Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57

From 78.4 to 78.5 From 86.1 to 86.2

From version 78.5

edited by lzehl
on 2021/07/05 10:21

Change comment: There is no comment for this version

To version 86.1

edited by lzehl
on 2021/07/05 14:01

Change comment: There is no comment for this version

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@@ -42,52 +42,36 @@
  (% style="text-align: justify;" %)
  **(3)** The version branch should have the following **folders** & **files**:
--* **##schemas/##** (required) - contains the schemas of that metadata model implemented in the reduced openMINDS syntax (cf. below). The sub-directory of the "schemas" folder can be further structured or flat.
--* **##tests/##** (recommended) - contains test-instances (JSON-LDs) for checking the constraints defined in the schemas of the metadata model. The sub-directory of the "tests" folder should follow the same structure as the "schemas" folder. The file names of the test-instances should state in lowerCamelCase first the name of the respectively tested schema and second, separated with an underscore, what schema constrain is tested (e.g., **##contactInformation_validEmail.jsonld##**). If a test-instance is expected to fail the schema validation the file name should receive the postfix **##"_nok"##** (e.g., **##contactInformation_invalidEmail_nok.jsonld##**).
--* **##examples/##** (recommended)
++* **##schemas/##** (required) - contains the schemas of the respective metadata model implemented in the reduced openMINDS syntax (cf. below). The sub-directory of the "schemas" folder can be further structured or flat.
++* **##tests/##** (recommended) - contains test-instances (JSON-LDs) for checking the constraints defined in the schemas of the respective metadata model. The sub-directory of the "tests" folder should follow the same structure as the "schemas" folder with an additional sub-directory for each schema. The file names of the test-instances should be written in lowerCamelCase and state first the name of the respectively tested schema and second, separated with an underscore, what schema constrain is tested (e.g., **##contactInformation_validEmail.jsonld##**). If a test-instance is expected to fail the schema validation the file name should receive the postfix **##"_nok"##** (e.g., **##contactInformation_invalidEmail_nok.jsonld##**).
++* **##examples/##** (recommended) - contains examples for valid instance collections for the respective metadata model. Each example should receive its own directory (folder) with a **##README.md##** describing the example, and an **##metadataCollection##** subfolder containing the openMINDS instances (JSON-LDs). This subfolder can be further structured or flat.
  * **##img/##** (optional) - contains typically the logo of the openMINDS submodule.
--* **##instances/##** (optional) - contains the controlled metadata instances (JSON-LDs) for selected schemas of the metadata model. The sub-directory of the "instances" folder should follow the same structure as the "schemas" folder.
--* **##version.txt##** (required)
--* **##README.md##** (required)
--* **##LICENSE.txt##** (required)
++* **##instances/##** (optional) - contains the controlled metadata instances (JSON-LDs) for selected schemas of the respective metadata model. The sub-directory of the "instances" folder should follow the same structure as the "schemas" folder with an additional sub-directory for each schema. The file names of the controlled instances should be written in lowerCamelCase and state the simple, human-readable identifier of the instance (e.g., **##homoSapiens.jsonld##** for the controlledTerms schema **##Species##**).
++* **##version.txt##** (required) - states the identifier of the version branch (e.g., **##v1##**) of the respective metadata model.
++* **##README.md##** (required) - contains a short content description of the respective metadata model.
++* **##LICENSE.txt##** (required) - defines the MIT license for the respective metadata model.
++For more information on the content of the existing openMINDS metadata models, please go to [[Metadata models & schemas>>doc:Collabs.openminds.Documentation.Metadata models and schemas.WebHome||target="_blank"]].
--(% style="text-align: justify;" %)
--**(5)** The **##tests##** folder should for the schemas in a flat directory. The file names for these test-instances should follow the convention of
--
--(% style="text-align: center;" %)
--**##<<XXX>>-<<YYY>>.jsonld##**
--
--(% style="text-align: justify;" %)
--for files that should pass the tests, and
--
--(% style="text-align: center;" %)
--**##<<XXX>>-<<YYY>>-nok.jsonld##**
--
--(% style="text-align: justify;" %)
--for files that should fail the test. In both cases, **##<<XXX>>##** should be replaced with the label of the schema that is tested, and **##<<YYY>>##** with a user defined label for what aspect is tested (e.g., **##person-withoutCI.jsonld##**).
--
--(% style="text-align: justify;" %)
--**(6)** The **##examples##** folder should contain examples for valid instance collections for that metadata model. Each example should receive its own directory (folder) with a **##README.md##** describing the example, and an **##metadataCollection##** subfolder containing the openMINDS instances (JSON-LDs). This subfolder can be further structured or flat.
--
--(% style="text-align: justify;" %)
