@nfdi4plants/arctrl 2.1.0-alpha.4 → 2.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (88) hide show
  1. package/CWL/CWLTypes.js +135 -0
  2. package/CWL/Decode.js +585 -0
  3. package/CWL/Inputs.js +62 -0
  4. package/CWL/Outputs.js +59 -0
  5. package/CWL/Requirements.js +72 -0
  6. package/CWL/ToolDescription.js +81 -0
  7. package/CWL/WorkflowDescription.js +81 -0
  8. package/CWL/WorkflowSteps.js +98 -0
  9. package/Core/ArcTypes.js +76 -87
  10. package/Core/Helper/Identifier.js +2 -2
  11. package/Core/OntologyAnnotation.js +8 -5
  12. package/Core/Table/ArcTable.js +15 -7
  13. package/Core/Table/CompositeHeader.js +4 -0
  14. package/Core/Template.js +8 -0
  15. package/Json/{ROCrateObject.js → LDObject.js} +66 -17
  16. package/Json/Process/Material.js +32 -8
  17. package/Json/Process/ProcessInput.js +3 -3
  18. package/Json/Process/Sample.js +32 -8
  19. package/Json/Process/Source.js +32 -8
  20. package/Json/context/rocrate/isa_assay_context.js +4 -4
  21. package/JsonIO/LDObject.js +31 -0
  22. package/ROCrate/ArcROCrateMetadata.js +35 -0
  23. package/ROCrate/ISAProfile/Assay.js +30 -2
  24. package/ROCrate/ISAProfile/Data.js +32 -5
  25. package/ROCrate/ISAProfile/Dataset.js +3 -3
  26. package/ROCrate/ISAProfile/Investigation.js +30 -2
  27. package/ROCrate/ISAProfile/LabProcess.js +113 -5
  28. package/ROCrate/ISAProfile/LabProtocol.js +4 -4
  29. package/ROCrate/ISAProfile/Person.js +32 -5
  30. package/ROCrate/ISAProfile/PropertyValue.js +59 -5
  31. package/ROCrate/ISAProfile/Sample.js +32 -5
  32. package/ROCrate/ISAProfile/ScholarlyArticle.js +59 -5
  33. package/ROCrate/ISAProfile/Study.js +30 -2
  34. package/ROCrate/LDObject.js +105 -0
  35. package/Spreadsheet/AnnotationTable/ArcTable.js +8 -5
  36. package/Spreadsheet/Template.js +29 -11
  37. package/Yaml/ValidationPackage.js +6 -6
  38. package/Yaml/ValidationPackagesConfig.js +6 -6
  39. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/DynObj.fs +4 -4
  40. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/DynObj.fs.js +0 -44
  41. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/HashCodes.fs +4 -1
  42. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/HashCodes.fs.js +8 -3
  43. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/obj/Debug/netstandard2.0/DynamicObj.AssemblyInfo.fs +1 -1
  44. package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/obj/Release/netstandard2.0/DynamicObj.AssemblyInfo.fs +3 -3
  45. package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Decode.fs +398 -373
  46. package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Decode.fs.js +35 -2
  47. package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/obj/Debug/netstandard2.0/YAMLicious.AssemblyInfo.fs +1 -1
  48. package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/obj/Release/netstandard2.0/YAMLicious.AssemblyInfo.fs +1 -1
  49. package/fable_modules/project_cracked.json +1 -1
  50. package/package.json +1 -1
  51. package/JsonIO/ROCrateObject.js +0 -146
  52. package/ROCrate/ROCrateObject.js +0 -61
  53. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/DynamicObj.fableproj +0 -0
  54. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/DynamicObj.fs +0 -0
  55. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/DynamicObj.fs.js +0 -0
  56. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/FableJS.fs +0 -0
  57. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/FableJS.fs.js +0 -0
  58. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/FablePy.fs +0 -0
  59. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/PropertyHelper.fs +0 -0
  60. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/PropertyHelper.fs.js +0 -0
  61. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/ReflectionUtils.fs +0 -0
  62. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/ReflectionUtils.fs.js +0 -0
  63. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/obj/Debug/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
  64. /package/fable_modules/{DynamicObj.4.0.0 → DynamicObj.4.0.3}/obj/Release/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
  65. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Encode.fs +0 -0
  66. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Encode.fs.js +0 -0
  67. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Interop/JsInterop.fs +0 -0
  68. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Interop/JsInterop.fs.js +0 -0
  69. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Interop/PyInterop.fs +0 -0
  70. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Library.fs +0 -0
  71. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Library.fs.js +0 -0
  72. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Persil.fs +0 -0
  73. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Persil.fs.js +0 -0
  74. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Preprocessing.fs +0 -0
  75. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Preprocessing.fs.js +0 -0
  76. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Reader.fs +0 -0
  77. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Reader.fs.js +0 -0
  78. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Regex.fs +0 -0
  79. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Regex.fs.js +0 -0
  80. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/RegexActivePatterns.fs +0 -0
  81. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/RegexActivePatterns.fs.js +0 -0
  82. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Writer.fs +0 -0
  83. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/Writer.fs.js +0 -0
  84. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/YAMLicious.fableproj +0 -0
  85. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/YAMLiciousTypes.fs +0 -0
  86. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/YAMLiciousTypes.fs.js +0 -0
  87. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/obj/Debug/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
  88. /package/fable_modules/{YAMLicious.0.0.1 → YAMLicious.0.0.3}/obj/Release/netstandard2.0/.NETStandard,Version=v2.0.AssemblyAttributes.fs +0 -0
@@ -95,7 +95,7 @@ module DynObj =
95
95
  /// <param name="propertyValue">The value of the property to set</param>
96
96
  /// <param name="dynObj">The DynamicObj to set the property on</param>
97
97
  /// <remarks>This function mutates the input DynamicObj</remarks>
98
- let withProperty (propertyName:string) (propertyValue:'TPropertyValue) (dynObj: DynamicObj) =
98
+ let inline withProperty (propertyName:string) (propertyValue:'TPropertyValue) (dynObj: #DynamicObj) =
99
99
  setProperty propertyName propertyValue dynObj
100
100
  dynObj
101
101
 
