Wiki source code of Technical details

Version 29.1 by lzehl on 2021/03/08 22:08
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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 7.1 13 === Overview of the openMINDS layout ===
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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 7.1 18 === The openMINDS schema template syntax ===
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lzehl 11.1 21 All openMINDS metadata models use a light-weighted schema template syntax for defining the metadata. The correspondingly formatted schema files use the extension: **##.schema.tpl.json##**.
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lzehl 26.1 24 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 27 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 30 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 14.1 33 ===== Target & context templates =====
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lzehl 27.1 36 Same as in JSON-Schema, all openMINDS schema templates define the name (written in lowerCamelCase) and value of the metadata (typically called property) they expect under the key **##properties##** as nested dictionaries. Furthermore, the names of obligatory metadata/properties can be listed under the key **##required##**. Here a generalized example:
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lzehl 22.1 38 {{code language="json"}}
39 {
lzehl 26.1 40 "properties": {
41 "propertyNameA": {},
42 "propertyNameB": {},
43 "propertyNameC": {}
44 },
45 "required": [
46 "propertyNameA",
47 "propertyNameC"
48 ]
lzehl 22.1 49 }
50 {{/code}}
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lzehl 27.1 53 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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55 {{code language="json"}}
56 {
57 "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
lzehl 28.1 58 "properties": {}
lzehl 26.1 59 }
60 {{/code}}
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lzehl 27.1 63 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 26.1 66 If an openMINDS schema template //does not// define a key **##"_type"##** (as in the first example above), it is interpreted as a **context template** which //has to be// extended to a target template.
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lzehl 26.1 69 Context templates are and should be used when multiple openMINDS schemas (target templates) have the same subset of properties. Such a common subset of properties can then be defined within a single context schema instead of each target template which facilitates the long-term maintenance of these properties.
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lzehl 27.1 72 To define that a target template is the extension of a context template, the target template can state under **##"_extends"##** the relative path to the context 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 74 {{code language="json"}}
75 {
lzehl 24.1 76 "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
lzehl 28.1 77 "_extends": "products/researchProduct.schema.tpl.json"
lzehl 23.1 78 }
79 {{/code}}
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lzehl 29.1 81 Note that this convention requires the context 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 83 1. A concept template has to define some properties which will be inherited by all extending target templates.
lzehl 28.1 84 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 85 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.
86 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 88 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 15.1 91 ===== String properties =====
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94 (//**coming soon**//)
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97 ===== Numerical properties =====
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100 (//**coming soon**//)
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103 ===== Object properties =====
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106 (//**coming soon**//)
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109 ===== Property arrays =====
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112 (//**coming soon**//)
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lzehl 6.1 115 === The openMINDS integration pipeline ===
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117 (//**coming soon**//)
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