--**(7)** The **##img##** folder should contain image files used on that GitHub repository (e.g., the logo of the new openMINDS metadata model). The directory of the images can be further structured or flat.
--
  === The openMINDS vocabulary ===
  (% style="text-align: justify;" %)
--Located under the folder **##vocab##** in the main openMINDS GitHub directory, the openMINDS vocabulary is semi-automatically gathered and stored in dedicated JSON files ([[**##types.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/types.json||rel="noopener noreferrer" target="_blank"]] and [[**##properties.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/properties.json||rel="noopener noreferrer" target="_blank"]]). The openMINDS integration pipeline makes sure that both files are updated with each commit to any of the GitHub repositories for the openMINDS metadata models. With that, the openMINDS vocab reflects always an up-to-date status of the general attributes of existing **schemas** and **properties** across all openMINDS metadata models, while providing the opportunity to centrally review and maintain their consistency. In addition, this design allows us to centrally define and maintain multiple references to related schemas and matching schema properties of other metadata initiatives. How this works in detail is explained in the following.
++Located under the folder **##vocab##** in the main branch of the central openMINDS GitHub directory, the openMINDS vocabulary is semi-automatically gathered and stored in dedicated JSON files ([[**##types.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/types.json||rel="noopener noreferrer" target="_blank"]] and [[**##properties.json##**>>https://raw.githubusercontent.com/HumanBrainProject/openMINDS/v2/vocab/properties.json||rel="noopener noreferrer" target="_blank"]]). The openMINDS integration pipeline makes sure that both files are updated with each commit to any of the GitHub repositories for the openMINDS metadata models. With that, the openMINDS vocab reflects always an up-to-date status of the general attributes of existing **schema types** and **properties** across all openMINDS metadata models, while providing the opportunity to centrally review and maintain their consistency. In addition, this design allows us to centrally define and maintain multiple references to related schemas and matching schema properties of other metadata initiatives. How this works in detail is explained in the following.
  (% style="text-align: justify;" %)
--The **##types.json##** file is an associative array listing all existing openMINDS schemas (via their type). For each openMINDS schema, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
++The **##types.json##** file is an associative array listing all existing openMINDS schema types. For each openMINDS schema type, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
  {{code language="json"}}
  {
--  "OPENMINDS_SCHEMA_TYPE": {
--    "description": "GENERAL_DESCRIPTION",
--    "name": "DISPLAY_LABEL",
++  "https://openminds.ebrains.eu/«METADATA_MODEL_LABEL»/«SCHEMA_NAME»": {
++    "description": "«GENERAL_DESCRIPTION»",
++    "label": "«HUMAN-READABLE_LABEL»",
++    "name": "«SCHEMA_NAME»",
++    "schemas": [
++      "«RELATIVE_PATH_TO_SCHEMA_FILE_OF_THAT_TYPE»"
++    ],
      "translatableTo": [
--      "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
++      "«REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE»"
      ]
    }
  }
@@ -94,22 +94,23 @@
  {{/code}}
  (% style="text-align: justify;" %)
--With each new schema committed to one of the openMINDS metadata models, a new entry is appended to the **##types.json##** file, with the display label automatically derived from the respective schema type and the remaining attributes predefined with a null value. Once an entry for a schema is made in the **##types.json##** file, the values of all attributes (**##"name"##**, **##"description"##**, and **##"translatableTo"##**) can be manually edited. All manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a schema is deleted from the openMINDS metadata models, the corresponding entry in the **##types.json##** file is marked as being deprecated (additional attribute-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##types.json##** file, if the entry is manually deleted.
++With each new schema committed to one of the openMINDS metadata models, a new entry is appended to the **##types.json##** file, with the values for **##"name"##**, **##"label"##**, and **##"schemas"##** automatically derived. The remaining attributes are predefined with a null value and frequently, manually edited by a corresponding expert of the openMINDS development team. If necessary the auto-derived **##"label"##** value can be edited as well. All manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a schema is deleted from the openMINDS metadata models, the corresponding entry in the **##types.json##** file is marked as being deprecated (additional attribute-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##types.json##** file, if the entry is manually deleted.
  (% style="text-align: justify;" %)
--Similar to the **##types.json##** file, the **##properties.json##** file is an associative array listing all properties across all existing openMINDS schemas (via the property name). For each openMINDS property, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
