, processingUnit);
-  }
+function cacheResolvedProcessingUnit(state, key, processingUnit) {
+  state.Cache = FSharpMap__Add(state.Cache, key, processingUnit);
 }
-function runFromProcessingUnit(processingUnit) {
+function tryRunFromProcessingUnit(processingUnit) {
   switch (processingUnit.tag) {
     case /* Workflow */
     1:
@@ -58,93 +58,173 @@ function runFromProcessingUnit(processingUnit) {
     case /* Operation */
     3:
       return WorkflowStepRunOps_fromOperation(processingUnit.fields[0]);
+    case /* RawProcess */
+    4:
+      return void 0;
     default:
       return WorkflowStepRunOps_fromTool(processingUnit.fields[0]);
   }
 }
-function resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, activePathKeys, state, workflow, tryResolveRunPath) {
-  let enumerator = getEnumerator(workflow.Steps);
+function reaches(isTarget, processingUnit) {
+  const visited = [];
+  const visit = (candidate) => {
+    if (isTarget(candidate)) {
+      return true;
+    } else if (exists((right) => CWLProcessingUnit.isSameObject(candidate, right), visited)) {
+      return false;
+    } else {
+      void visited.push(candidate);
+      if (candidate.tag === /* Workflow */
+      1) {
+        const workflow = candidate.fields[0];
+        return exists((step) => {
+          let option_1 = void 0;
+          return exists$1((workflow_1) => visit(CWLProcessingUnit_Workflow(workflow_1)), choose((x) => x, ofArray([WorkflowStepRunOps_tryGetWorkflow(step.Run), (option_1 = step.ResolvedRun.Run, option_1 != null ? WorkflowStepRunOps_tryGetWorkflow(option_1) : void 0)])));
+        }, CWLWorkflowDescription.getStepValues(workflow));
+      } else {
+        return false;
+      }
+    }
+  };
+  return visit(processingUnit);
+}
+function reachesAny(targets, processingUnit) {
+  return reaches((candidate) => exists$1((right) => CWLProcessingUnit.isSameObject(candidate, right), targets), processingUnit);
+}
+function resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, activePathKeys, activeWorkflows, state, workflow, tryResolveRunPath) {
+  const activeWorkflows_1 = cons(CWLProcessingUnit_Workflow(workflow), activeWorkflows);
+  let enumerator = getEnumerator(CWLWorkflowDescription.getStepValues(workflow));
   try {
     while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      let left = void 0;
       const step = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-      const resolvedRun = resolveWorkflowStepRunRecursiveWithResolver(workflowFilePath, activePathKeys, state, step.Run, tryResolveRunPath);
-      step.Run = resolvedRun;
+      const matchValue = step.Run;
+      let matchResult = void 0, runPath_2 = void 0;
+      switch (matchValue.tag) {
+        case /* RunString */
+        0: {
+          if (matchValue.fields[0], step.ResolvedRun.Run == null) {
+            matchResult = 0;
+            runPath_2 = matchValue.fields[0];
+          } else {
+            matchResult = 1;
+          }
+          break;
+        }
+        case /* RunImport */
+        1: {
+          if (matchValue.fields[0], step.ResolvedRun.Run == null) {
+            matchResult = 0;
+            runPath_2 = matchValue.fields[0];
+          } else {
+            matchResult = 1;
+          }
+          break;
+        }
+        default:
+          matchResult = 1;
+      }
+      switch (matchResult) {
+        case 0: {
+          step.ResolvedRun = new ResolvedRun(resolveRunReferenceWithResolver(workflowFilePath, activePathKeys, activeWorkflows_1, state, runPath_2, tryResolveRunPath));
+          break;
+        }
+        case 1: {
+          if (matchValue.tag === /* RunWorkflow */
+          5) {
+            const matchValue_1 = WorkflowStepRunOps_tryGetWorkflow(step.Run);
+            let matchResult_1 = void 0, inlineWorkflow_1 = void 0;
+            if (matchValue_1 != null) {
+              if (!exists$1((left = CWLProcessingUnit_Workflow(matchValue_1), (right) => CWLProcessingUnit.isSameObject(left, right)), activeWorkflows_1)) {
+                matchResult_1 = 0;
+                inlineWorkflow_1 = matchValue_1;
+              } else {
+                matchResult_1 = 1;
+              }
+            } else {
+              matchResult_1 = 1;
+            }
+            switch (matchResult_1) {
+              case 0: {
+                resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, activePathKeys, activeWorkflows_1, state, inlineWorkflow_1, tryResolveRunPath);
+                break;