@@ -120,7 +120,7 @@ module DynObj =
120
120
  /// <param name="propertyValue">The value of the property to set</param>
121
121
  /// <param name="dynObj">The DynamicObj to set the property on</param>
122
122
  /// <remarks>This function mutates the input DynamicObj</remarks>
123
- let withOptionalProperty (propertyName: string) (propertyValue: 'TPropertyValue option) (dynObj: DynamicObj) =
123
+ let inline withOptionalProperty (propertyName: string) (propertyValue: 'TPropertyValue option) (dynObj: #DynamicObj) =
124
124
  match propertyValue with
125
125
  | Some pv -> dynObj |> withProperty propertyName pv
126
126
  | None -> dynObj
@@ -148,7 +148,7 @@ module DynObj =
148
148
  /// <param name="mapping">A function to apply to the property value before setting it on the DynamicObj</param>
149
149
  /// <param name="dynObj">The DynamicObj to set the property on</param>
150
150
  /// <remarks>This function mutates the input DynamicObj</remarks>
151
- let withOptionalPropertyBy (propertyName: string) (propertyValue: 'TPropertyValue option) (mapping: 'TPropertyValue -> 'UPropertyValue) (dynObj: DynamicObj) =
151
+ let inline withOptionalPropertyBy (propertyName: string) (propertyValue: 'TPropertyValue option) (mapping: 'TPropertyValue -> 'UPropertyValue) (dynObj: #DynamicObj) =
152
152
  match propertyValue with
153
153
  | Some pv -> dynObj |> withProperty propertyName (mapping pv)
154
154
  | None -> dynObj
@@ -182,7 +182,7 @@ module DynObj =
182
182
  /// <param name="dynObj">The DynamicObj to remove the property from</param>
183
183
  /// <remarks>This function mutates the input DynamicObj</remarks>
184
184
  /// <exception cref="System.MemberAccessException">Thrown if the dynamic property does not exist</exception>
185
- let withoutProperty(propertyName: string) (dynObj: DynamicObj) =
185
+ let inline withoutProperty(propertyName: string) (dynObj: #DynamicObj) =
186
186
  dynObj |> removeProperty propertyName
187
187
  dynObj
188
188
 