++Similar to the **##types.json##** file, the **##properties.json##** file is an associative array listing all properties across all existing openMINDS schemas. For each openMINDS property, a small list of general attributes are provided in a nested associative array. Currently, the following attributes are captured:
  {{code language="json"}}
  {
--  "PROPERTY_NAME": {
--    "description": "GENERAL_DESCRIPTION",
--    "name": "DISPLAY_LABEL",
--    "nameForReverseLink": "DISPLAY_LABEL_OF_REVERSED_LINK",
++  "https://openminds.ebrains.eu/vocab/«PROPERTY_NAME»": {
++    "description": "«GENERAL_DESCRIPTION",
++    "label": "«HUMAN-READABLE_LABEL",
++    "labelForReverseLink": "«HUMAN-READABLE_LABEL_OF_REVERSED_LINK",
++    "name": "«PROPERTY_NAME»",
      "sameAs": [
--      "REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
++      "«REFERENCE_TO_MATCHING_SCHEMA-PROPERTY_OF_OTHER_INITIATIVE"
      ],
      "schemas": [
--      "RELATIVE_PATH_TO_OPENMINDS-SCHEMA_USING_THIS_PROPERTY"
++      "«RELATIVE_PATH_TO_SCHEMA_FILE_CONTAINING_THIS_PROPERTY»"
      ]
    }
  }
@@ -116,7 +116,7 @@
  {{/code}}
  (% style="text-align: justify;" %)
--With each new property committed to a schema of one of the openMINDS metadata models, a new entry is appended to the **##properties.json##** file, with the display label and list of schemas in which this property occurs automatically derived. The remaining attributes are initially provided with a null value. Once an entry for a property is made in the **##properties.json##** file, the values of all attributes (**##"name"##**, **##"description"##**, **##"nameForReversedLink"##**, and **##"sameAs"##**) can be manually edited, except for **##"schemas"##** which will be always automatically updated. All those manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a property is not used anymore in any of the schemas from the openMINDS metadata models, the corresponding entry in the **##properties.json##** file is marked as being deprecated (additional attribute-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##properties.json##** file, if the entry is manually deleted.
++With each new property committed to a schema of one of the openMINDS metadata models, a new entry is appended to the **##properties.json##** file, with the **##"name"##**, **##"label"##** and **##"labelForReversedLink"##** automatically derived. The remaining attributes are predefined with a null value and frequently, manually edited by a corresponding expert of the openMINDS development team. If necessary the auto-derived values for **##"label"##** and **##"labelForReversedLink"##** can be edited as well. All manual editions will be preserved and not overwritten when the file is updated again with a new commit. In case a property is not used anymore in any of the schemas from the openMINDS metadata models, the corresponding entry in the **##properties.json##** file is marked as being deprecated (additional attribute-value pair; **##"deprecated": true##**). It only can be permanently removed from the **##properties.json##** file, if the entry is manually deleted.
  === The openMINDS syntax ===
@@ -139,6 +139,7 @@
      "PROPERTY_NAME": {
        "type": "DATA_TYPE",
        "_instruction": "METADATA_ENTRY_INSTRUCTION"
++    }
    },
    "required": [
      "PROPERTY_NAME"
@@ -177,8 +177,42 @@
  Depending on the expected data **##"type"##** additional constraints can be made for the metadata entry of a respective property. Currently, the openMINDS schema template syntax supports the following data types: **##"string"##**, ##**"integer"**##, **##"float"##**, **##"boolean"##**, **##"array"##** and **##"object"##**.
  (% style="text-align: justify;" %)
--If the expected data **##"type"##** is a **##"string"##** the expected number of characters, the format or a regular expression pattern of the string can be further defined.
++If the expected data **##"type"##** is a **##"string"##** the expected number of characters, the format or a regular expression pattern of the string can be further defined. Here an abstract example for all possible string constraints:
++{{code language="json"}}
++{
++  "_type": "https://openminds.ebrains.eu/LABEL_OF_METADATA_MODEL/SCHEMA_NAME",
++  "properties": {
++    "stringProperty_noConstraints": {
++      "type": "string",
++      "_instruction": "Enter a free text."
++    },
++    "stringProperty_lengthConstraints": {
++      "maxLength": 6,
++      "minLength": 2,
++      "type": "string",
++      "_instruction": "Enter a free text (allowed numbers of characters: 2 - 6)."
++    },
++    "stringProperty_formatConstraints": {
++      "type": "string",
++      "_formats": [
++        "email",
++        "date",
++        "time",
++        "date-time",
++        "iri"
++      ]
++      "_instruction": "Enter a string matching one of the given formats."
++    },
++    "stringProperty_patternConstraints": {
++      "pattern": "«regular_expression»"
++      "type": "string",
++      "_instruction": "Enter a string matching the given regex pattern (ECMA 262 dialect)."
++    }
++  }
++}
++{{/code}}
++
  === The openMINDS integration pipeline ===
  (//**coming soon**//) If you'd like to learn more about the openMINDS integration pipeline, especially if you'd like to contribute to it, please get in touch with us (the openMINDS development team) via the issues on the openMINDS or openMINDS_generator GitHub or the support email: openminds@ebrains.eu