+              }
+            }
+          }
+          break;
+        }
+      }
     }
   } finally {
     disposeSafe(enumerator);
   }
 }
-function resolveWorkflowStepRunRecursiveWithResolver(workflowFilePath, activePathKeys, state, run, tryResolveRunPath) {
-  switch (run.tag) {
-    case /* RunWorkflow */
-    2: {
-      const matchValue_2 = WorkflowStepRunOps_tryGetWorkflow(run);
-      if (matchValue_2 == null) {
-        return run;
-      } else {
-        const workflow_1 = value(matchValue_2);
-        resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, activePathKeys, state, workflow_1, tryResolveRunPath);
-        return WorkflowStepRunOps_fromWorkflow(workflow_1);
-      }
-    }
-    case /* RunCommandLineTool */
-    1:
-      return run;
-    case /* RunExpressionTool */
-    3:
-      return run;
-    case /* RunOperation */
-    4:
-      return run;
-    default: {
-      const runPath = run.fields[0];
-      const candidates = getRunNodeCandidates(workflowFilePath, runPath);
-      const candidateKeys = Array_distinct(map(pathKey, candidates), {
-        Equals: (x, y) => x === y,
-        GetHashCode: (x) => stringHash(x) | 0
-      });
-      const tryResolveCandidate = (index_mut) => {
-        tryResolveCandidate:
-          while (true) {
-            const index = index_mut;
-            if (index >= candidates.length) {
-              return WorkflowStepRun_RunString(runPath);
-            } else {
-              const candidate = item(index, candidates);
-              const key = pathKey(candidate);
-              if (FSharpSet__Contains(activePathKeys, key)) {
-                index_mut = index + 1;
-                continue tryResolveCandidate;
+function resolveRunReferenceWithResolver(workflowFilePath, activePathKeys, activeWorkflows, state, runPath, tryResolveRunPath) {
+  const candidates = getRunNodeCandidates(workflowFilePath, runPath);
+  const tryResolveCandidate = (index_mut) => {
+    tryResolveCandidate:
+      while (true) {
+        const index = index_mut;
+        if (index >= candidates.length) {
+          return void 0;
+        } else {
+          const candidate = item(index, candidates);
+          const key = pathKey(candidate);
+          if (FSharpSet__Contains(activePathKeys, key)) {
+            index_mut = index + 1;
+            continue tryResolveCandidate;
+          } else {
+            const matchValue = FSharpMap__TryFind(state.Cache, key);
+            if (matchValue == null) {
+              let matchValue_1;
+              const option_3 = tryResolveRunPath(candidate);
+              if (option_3 != null) {
+                const found = option_3;
+                const option_1 = tryRunFromProcessingUnit(found);
+                matchValue_1 = option_1 != null ? [found, option_1] : void 0;
               } else {
-                const matchValue = FSharpMap__TryFind(state.Cache, key);
-                if (matchValue == null) {
-                  const matchValue_1 = tryResolveRunPath(candidate);
-                  if (matchValue_1 == null) {
-                    index_mut = index + 1;
-                    continue tryResolveCandidate;
-                  } else if (value(matchValue_1).tag === /* Workflow */
+                matchValue_1 = void 0;
+              }
+              let matchResult = void 0, processingUnit_1 = void 0, run_2 = void 0;
+              if (matchValue_1 != null) {
+                if (matchValue_1[1], !reachesAny(activeWorkflows, matchValue_1[0])) {
+                  matchResult = 0;
+                  processingUnit_1 = matchValue_1[0];
+                  run_2 = matchValue_1[1];
+                } else {
+                  matchResult = 1;
+                }
+              } else {
+                matchResult = 1;
+              }
+              switch (matchResult) {
+                case 0: {
+                  if (processingUnit_1.tag === /* Workflow */
                   1) {
-                    const workflow = value(matchValue_1).fields[0];
-                    resolveWorkflowRunsRecursiveWithResolver(candidate, FSharpSet__Add(activePathKeys, key), state, workflow, tryResolveRunPath);
-                    const resolved = CWLProcessingUnit_Workflow(workflow);
-                    cacheResolvedProcessingUnit(state, candidateKeys, resolved);
-                    return runFromProcessingUnit(resolved);
-                  } else {
-                    const processingUnit = value(matchValue_1);
