Output content

.eslintrc.js

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+module.exports = {
+  root: true,
+  env: {
+    node: true,
+    es6: true,
+  },
+  'extends': [
+    'eslint:recommended'
+  ],
+  parserOptions: {
+    parser: 'babel-eslint',
+    ecmaVersion: 11
+  }
+}

notes.md

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+# TODO LIST:
+
+- in protocol schema manualy create the "components" relationship and the corresponding file.
+
+```
+component model
+"properties": {
+		"componentName": {
+				"type": "string"
+		},
+		"componentType": {
+				"$ref": "ontology_annotation_schema.json#"
+		},
+		"comments" : {
+				"type": "array",
+				"items": {
+							"$ref": "comment_schema.json#"
+				}
+		}
+}
+```
+
+- manually curate `x_to_many` relations

package.json

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+{
+  "name": "isa2zendro",
+  "license": "MIT",
+  "repository": "https://github.com/Zendro-dev/ISA_Schema_to_Zendro_Definition",
+  "devDependencies": {
+    "eslint": "^6.7.2"
+  },
+  "scripts": {
+    "lint": "eslint utils.js",
+    "exec:silent": "node src/index.js",
+    "exec": "node src/index.js",
+    "exec:verbose": "node src/index.js mode=verbose"
+  }
+}

src/index.js

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+const fs = require("fs");
+const utils = require("./utils.js");
+
+if (require.main === module) {
+  const params = parseParams();
+  if (params.verbose) utils.setVerbose(true)
+  else utils.setVerbose(false)
+  fs.readdir("./src/isa_1_0_core/", (err, files) => {
+    let output = {};
+    files.forEach((file) => {
+      // console.log(`PROCESSING FILE ${file}`);
+      const schemaName = utils.getSchemaName(file),
+          i = require(`./isa_1_0_core/${file}`);
+      output[schemaName] = utils.processProperties(i.properties, schemaName);
+      utils.writeToFile({
+        name: schemaName,
+        value: output[schemaName]
+      })
+    });
+    utils.writeToFile({
+      name: "reverseRelations",
+      value: utils.relationMapping
+    })
+  });
+}
+
+function parseParams() {
+  const args = process.argv.slice(2);
+  let params = {
+    verbose: false
+  }
+  args.forEach((arg) => {
+    const split = arg.split("=");
+    if (split[0] === "mode" && split[1] === "verbose") params.verbose = true
+  });
+  return params;
+}

src/isa_1_0_core/assay_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-04/schema#",
+  "title": "Assay JSON Schema",
+  "name": "Assay JSON Schema",
+  "description": "JSON Schema describing an Assay",
+  "@context": {
+    "@base": "http://purl.org/isaterms/",
+    "xsd": "http://www.w3.org/2001/XMLSchema#"
+  },
+  "type": "object",
+  "properties": {
+    "@id": { "type": "string", "format": "uri" },
+    "filename" : { "type" : "string" },
+    "measurementType" : {
+      "$ref": "ontology_annotation_schema.json#"
+    },
+    "technologyType" : {
+      "type" : "object",
+      "properties": {
+        "ontologyAnnotation" : {
+          "$ref": "ontology_annotation_schema.json#"
+        }
+      }
+    },
+    "technologyPlatform" : { "type" : "string"},
+    "dataFiles" : {
+      "type": "array",
+      "items" : {
+        "$ref": "data_schema.json#"
+      }
+    },
+    "materials": {
+      "type": "object",
+      "properties": {
+        "samples": {
+          "type": "array",
+          "items": {
+            "$ref": "sample_schema.json#"
+          }
+        },
+        "otherMaterials": {
+          "type": "array",
+          "items": {
+            "$ref": "material_schema.json#"
+          }
+        }
+      }
+    },
+    "characteristicCategories": {
+      "description": "List of all the characteristics categories (or material attributes) defined in the study, used to avoid duplication of their declaration when each material_attribute_value is created. ",
+      "type": "array",
+      "items": {
+        "$ref": "material_attribute_schema.json#"
+      }
+    },
+    "unitCategories": {
+      "description": "List of all the unitsdefined in the study, used to avoid duplication of their declaration when each value is created. ",
+      "type": "array",
+      "items": {
+        "$ref": "ontology_annotation_schema.json#"
+      }
+    },
+    "processSequence": {
+      "type": "array",
+      "items" : {
+        "$ref" : "process_schema.json#"
+      }
+    },
+    "comments" : {
+      "type": "array",
+      "items": {
+        "$ref": "comment_schema.json#"
+      }
+    }
+  },
+  "additionalProperties": false
+}

