Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 43.1
edited by lzehl
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To version 35.1
edited by lzehl
on 2021/03/08 22:31
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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  
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19 -The main (or central) [[openMINDS GitHub repository>>https://github.com/HumanBrainProject/openMINDS||rel="noopener noreferrer" target="_blank"]] ingests all these GitHub repositories as submodules. 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 generator pipeline.
20 -
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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:
23 -((% style="color:#7f8c8d" %)//**coming soon**//(%%))
24 -
25 -=== The openMINDS vocabulary ===
26 -
27 -(% style="text-align: justify;" %)
28 -((% style="color:#7f8c8d" %)//**coming soon**//(%%))
29 -
30 30  === The openMINDS schema template syntax ===
31 31  
32 32  (% style="text-align: justify;" %)
33 -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##**.
34 34  
35 35  (% style="text-align: justify;" %)
36 36  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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42 42  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.
43 43  
44 44  (% style="text-align: justify;" %)
45 -===== Target & concept templates =====
33 +===== Target & context templates =====
46 46  
47 47  (% style="text-align: justify;" %)
48 48  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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50 50  {{code language="json"}}
51 51  {
52 52   "properties": {
53 - "propertyNameA": {},
54 - "propertyNameB": {},
55 - "propertyNameC": {}
41 + "propertyNameA": {},
42 + "propertyNameB": {},
43 + "propertyNameC": {}
56 56   },
57 57   "required": [
58 - "propertyNameA",
59 - "propertyNameC"
46 + "propertyNameA",
47 + "propertyNameC"
60 60   ]
61 61  }
62 62  {{/code}}
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75 75  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##**).
76 76  
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78 -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.
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.
79 79  
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81 -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.
69 +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 context template and passed on to all extending target templates.
82 82  
83 83  (% style="text-align: justify;" %)
84 -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:
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:
85 85  
86 86  {{code language="json"}}
87 87  {
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90 90  }
91 91  {{/code}}
92 92  
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94 -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: 
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: 
95 95  
96 96  1. A concept template has to define some properties which will be inherited by all extending target templates.
97 97  1. If a concept template additionally states that some of these properties are required, all extending target templates will require the same properties. 
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98 98  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.
99 99  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.
100 100  
101 -(% style="text-align: justify;" %)
102 102  How to define the expected value of a property will be explained for the different property types in the following sections.
103 103  
104 104  (% style="text-align: justify;" %)
105 -===== Defining expected values =====
91 +===== String properties =====
106 106  
107 107  (% style="text-align: justify;" %)
108 -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.
94 +(//**coming soon**//)
109 109  
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111 -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:
112 -+ **##"string"##**
113 -+ **##"number"##**
114 -+ **##"integer"##**
115 -+ **##"array"##**
116 -+ **##"boolean"##**
117 -+ **##"null"##**
118 -+ **##"object"##** 
97 +===== Numerical properties =====
119 119  
120 -Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H
99 +(% style="text-align: justify;" %)
100 +(//**coming soon**//)
121 121  
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103 +===== Object properties =====
122 122  
105 +(% style="text-align: justify;" %)
106 +(//**coming soon**//)
107 +
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109 +===== Property arrays =====
110 +
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112 +(//**coming soon**//)
113 +
114 +
123 123  === The openMINDS integration pipeline ===
124 124  
125 125  (//**coming soon**//)
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