-                    cacheResolvedProcessingUnit(state, candidateKeys, processingUnit);
-                    return runFromProcessingUnit(processingUnit);
+                    const workflow = processingUnit_1.fields[0];
+                    resolveWorkflowRunsRecursiveWithResolver(candidate, FSharpSet__Add(activePathKeys, key), activeWorkflows, state, workflow, tryResolveRunPath);
                   }
-                } else {
-                  return runFromProcessingUnit(value(matchValue));
+                  cacheResolvedProcessingUnit(state, key, processingUnit_1);
+                  return run_2;
+                }
+                default: {
+                  index_mut = index + 1;
+                  continue tryResolveCandidate;
                 }
               }
+            } else if (!reachesAny(activeWorkflows, matchValue)) {
+              const cached_1 = matchValue;
+              return tryRunFromProcessingUnit(cached_1);
+            } else {
+              index_mut = index + 1;
+              continue tryResolveCandidate;
             }
-            break;
           }
-      };
-      return tryResolveCandidate(0);
-    }
-  }
+        }
+        break;
+      }
+  };
+  return tryResolveCandidate(0);
 }
 function resolveRunReferencesFromLookup(workflowFilePath, processingUnit, tryResolveRunPath) {
   switch (processingUnit.tag) {
@@ -157,25 +237,80 @@ function resolveRunReferencesFromLookup(workflowFilePath, processingUnit, tryRes
     case /* Operation */
     3:
       return processingUnit;
+    case /* RawProcess */
+    4:
+      return processingUnit;
     default: {
       const workflow = processingUnit.fields[0];
       const state = new RunResolutionState(empty({
         Compare: (x, y) => comparePrimitives(x, y) | 0
       }));
-      resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, empty$1({
+      resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, ofList(singleton(pathKey(workflowFilePath)), {
         Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
-      }), state, workflow, tryResolveRunPath);
+      }), empty$1(), state, workflow, tryResolveRunPath);
       return CWLProcessingUnit_Workflow(workflow);
     }
   }
 }
-function resolveWorkflowStepRunFromLookup(workflowFilePath, run, tryResolveRunPath) {
+function resolveWorkflowStepFromLookup(workflowFilePath, step, tryResolveRunPath) {
+  let option_2 = void 0;
   const state = new RunResolutionState(empty({
     Compare: (x, y) => comparePrimitives(x, y) | 0
   }));
-  return resolveWorkflowStepRunRecursiveWithResolver(workflowFilePath, empty$1({
-    Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
-  }), state, run, tryResolveRunPath);
+  const matchValue = step.Run;
+  let matchResult = void 0, runPath = void 0;
+  switch (matchValue.tag) {
+    case /* RunString */
+    0: {
+      matchResult = 0;
+      runPath = matchValue.fields[0];
+      break;
+    }
+    case /* RunImport */
+    1: {
+      matchResult = 0;
+      runPath = matchValue.fields[0];
+      break;
+    }
+    case /* RunWorkflow */
+    5: {
+      matchResult = 1;
+      break;
+    }
+    default:
+      matchResult = 2;
+  }
+  switch (matchResult) {
+    case 0: {
+      const resolved = resolveRunReferenceWithResolver(workflowFilePath, empty$2({
+        Compare: (x_1, y_1) => comparePrimitives(x_1, y_1) | 0
+      }), empty$1(), state, runPath, tryResolveRunPath);
+      step.ResolvedRun = new ResolvedRun((option_2 = resolved, option_2 != null ? !exists((workflow_1) => reaches((processingUnit) => {
+        if (processingUnit.tag === /* Workflow */
+        1) {
+          const workflow = processingUnit.fields[0];
+          return exists((other) => other === step, CWLWorkflowDescription.getStepValues(workflow));
+        } else {
+          return false;
+        }
+      }, CWLProcessingUnit_Workflow(workflow_1)), toArray(WorkflowStepRunOps_tryGetWorkflow(option_2))) ? option_2 : void 0 : void 0));
+      break;
+    }
+    case 1: {
+      const matchValue_1 = WorkflowStepRunOps_tryGetWorkflow(step.Run);
+      if (matchValue_1 == null) {
+      } else {
+        const inlineWorkflow = matchValue_1;
+        resolveWorkflowRunsRecursiveWithResolver(workflowFilePath, empty$2({
+          Compare: (x_2, y_2) => comparePrimitives(x_2, y_2) | 0
+        }), empty$1(), state, inlineWorkflow, tryResolveRunPath);
+      }
+      break;
+    }
+    case 2: {
+      break;
+    }
+  }
 }
 
