Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 78.4
edited by lzehl
on 2021/07/05 09:55
Change comment: There is no comment for this version
To version 82.1
edited by lzehl
on 2021/07/05 12:13
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -16,19 +16,19 @@
16 16  openMINDS is the overall umbrella for a set of integrated metadata models for describing neuroscience research products in graph databases. The correct integration of these metadata models as well as the provision of a central access point is handled by an integration pipeline. All metadata models are developed on separate GitHub repositories, in order to facilitate extensions and maintenance of existing, as well as development and integration of new openMINDS metadata models and schemas. The integration pipeline ensures that the central openMINDS GitHub repository ingests all these GitHub repositories as [[git-submodules>>https://git-scm.com/docs/git-submodule||rel="noopener noreferrer" target="_blank"]], integrates the respective metadata models and builds the openMINDS GitHub pages, as well as ZIP files containing the respective openMINDS schemas in the supported formats, such as the openMINDS syntax (cf. below), JSON-Schema, or HTML. In the following we will summarize the contents and requirements for the central openMINDS GitHub repository as well as all metadata model git-submodules. The openMINDS integration pipeline will be handled in a separate chapter (cf. below).
17 17  
18 18  (% style="text-align: justify;" %)
19 -Let us start with the [[central openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel=" noopener noreferrer" target="_blank"]] which has a **main branch**, a **documentation branch**, and **version branches** (naming convention: vX; e.g., v1). Official releases (naming convention: vX.Y; e.g., v1.0) are tagged and provided as release packages.
19 +Let us start with the [[central openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel="noopener noreferrer" target="_blank"]] which has a **main branch**, a **documentation branch**, and **version branches** (naming convention: vX; e.g., v1). Official releases (naming convention: vX.Y; e.g., v1.0) are tagged and provided as release packages.
20 20  
21 21  (% style="text-align: justify;" %)
22 22  The **main branch** hosts the general README, the LICENSE document, the CONTRIBUTING document, and the general openMINDS logo. In addition, it maintains the openMINDS vocabulary (vocab; cf. below) which provides general definitions and references for schema types and properties used across all openMINDS metadata models and their versions, as well as the bash script that builds the content of the documentation and version branches.
23 23  
24 24  (% style="text-align: justify;" %)
25 -The **documentation** branch hosts the HTML files that build the [[openMINDS GitHub pages>>https://humanbrainproject.github.io/openMINDS/||rel=" noopener noreferrer" target="_blank"]], as well as a ZIP file for each version branch and official release containing the respective openMINDS schemas in the currently supported formats, such as the openMINDS syntax (`.schema.tpl.json`; cf. below), JSON-Schema (`.schema.json`), or HTML (`.html`).
25 +The **documentation** branch hosts the HTML files that build the [[openMINDS GitHub pages>>https://humanbrainproject.github.io/openMINDS/||rel="noopener noreferrer" target="_blank"]], as well as a ZIP file for each version branch and official release containing the respective openMINDS schemas in the currently supported formats, such as the openMINDS syntax (`.schema.tpl.json`; cf. below), JSON-Schema (`.schema.json`), or HTML (`.html`).
26 26  
27 27  (% style="text-align: justify;" %)
28 28  The **version** branches host the respective openMINDS schemas of a major version by ingesting the corresponding metadata models as git-submodules. Note that these version branches can have official release tags. If a version branch has an official release tag, only backwards compatible changes can be merged on this branch. This can include corrections of typos in instructions, introduction of additional properties to schemas, loosening constraints on expected value numbers or formats, granting additional relations between schemas, and adding new schemas (if they do not require relational changes in existing schemas). Except for typo corrections, these changes are typically tagged as sub-releases for the respective major version (e.g., v1.1). If a version branch does not have an official release tag, yet, also non-backwards compatible changes can be merged on this branch. This can include renaming of existing properties, increasing constraints on expected value numbers or formats, removing relations between schemas and adding new schemas, if they cause relational changes in existing schemas. In case all version branches have official release tags, a new non-backwards compatible change would lead to the creation of a new version branch (with a respectively increased major version number).
29 29  
30 30  (% style="text-align: justify;" %)
31 -As mentioned already above, the setup of the central openMINDS GitHub repository is maintained by the openMINDS integration pipeline (cf. [openMINDS_generator](https:~/~/github.com/HumanBrainProject/openMINDS_generator) GitHub repository). Note that the pipeline is configured in such a way, that each commit on one of the openMINDS submodules will trigger a new build of the central openMINDS repository ensuring that its content is always up-to-date.