@@ -75,14 +75,6 @@ export function setProperty(propertyName, propertyValue, dynObj) {
75
75
  dynObj.SetProperty(propertyName, propertyValue);
76
76
  }
77
77
 
78
- /**
79
- * Sets the dynamic (or static) property value with the given name, creating a new dynamic property if none exists on the given DynamicObj and returns it.
80
- */
81
- export function withProperty(propertyName, propertyValue, dynObj) {
82
- setProperty(propertyName, propertyValue, dynObj);
83
- return dynObj;
84
- }
85
-
86
78
  /**
87
79
  * Sets the dynamic (or static) property value with the given name on the given DynamicObj if the value is Some('TPropertyValue), creating a new dynamic property if none exists.
88
80
  * If the given propertyValue is None, does nothing to the input DynamicObj.
@@ -95,19 +87,6 @@ export function setOptionalProperty(propertyName, propertyValue, dynObj) {
95
87
  }
96
88
  }
97
89
 
98
- /**
99
- * Sets the dynamic (or static) property value with the given name on the given DynamicObj if the value is Some('TPropertyValue), creating a new dynamic property if none exists, and returns it.
100
- * If the given propertyValue is None, does nothing to the input DynamicObj.
101
- */
102
- export function withOptionalProperty(propertyName, propertyValue, dynObj) {
103
- if (propertyValue == null) {
104
- return dynObj;
105
- }
106
- else {
107
- return withProperty(propertyName, value_1(propertyValue), dynObj);
108
- }
109
- }
110
-
111
90
  /**
112
91
  * Sets the given dynamic (or static) property with the result of a mapping function applied to the given property value on the given DynamicObj if the value is Some('TPropertyValue).
113
92
  * If the given propertyValue is None, does nothing to the input DynamicObj.
@@ -120,19 +99,6 @@ export function setOptionalPropertyBy(propertyName, propertyValue, mapping, dynO
120
99
  }
121
100
  }
122
101
 
123
- /**
124
- * Sets the given dynamic (or static) property with the result of a mapping function applied to the given property value on the given DynamicObj if the value is Some('TPropertyValue) and returns it.
125
- * If the given propertyValue is None, returns the unchanged DynamicObj.
126
- */
127
- export function withOptionalPropertyBy(propertyName, propertyValue, mapping, dynObj) {
128
- if (propertyValue == null) {
129
- return dynObj;
130
- }
131
- else {
132
- return withProperty(propertyName, mapping(value_1(propertyValue)), dynObj);
133
- }
134
- }
135
-
136
102
  /**
137
103
  * Returns Some(boxed property value) if a dynamic (or static) property with the given name exists on the input, otherwise None.
138
104
  */
@@ -149,16 +115,6 @@ export function removeProperty(propertyName, dynObj) {
149
115
  dynObj.RemoveProperty(propertyName);
150
116
  }
151
117
 
152
- /**
153
- * Removes any dynamic property with the given name from the input DynamicObj and returns it.
154
- * If the property is static and mutable, it will be set to null.
155
- * Static immutable properties cannot be removed.
156
- */
157
- export function withoutProperty(propertyName, dynObj) {
158
- removeProperty(propertyName, dynObj);
159
- return dynObj;
160
- }
161
-
162
118
  /**
163
119
  * Returns a formatted string containing all static and dynamic properties of the given DynamicObj
164
120
  */
@@ -15,7 +15,10 @@ let hashDateTime (dt : System.DateTime) : int =
15
15
 
16
16
 
17
17
  let hash obj =
18
- obj.GetHashCode()
18
+ if obj = null then
19
+ 0
20
+ else
21
+ obj.GetHashCode()
19
22
 