-export { RunResolutionState, RunResolutionState_$reflection, cacheResolvedProcessingUnit, getRunNodeCandidates, pathKey, resolveRunReferencesFromLookup, resolveWorkflowRunsRecursiveWithResolver, resolveWorkflowStepRunFromLookup, resolveWorkflowStepRunRecursiveWithResolver, runFromProcessingUnit };
+export { RunResolutionState, RunResolutionState_$reflection, cacheResolvedProcessingUnit, getRunNodeCandidates, pathKey, resolveRunReferenceWithResolver, resolveRunReferencesFromLookup, resolveWorkflowRunsRecursiveWithResolver, resolveWorkflowStepFromLookup, tryRunFromProcessingUnit };

package/dist/ts/ts/Contract/ARC.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ARC.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ARC.ts"],"names":[],"mappings":"AAIA,OAAO,EAAS,MAAM,EAAE,MAAM,uCAAuC,CAAC;AACtE,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAQzC;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC,QAAQ,CAAC,CAyEzE"}
+{"version":3,"file":"ARC.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ARC.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAC/D,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAQzC;;GAEG;AACH,wBAAgB,0BAA0B,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAC,QAAQ,CAAC,CAyEzE"}

package/dist/ts/ts/Contract/ARC.js

@@ -1,10 +1,9 @@
 import { split } from '../FileSystem/Path.js';
 import { $007CInvestigationPath$007C_$007C } from './ArcInvestigation.js';
-import { value } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { Contract } from './Contract.js';
 import { $007CAssayPath$007C_$007C } from './ArcAssay.js';
 import { $007CStudyPath$007C_$007C } from './ArcStudy.js';
-import { $007CWorkflowPath$007C_$007C, $007CWorkflowCWLPath$007C_$007C } from './ArcWorkflow.js';
+import { WorkflowContractExtensions_$007CWorkflowPath$007C_$007C, WorkflowContractExtensions_$007CWorkflowCWLPath$007C_$007C } from './ArcWorkflow.js';
 import { $007CRunPath$007C_$007C, $007CRunCWLPath$007C_$007C, $007CRunYMLPath$007C_$007C } from './ArcRun.js';
 import { $007CDatamapPath$007C_$007C } from './Datamap.js';
 import { LicenseContractExtensions_$007CLicensePath$007C_$007C } from './License.js';
@@ -13,52 +12,52 @@ function tryISAReadContractFromPath(path) {
   const split$1 = split(path);
   const activePatternResult = $007CInvestigationPath$007C_$007C(split$1);
   if (activePatternResult != null) {
-    const p = value(activePatternResult);
+    const p = activePatternResult;
     return Contract.createRead(p, "ISA_Investigation");
   } else {
     const activePatternResult_1 = $007CAssayPath$007C_$007C(split$1);
     if (activePatternResult_1 != null) {
-      const p_1 = value(activePatternResult_1);
+      const p_1 = activePatternResult_1;
       return Contract.createRead(p_1, "ISA_Assay");
     } else {
       const activePatternResult_2 = $007CStudyPath$007C_$007C(split$1);