31 +As mentioned already above, the setup of the central openMINDS GitHub repository is maintained by the openMINDS integration pipeline (cf. below). Note that the pipeline is configured in such a way, that each commit on one of the openMINDS submodules will trigger a new build of the central openMINDS repository ensuring that its content is always up-to-date.
32 32  
33 33  (% style="text-align: justify;" %)
34 34  For this to work smoothly for the existing, but also for all new openMINDS metadata models, the corresponding openMINDS submodules (GitHub repositories) have to meet the following requirements:
... ... @@ -37,39 +37,26 @@
37 37  **(1)** The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
38 38  
39 39  (% style="text-align: justify;" %)
40 -**(2)** The GitHub repository should have at least one **version branch** (e.g., "v1").
40 +**(2)** The GitHub repository of such a metadata model should have at least one **version branch** (naming convention: vX, where X is a major version number).
41 41  
42 42  (% style="text-align: justify;" %)
43 -**(3)** The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
43 +**(3)** The version branch should have the following **folders** & **files**:
44 44  
45 -(% style="text-align: justify;" %)
46 -**(4)** The **##schemas##** folder should contain the schemas of that metadata model implemented in the **openMINDS schema template syntax** (cf. below). The directory of the schemas can be further structured or flat.
45 +* **##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.
46 +* **##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##**).
47 +* **##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.
48 +* **##img/##** (optional) - contains typically the logo of the openMINDS submodule.
49 +* **##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##**).
50 +* **##version.txt##** (required) - states the identifier of the version branch (e.g., **##v1##**) of the respective metadata model.
51 +* **##README.md##** (required) - contains a short content description of the respective metadata model.
52 +* **##LICENSE.txt##** (required) - defines the MIT license for the respective metadata model.
47 47  
48 -(% style="text-align: justify;" %)
49 -**(5)** The **##tests##** folder should contain test-instances (JSON-LDs) for the schemas in a flat directory. The file names for these test-instances should follow the convention of
54 +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"]].
50 50  
51 -(% style="text-align: center;" %)
52 -**##<<XXX>>-<<YYY>>.jsonld##**
53 -
54 -(% style="text-align: justify;" %)
55 -for files that should pass the tests, and
56 -
57 -(% style="text-align: center;" %)
58 -**##<<XXX>>-<<YYY>>-nok.jsonld##**
59 -
60 -(% style="text-align: justify;" %)
61 -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##**).
62 -
63 -(% style="text-align: justify;" %)
64 -**(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.
65 -
66 -(% style="text-align: justify;" %)
67 -**(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.
68 -
69 69  === The openMINDS vocabulary ===
70 70  
71 71  (% style="text-align: justify;" %)
72 -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.
59 +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 **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.
73 73  
74 74  (% style="text-align: justify;" %)
75 75  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:
... ... @@ -78,7 +78,8 @@
78 78  {
79 79   "OPENMINDS_SCHEMA_TYPE": {
80 80   "description": "GENERAL_DESCRIPTION",
81 - "name": "DISPLAY_LABEL",
68 + "label": "HUMAN-READABLE_LABEL",
69 + "name": "SIMPLIFIED_SCHEMA_TYPE",
82 82   "translatableTo": [
83 83   "REFERENCE_TO_RELATED_SCHEMA_OF_OTHER_INITIATIVE"
84 84   ]
... ... @@ -87,9 +87,15 @@
87 87  {{/code}}
88 88  
89 89  (% style="text-align: justify;" %)
90 -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.
78 +With each new schema committed to one of the openMINDS metadata models, a new entry is appended to the **##types.json##** file, with the "name" and "label" automatically derived from the respective schema type, because it has a consistent naming convention:
91 91  
80 +(% style="text-align: center;" %)
81 +**##"https:~/~/openminds.ebrains.eu/METADATA_MODEL_LABEL/SIMPLIFIED_SCHEMA_NAME"##**
82 +
92 92  (% style="text-align: justify;" %)
84 +The remaining attributes are predefined with a null value and frequently, manually edited by a corresponding expert of the openMINDS development team. Once an entry for a schema is made in the **##types.json##** file, the values of attributes (**##"label"##**, **##"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.
85 +
86 +(% style="text-align: justify;" %)
93 93  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:
94 94  
95 95  {{code language="json"}}
Public

openMINDS