src/isa_1_0_core/comment_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title": "ISA comment schema - it corresponds to ISA Comment[] construct",
+    "description": "JSON-schema representing a comment in the ISA model",
+    "type": "object",
+    "properties": {
+        "@id": { "type": "string", "format": "uri" },
+        "name": {
+            "type": "string"
+        },
+        "value": {
+            "type": "string"
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/data_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title": "ISA data schema",
+    "description": "JSON-schema representing a data file in the ISA model",
+    "type": "object",
+    "properties": {
+        "@id": { "type": "string", "format": "uri" },
+        "name": {
+            "type": "string"
+        },
+        "type": {
+            "type": "string",
+            "enum": [
+                "Raw Data File",
+                "Derived Data File",
+                "Image File",
+                "Acquisition Parameter Data File",
+                "Derived Spectral Data File",
+                "Protein Assignment File",
+                "Raw Spectral Data File",
+                "Peptide Assignment File",
+                "Array Data File",
+                "Derived Array Data File",
+                "Post Translational Modification Assignment File",
+                "Derived Array Data Matrix File",
+                "Free Induction Decay Data File",
+                "Metabolite Assignment File",
+                "Array Data Matrix File"
+            ]
+        },
+        "comments" : {
+            "type": "array",
+            "items": {
+                "$ref": "comment_schema.json#"
+            }
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/factor_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title": "ISA factor schema",
+    "name": "ISA factor schema",
+    "description": "JSON-schema representing a factor value in the ISA model",
+    "type": "object",
+    "properties": {
+        "@id": { "type": "string", "format": "uri" },
+        "factorName": {
+            "type": "string"
+        },
+        "factorType": {
+            "$ref": "ontology_annotation_schema.json#"
+        },
+        "comments" : {
+            "type": "array",
+            "items": {
+                 "$ref": "comment_schema.json#"
+            }
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/factor_value_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title": "ISA factor value schema",
+    "description": "JSON-schema representing a factor value in the ISA model",
+    "type": "object",
+    "properties": {
+         "@id": { "type": "string", "format": "uri" },
+         "category" : {
+             "$ref": "factor_schema.json#"
+        },
+        "value": {
+            "anyOf" : [
+                { "$ref": "ontology_annotation_schema.json#"},
+                { "type": "string"},
+                { "type": "number"}
+                ]
+        },
+        "unit": {
+            "$ref": "ontology_annotation_schema.json#"
+        },
+        "comments" : {
+            "type": "array",
+            "items": {
+                 "$ref": "comment_schema.json#"
+            }
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/investigation_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title" : "ISA investigation schema",
+    "description" : "JSON-schema representing an investigation in the ISA model",
+    "type" : "object",
+    "properties" : {
+         "@id": { "type": "string", "format": "uri" },
+        "filename": { "type" : "string"},
+        "identifier" : { "type" : "string" },
+        "title" : { "type" : "string"},
+        "description" : { "type" : "string"},
+        "submissionDate" : { "type" : "string", "format" : "date-time"},
+        "publicReleaseDate" : { "type" : "string", "format" : "date-time"},
+        "ontologySourceReferences" : {
+            "type" : "array",
+            "items" : {
+                "$ref": "ontology_source_reference_schema.json#"
+            }
+        },
+        "publications" : {
+            "type" : "array",
+            "items" : {
+                 "$ref": "publication_schema.json#"
+
+            }
+        },
+        "people" : {
+            "type" : "array",
+            "items" : {
+                 "$ref": "person_schema.json#"
+
+            }
+        },
+        "studies" : {
+            "type" : "array",
+            "items" : {
+                 "$ref": "study_schema.json#"
+
+            }
+        },
+        "comments" : {
+            "type": "array",
+            "items": {
+                 "$ref": "comment_schema.json#"
+            }
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/material_attribute_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title" : "ISA material attribute schema",
+    "description" : "JSON-schema representing a characteristics category (what appears between the brackets in Charactersitics[]) in the ISA model",
+    "type" : "object",
+    "properties" : {
+        "@id": { "type": "string", "format": "uri" },
+        "characteristicType": {
+            "$ref": "ontology_annotation_schema.json#"
+        }
+    },
+    "additionalProperties": false
+}

src/isa_1_0_core/material_attribute_value_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-04/schema",
+    "title" : "ISA material attribute schema",
+    "description" : "JSON-schema representing a material attribute (or characteristic) value in the ISA model",
+    "type" : "object",
+    "properties" : {
+        "@id": { "type": "string", "format": "uri" },
+        "category" : {
+             "$ref": "material_attribute_schema.json#"
+        },
+        "value": {
+            "anyOf" : [
+                { "$ref": "ontology_annotation_schema.json#"},
+                { "type": "string"},
+                { "type": "number"}
+                ]
+        },
+        "unit": {
+            "$ref": "ontology_annotation_schema.json#"
+        },
+        "comments" : {
+            "type": "array",
+            "items": {
+                 "$ref": "comment_schema.json#"
+            }
+        }
+    },
+    "additionalProperties": false
+}