       if (activePatternResult_2 != null) {
-        const p_2 = value(activePatternResult_2);
+        const p_2 = activePatternResult_2;
         return Contract.createRead(p_2, "ISA_Study");
       } else {
-        const activePatternResult_3 = $007CWorkflowPath$007C_$007C(split$1);
+        const activePatternResult_3 = WorkflowContractExtensions_$007CWorkflowPath$007C_$007C(split$1);
         if (activePatternResult_3 != null) {
-          const p_3 = value(activePatternResult_3);
+          const p_3 = activePatternResult_3;
           return Contract.createRead(p_3, "ISA_Workflow");
         } else {
-          const activePatternResult_4 = $007CWorkflowCWLPath$007C_$007C(split$1);
+          const activePatternResult_4 = WorkflowContractExtensions_$007CWorkflowCWLPath$007C_$007C(split$1);
           if (activePatternResult_4 != null) {
-            const p_4 = value(activePatternResult_4);
+            const p_4 = activePatternResult_4;
             return Contract.createRead(p_4, "CWL");
           } else {
             const activePatternResult_5 = $007CRunPath$007C_$007C(split$1);
             if (activePatternResult_5 != null) {
-              const p_5 = value(activePatternResult_5);
+              const p_5 = activePatternResult_5;
               return Contract.createRead(p_5, "ISA_Run");
             } else {
               const activePatternResult_6 = $007CRunCWLPath$007C_$007C(split$1);
               if (activePatternResult_6 != null) {
-                const p_6 = value(activePatternResult_6);
+                const p_6 = activePatternResult_6;
                 return Contract.createRead(p_6, "CWL");
               } else {
                 const activePatternResult_7 = $007CRunYMLPath$007C_$007C(split$1);
                 if (activePatternResult_7 != null) {
-                  const p_7 = value(activePatternResult_7);
+                  const p_7 = activePatternResult_7;
                   return Contract.createRead(p_7, "YAML");
                 } else {
                   const activePatternResult_8 = $007CDatamapPath$007C_$007C(split$1);
                   if (activePatternResult_8 != null) {
-                    const p_8 = value(activePatternResult_8);
+                    const p_8 = activePatternResult_8;
                     return Contract.createRead(p_8, "ISA_Datamap");
                   } else {
                     const activePatternResult_9 = LicenseContractExtensions_$007CLicensePath$007C_$007C(split$1);
                     if (activePatternResult_9 != null) {
-                      const p_9 = value(activePatternResult_9);
+                      const p_9 = activePatternResult_9;
                       return Contract.createRead(p_9, "PlainText");
                     } else {
                       return void 0;