20
23
  let boxHashOption (a: 'a option) : obj =
21
24
  if a.IsSome then a.Value.GetHashCode() else (0).GetHashCode()
@@ -1,5 +1,5 @@
1
1
  import { second, minute, hour, day, month, year } from "../fable-library-js.4.22.0/Date.js";
2
- import { numberHash, identityHash } from "../fable-library-js.4.22.0/Util.js";
2
+ import { numberHash, identityHash, defaultOf, equals } from "../fable-library-js.4.22.0/Util.js";
3
3
  import { value as value_1 } from "../fable-library-js.4.22.0/Option.js";
4
4
  import { fold } from "../fable-library-js.4.22.0/Array.js";
5
5
  import { fold as fold_1 } from "../fable-library-js.4.22.0/Seq.js";
@@ -20,8 +20,13 @@ export function hashDateTime(dt) {
20
20
  }
21
21
 
22
22
  export function hash(obj) {
23
- let copyOfStruct = obj;
24
- return identityHash(copyOfStruct) | 0;
23
+ if (equals(obj, defaultOf())) {
24
+ return 0;
25
+ }
26
+ else {
27
+ let copyOfStruct = obj;
28
+ return identityHash(copyOfStruct) | 0;
29
+ }
25
30
  }
26
31
 
27
32
  export function boxHashOption(a) {
@@ -11,7 +11,7 @@ open System.Reflection
11
11
  [<assembly: System.Reflection.AssemblyConfigurationAttribute("Debug")>]
12
12
  [<assembly: System.Reflection.AssemblyDescriptionAttribute("F# library supporting Dynamic Objects including inheritance in functional style. Compatible with Fable javascript and python transpilation.")>]
13
13
  [<assembly: System.Reflection.AssemblyFileVersionAttribute("1.0.0.0")>]
14
- [<assembly: System.Reflection.AssemblyInformationalVersionAttribute("1.0.0+1d5799f222ea3f1f0885bc3e0efcee4fd0473a4c")>]
14
+ [<assembly: System.Reflection.AssemblyInformationalVersionAttribute("1.0.0+36c543f1c23ec27364ae79a3905daa1ac18c8887")>]
15
15
  [<assembly: System.Reflection.AssemblyProductAttribute("DynamicObj")>]
16
16
  [<assembly: System.Reflection.AssemblyTitleAttribute("DynamicObj")>]
17
17
  [<assembly: System.Reflection.AssemblyVersionAttribute("1.0.0.0")>]
@@ -10,10 +10,10 @@ open System.Reflection
10
10
  [<assembly: System.Reflection.AssemblyCompanyAttribute("Timo Mühlhaus, Kevin Schneider, Heinrich Lukas Weil, F# open source contributors")>]
11
11
  [<assembly: System.Reflection.AssemblyConfigurationAttribute("Release")>]
12
12
  [<assembly: System.Reflection.AssemblyDescriptionAttribute("F# library supporting Dynamic Objects including inheritance in functional style. Compatible with Fable javascript and python transpilation.")>]
13
- [<assembly: System.Reflection.AssemblyFileVersionAttribute("4.0.0.0")>]
14
- [<assembly: System.Reflection.AssemblyInformationalVersionAttribute("4.0.0+1d5799f222ea3f1f0885bc3e0efcee4fd0473a4c")>]
13
+ [<assembly: System.Reflection.AssemblyFileVersionAttribute("4.0.3.0")>]
14
+ [<assembly: System.Reflection.AssemblyInformationalVersionAttribute("4.0.3+36c543f1c23ec27364ae79a3905daa1ac18c8887")>]
15
15
  [<assembly: System.Reflection.AssemblyProductAttribute("DynamicObj")>]
16
16
  [<assembly: System.Reflection.AssemblyTitleAttribute("DynamicObj")>]
17
- [<assembly: System.Reflection.AssemblyVersionAttribute("4.0.0.0")>]
17
+ [<assembly: System.Reflection.AssemblyVersionAttribute("4.0.3.0")>]
18
18
  [<assembly: System.Reflection.AssemblyMetadataAttribute("RepositoryUrl", "https://github.com/CSBiology/DynamicObj")>]
19
19
  do()