Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 45.1
edited by lzehl
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To version 26.1
edited by lzehl
on 2021/03/08 21:38
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10 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.
11 11  )))
12 12  
13 -=== The openMINDS umbrella ===
13 +=== Overview of the openMINDS layout ===
14 14  
15 15  (% style="text-align: justify;" %)
16 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.
17 17  
18 -(% style="text-align: justify;" %)
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).
20 -
21 -(% style="text-align: justify;" %)
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:
23 -
24 -(% style="text-align:justify" %)
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.
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-withoutContactInformation.jsonld##**).
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.
31 -
32 -=== The openMINDS vocabulary ===
33 -
34 -(% style="text-align: justify;" %)
35 -((% style="color:#7f8c8d" %)//**coming soon**//(%%))
36 -
37 37  === The openMINDS schema template syntax ===
38 38  
39 39  (% style="text-align: justify;" %)
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##**.
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##**.
41 41  
42 42  (% style="text-align: justify;" %)
43 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).
... ... @@ -49,84 +49,89 @@
49 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.
50 50  
51 51  (% style="text-align: justify;" %)
52 -===== Target & concept templates =====
33 +===== Target & context templates =====
53 53  
54 54  (% style="text-align: justify;" %)
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:
36 +Same as in JSON-Schema, all openMINDS schemas define the name and value of the metadata they expect under the key **##properties##** as nested dictionaries, and which of those properties is obligatory under the key **##required##** listing the corresponding property names, as depicted here:
56 56  
57 57  {{code language="json"}}
58 58  {
59 59   "properties": {
60 - "propertyNameA": {},
61 - "propertyNameB": {},
62 - "propertyNameC": {}
41 + "propertyNameA": {},
42 + "propertyNameB": {},
43 + "propertyNameC": {}
63 63   },
64 64   "required": [
65 - "propertyNameA",
66 - "propertyNameC"
46 + "propertyNameA",
47 + "propertyNameC"
67 67   ]
68 68  }
69 69  {{/code}}
70 70  
71 71  (% style="text-align: justify;" %)
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:
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, as depicted here:
73 73  
74 74  {{code language="json"}}
75 75  {
76 76   "_type": "https:~/~/openminds.ebrains.eu/<<schema-model>>/<<schema-name>>",
77 - "properties": {}
58 + "properties": {},
59 + "required": []
78 78  }
79 79  {{/code}}
80 80  
81 81  (% style="text-align: justify;" %)
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##**).
64 +where **##<<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 that schema (written in **##CamelCase##**).
83 83  
84 84  (% style="text-align: justify;" %)
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.
67 +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.
86 86  
87 87  (% style="text-align: justify;" %)
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.
70 +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.
89 89  
90 90  (% style="text-align: justify;" %)
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:
73 +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##**:
92 92  
93 93  {{code language="json"}}
94 94  {
95 95   "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
96 - "_extends": "products/researchProduct.schema.tpl.json"
78 + "_extends": "products/researchProduct.schema.tpl.json",
79 + "properties": []
97 97  }
98 98  {{/code}}
99 99  
83 +Note that this convention requires the context and corresponding target templates to be located in the same openMINDS metadata model repository. Note also that both, target and concept template, can or cannot define required properties. In this context, the following rules apply: 
84 +
85 +1. If a concept template requires properties, the target templates extending this concept template require the same properties.
86 +1. A target template can require properties of the concept template, that are not explicitly required within the concept template. Other target templates extending the same concept template will not require those properties.
87 +1. A target template can define and require additional properties that were not defined and required in the concept template. These properties are not shared with the other target templates that extend the same concept template.
88 +
89 +How to define the expected value of a property will be explained for the different property types in the following sections.
90 +
100 100  (% style="text-align: justify;" %)
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: 
92 +===== String properties =====
102 102  
103 -1. A concept template has to define some properties which will be inherited by all extending target templates.
104 -1. If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties. 
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.
94 +(% style="text-align: justify;" %)
95 +(//**coming soon**//)
107 107  
108 108  (% style="text-align: justify;" %)
109 -How to define the expected value of a property will be explained for the different property types in the following sections.
98 +===== Numerical properties =====
110 110  
111 111  (% style="text-align: justify;" %)
112 -===== Defining expected values =====
101 +(//**coming soon**//)
113 113  
114 114  (% style="text-align: justify;" %)
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.
104 +===== Object properties =====
116 116  
117 117  (% style="text-align: justify;" %)
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"##**
125 -+ **##"object"##** 
107 +(//**coming soon**//)
126 126  
127 -Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H
109 +(% style="text-align: justify;" %)
110 +===== Property arrays =====
128 128  
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113 +(//**coming soon**//)
129 129  
115 +
130 130  === The openMINDS integration pipeline ===
131 131  
132 132  (//**coming soon**//)
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openMINDS