package/dist/ts/ts/Contract/ArcAssay.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ArcAssay.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ArcAssay.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,YAAY,EAAa,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAA6B,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAE1F,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAIzC,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAG/C,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,CA0BrF;AAED,wBAAgB,mDAAmD,CAAC,KAAK,EAAE,QAAQ,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,YAAY,CAAC,QAAQ,CAAC,CAQjI;AAED,wBAAgB,0CAA0C,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAGpF;AAED,wBAAgB,0CAA0C,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAGpF;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAEpG;AAED,wBAAgB,2DAA2D,CAAC,KAAK,EAAE,QAAQ,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,YAAY,CAAC,QAAQ,CAAC,CAEzI;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAEpG;AAED,wBAAgB,6DAA6D,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC,CAmC3G"}
+{"version":3,"file":"ArcAssay.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ArcAssay.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,YAAY,EAAa,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAsB,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAEnF,OAAO,EAAgB,QAAQ,EAAE,MAAM,eAAe,CAAC;AAIvD,OAAO,EAAE,QAAQ,EAAE,MAAM,qBAAqB,CAAC;AAG/C,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,CA0BrF;AAED,wBAAgB,mDAAmD,CAAC,KAAK,EAAE,QAAQ,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,YAAY,CAAC,QAAQ,CAAC,CAQjI;AAED,wBAAgB,0CAA0C,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAGpF;AAED,wBAAgB,0CAA0C,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAGpF;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAEpG;AAED,wBAAgB,2DAA2D,CAAC,KAAK,EAAE,QAAQ,EAAE,UAAU,CAAC,EAAE,OAAO,GAAG,YAAY,CAAC,QAAQ,CAAC,CAEzI;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,QAAQ,GAAG,QAAQ,CAEpG;AAED,wBAAgB,6DAA6D,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC,CAmC3G"}

package/dist/ts/ts/Contract/ArcAssay.js

@@ -1,7 +1,7 @@
 import { equalsWith, item } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
 import { combineMany, getAssayFolderPath } from '../FileSystem/Path.js';
 import { defaultOf } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
-import { defaultArg, unwrap, value } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { defaultArg, unwrap } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { Assay_fileNameFromIdentifier } from '../Core/Helper/Identifier.js';
 import { Contract } from './Contract.js';
 import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F, ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D } from '../Spreadsheet/ArcAssay.js';
@@ -63,11 +63,11 @@ function ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F(c) {
   let matchResult = void 0, fsworkbook = void 0;
   if (c.Operation === "READ") {
     if (c.DTOType != null) {
-      if (value(c.DTOType) === "ISA_Assay") {
+      if (c.DTOType === "ISA_Assay") {
         if (c.DTO != null) {
-          if (value(c.DTO) instanceof FsWorkbook) {
+          if (c.DTO instanceof FsWorkbook) {
             matchResult = 0;
-            fsworkbook = value(c.DTO);
+            fsworkbook = c.DTO;
           } else {
             matchResult = 1;
           }

package/dist/ts/ts/Contract/ArcInvestigation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ArcInvestigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ArcInvestigation.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,YAAY,EAAa,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAS,MAAM,EAAE,MAAM,uCAAuC,CAAC;AACtE,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAGvD,wBAAgB,iCAAiC,CAAC,KAAK,EAAE,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,CAmB7F;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,gBAAgB,GAAG,QAAQ,CAE5G;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,gBAAgB,GAAG,QAAQ,CAE5G;AAED,wBAAgB,2EAA2E,CAAC,GAAG,EAAE,gBAAgB,GAAG,QAAQ,CAE3H;AAED,wBAAgB,2EAA2E,CAAC,GAAG,EAAE,gBAAgB,GAAG,QAAQ,CAE3H;AAED,wBAAgB,6EAA6E,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAAC,gBAAgB,CAAC,CAmCnI"}
+{"version":3,"file":"ArcInvestigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Contract/ArcInvestigation.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,YAAY,EAAa,MAAM,qCAAqC,CAAC;AAC9E,OAAO,EAAE,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAC/D,OAAO,EAAgB,QAAQ,EAAE,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAE,gBAAgB,EAAE,MAAM,qBAAqB,CAAC;AAGvD,wBAAgB,iCAAiC,CAAC,KAAK,EAAE,YAAY,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,CAmB7F;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,gBAAgB,GAAG,QAAQ,CAE5G;AAED,wBAAgB,0DAA0D,CAAC,KAAK,EAAE,gBAAgB,GAAG,QAAQ,CAE5G;AAED,wBAAgB,2EAA2E,CAAC,GAAG,EAAE,gBAAgB,GAAG,QAAQ,CAE3H;AAED,wBAAgB,2EAA2E,CAAC,GAAG,EAAE,gBAAgB,GAAG,QAAQ,CAE3H;AAED,wBAAgB,6EAA6E,CAAC,CAAC,EAAE,QAAQ,GAAG,MAAM,CAAC,gBAAgB,CAAC,CAmCnI"}

