Wiki source code of Technical details

Version 47.1 by lzehl on 2021/03/18 11:47
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lzehl 4.1 4 openMINDS is designed as modular as possible, in order to facilitate extensions and maintenance of existing, as well as development and integration of new metadata models and schemas. The layout and technical requirements for this modularity are described below.
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lzehl 4.1 7 In parallel, openMINDS tries to consider the various programming skills present in the neuroscience research community. For this reason, openMINDS established an integration pipeline which gradually increases the level of technical detail: starting from a user-friendly, lightweight schema template and ending with established, highly technical metadata schema formats (e.g., JSON-Schema).
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lzehl 8.1 10 Please find below a documentation of the layout and requirements needed to keep the openMINDS modularity, the syntax of the openMINDS schema template, as well as the openMINDS integration pipeline.
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lzehl 42.1 13 === The openMINDS umbrella ===
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lzehl 8.1 16 In summary, openMINDS is the overall umbrella for a set of distributed GitHub repositories, each defining a particular metadata model for neuroscience research products.
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lzehl 45.1 19 The main (or central) [[openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel="noopener noreferrer" target="_blank"]] ingests all these GitHub repositories as [[git-submodules>>https://git-scm.com/docs/git-submodule||rel="noopener noreferrer" target="_blank"]]. Furthermore it defines the openMINDS vocabulary (**##vocab##**) used for **##types##** and **##properties##** across all schemas independent of their original repository (cf. below). And last but not least, it holds the schema representations for all supported metadata formats created by the openMINDS integration pipeline (cf. below).
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22 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:
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25 * The openMINDS metadata model has to be located on a **public GitHub repository** and published under an **MIT license**.
26 * The GitHub repository should have at least one **version branch** (e.g. "v1").
27 * The version branch should have the following **main directory folders**: **##schemas##** (required), **##tests##** (recommended),  **##examples##** (recommended), and **##img##** (optional).
28 * 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.
lzehl 47.1 29 * 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 **##<<XXX>>-<<YYY>>.jsonld##** for files that should pass the tests, and **##<<XXX>>-<<YYY>>-nok.jsonld##** 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##**).
lzehl 45.1 30 * 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 to group related instances.
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lzehl 43.1 32 === The openMINDS vocabulary ===
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35 ((% style="color:#7f8c8d" %)//**coming soon**//(%%))
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lzehl 7.1 37 === The openMINDS schema template syntax ===
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lzehl 39.1 40 All openMINDS metadata models use a light-weighted schema template syntax for defining the expected metadata. The correspondingly formatted schema files use the extension: **##.schema.tpl.json##**.
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lzehl 26.1 43 Although, as the file extension suggests, this openMINDS schema template syntax is inspired by JSON-Schema, it facilitates or even excludes technical aspects that are generally expected for the openMINDS schemas making them more human-readable, especially for untrained eyes. Behind the scenes, within the openMINDS integration pipeline (cf. below), this schema template syntax is then interpreted and flexibly translated to various formal metadata formats (e.g., JSON-Schema).
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lzehl 18.1 46 Despite the simplification in comparison to JSON-Schema, the openMINDS schema templates are also, at the core, specially formatted JSON files using a particular syntax, meaning special key-value pairs that define the validation rules of a schema.
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lzehl 26.1 49 Please find in the following a full documentation of the openMINDS schema template syntax and how it's key-value pairs need to be defined and interpreted.
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lzehl 36.1 52 ===== Target & concept templates =====
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lzehl 32.1 55 Same as in JSON-Schema, all openMINDS schema templates define the expected name (written in **##lowerCamelCase##**) and value of the metadata, typically called property, under the key **##properties##** as nested dictionaries. Furthermore, the names of obligatory metadata can be listed under the key **##required##**. Here a generalized example:
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lzehl 22.1 57 {{code language="json"}}
58 {
lzehl 26.1 59 "properties": {
lzehl 41.1 60 "propertyNameA": {},
61 "propertyNameB": {},
62 "propertyNameC": {}
lzehl 26.1 63 },
64 "required": [
lzehl 41.1 65 "propertyNameA",
66 "propertyNameC"
lzehl 26.1 67 ]
lzehl 22.1 68 }
69 {{/code}}
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lzehl 27.1 72 In addition, an openMINDS schema //has to have// a key **##"_type"##** to be recognized as **target template**. In other words, the **##"_type"##** is used to define the openMINDS namespace of a corresponding schema using a particular naming convention. Here again a generalized example:
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74 {{code language="json"}}
75 {
76 "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
lzehl 28.1 77 "properties": {}
lzehl 26.1 78 }
79 {{/code}}
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lzehl 27.1 82 Note that **##<<schema-model>>##** has to be replaced with the label of the openMINDS metadata model to which the corresponding schema belongs to, and **##<<schema-name>>##** has to be replaced with the corresponding name of the schema (written in **##CamelCase##**).
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lzehl 36.1 85 If an openMINDS schema template //does not// define a key **##"_type"##** (as in the first example above), it is interpreted as a **concept template** which //has to be// extended to a target template.
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lzehl 36.1 88 Concept templates are and should be used when multiple target templates have the same subset of properties, because they facilitate the long-term maintenance of those shared properties: Instead of defining the same properties repeatedly within multiple target templates, the common subset can be defined within a single concept template and passed on to all extending target templates.
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lzehl 36.1 91 To define that a target template is the extension of a concept template, the target template can state under **##"_extends"##** the relative path to the concept template. For example, the openMINDS core target template **##Dataset##** extends the core concept template **##researchProduct##** as indicated here:
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lzehl 23.1 93 {{code language="json"}}
94 {
lzehl 41.1 95 "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
96 "_extends": "products/researchProduct.schema.tpl.json"
lzehl 23.1 97 }
98 {{/code}}
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lzehl 36.1 101 Note that this convention requires the concept and corresponding target templates to be located in the same openMINDS metadata model repository. Note also that for properties, the following rules apply for target and concept template: 
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lzehl 27.1 103 1. A concept template has to define some properties which will be inherited by all extending target templates.
lzehl 28.1 104 1. If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties. 
lzehl 27.1 105 1. A target template can require properties of the concept template, that are not explicitly required within the concept template. In such a case, the other target templates extending the same concept template will not require those properties.
106 1. A target template can (but does not have to) define and require additional properties that were not defined and required in the concept template. These additionally defined and required properties will not be shared with the other target templates extending the same concept template.
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lzehl 26.1 109 How to define the expected value of a property will be explained for the different property types in the following sections.
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lzehl 41.1 112 ===== Defining expected values =====
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lzehl 41.1 115 The expected value of a property can be defined in large parts in the same way as in JSON-Schema, with some openMINDS syntax specific simplifications and modifications.
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lzehl 41.1 118 On the first level, the **##"type"##** of the expected property value needs to be defined. In principle, the openMINDS template syntax supports the same value types as JSON-Schema Draft 7.0, meaning:
119 + **##"string"##**
120 + **##"number"##**
121 + **##"integer"##**
122 + **##"array"##**
123 + **##"boolean"##**
124 + **##"null"##**
lzehl 42.1 125 + **##"object"##** 
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lzehl 41.1 127 Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H
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lzehl 6.1 130 === The openMINDS integration pipeline ===
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132 (//**coming soon**//)
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openMINDS