package/dist/ts/ts/Contract/ArcInvestigation.js

@@ -1,7 +1,6 @@
 import { combineMany } from '../FileSystem/Path.js';
 import { equalsWith, item } from '../../node_modules/@fable-org/fable-library-ts/Array.js';
 import { defaultOf } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
-import { value } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { Contract } from './Contract.js';
 import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF, ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D } from '../Spreadsheet/ArcInvestigation.js';
 import { FsWorkbook } from '../fable_modules/FsSpreadsheet.7.0.1/FsWorkbook.fs.js';
@@ -40,11 +39,11 @@ function ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_75
   let matchResult = void 0, fsworkbook = void 0;
   if (c.Operation === "READ") {
     if (c.DTOType != null) {
-      if (value(c.DTOType) === "ISA_Investigation") {
+      if (c.DTOType === "ISA_Investigation") {
         if (c.DTO != null) {
-          if (value(c.DTO) instanceof FsWorkbook) {
+          if (c.DTO instanceof FsWorkbook) {
             matchResult = 0;
-            fsworkbook = value(c.DTO);
+            fsworkbook = c.DTO;
           } else {
             matchResult = 1;
           }

package/dist/ts/ts/Contract/ArcRun.d.ts

@@ -1,12 +1,22 @@
 import { MutableArray } from '@fable-org/fable-library-ts/Util.ts';
 import { Option } from '@fable-org/fable-library-ts/Option.ts';
-import { Contract } from './Contract.ts';
-import { ArcRun } from '../Core/ArcTypes.ts';
 import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.ts';
+import { Operation, Contract } from './Contract.ts';
+import { ArcRun } from '../Core/ArcTypes.ts';
 import { CWLParameterReference } from '../CWL/ParameterReference.ts';
 export declare function $007CRunPath$007C_$007C(input: MutableArray<string>): Option<string>;
 export declare function $007CRunCWLPath$007C_$007C(input: MutableArray<string>): Option<string>;
 export declare function $007CRunYMLPath$007C_$007C(input: MutableArray<string>): Option<string>;
+/**
+ * The contract that carries the CWL file of the run, or none for a run without a description. The operation is
+ * CREATE for a file that is new and UPDATE for a file that changed.
+ */
+export declare function ARCtrl_ArcRun__ArcRun_TryToCWLContract_Z2D283928(this$: ArcRun, operation: Operation): Option<Contract>;
+/**
+ * The contract that carries the parameter file run.yml of the run, or none for a run without parameter
+ * references. The operation is CREATE for a file that is new and UPDATE for a file that changed.
+ */
+export declare function ARCtrl_ArcRun__ArcRun_TryToYMLContract_Z2D283928(this$: ArcRun, operation: Operation): Option<Contract>;
 export declare function ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(this$: ArcRun, WithFolder?: boolean): MutableArray<Contract>;
 export declare function ARCtrl_ArcRun__ArcRun_ToUpdateContract(this$: ArcRun): Contract;
 export declare function ARCtrl_ArcRun__ArcRun_ToDeleteContract(this$: ArcRun): Contract;

package/dist/ts/ts/Contract/ArcRun.d.ts.map

@@ -1 +1 @@
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