Changes for page Technical details

Last modified by lzehl on 2021/07/05 18:57
From version 40.1
edited by lzehl
on 2021/03/09 16:52
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To version 47.1
edited by lzehl
on 2021/03/18 11:47
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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 -=== Overview of the openMINDS layout ===
13 +=== The openMINDS umbrella ===
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-withoutCI.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 +
18 18  === The openMINDS schema template syntax ===
19 19  
20 20  (% style="text-align: justify;" %)
... ... @@ -38,13 +38,13 @@
38 38  {{code language="json"}}
39 39  {
40 40   "properties": {
41 - "propertyNameA": {},
42 - "propertyNameB": {},
43 - "propertyNameC": {}
60 + "propertyNameA": {},
61 + "propertyNameB": {},
62 + "propertyNameC": {}
44 44   },
45 45   "required": [
46 - "propertyNameA",
47 - "propertyNameC"
65 + "propertyNameA",
66 + "propertyNameC"
48 48   ]
49 49  }
50 50  {{/code}}
... ... @@ -73,8 +73,8 @@
73 73  
74 74  {{code language="json"}}
75 75  {
76 - "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
77 - "_extends": "products/researchProduct.schema.tpl.json"
95 + "_type": "https:~/~/openminds.ebrains.eu/core/Dataset",
96 + "_extends": "products/researchProduct.schema.tpl.json"
78 78  }
79 79  {{/code}}
80 80  
... ... @@ -90,70 +90,24 @@
90 90  How to define the expected value of a property will be explained for the different property types in the following sections.
91 91  
92 92  (% style="text-align: justify;" %)
93 -===== Properties expecting a string value =====
112 +===== Defining expected values =====
94 94  
95 95  (% style="text-align: justify;" %)
96 -Properties that expect values of type string can be defined in large parts in the same way as in JSON-Schema. Without any further formatting requirements the definition of such a property looks like this:
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.
97 97  
98 -{{code language="json"}}
99 -{
100 - "properties": {
101 - "freeStringProperty": {
102 - "type": "string"
103 - }
104 - }
105 -}
106 -{{/code}}
107 -
108 108  (% style="text-align: justify;" %)
109 -In accordance with JSON-Schema, it is possible, though, to further define a selected list of built-in formats that are accepted for the expected string. Supported are all [[built-in formats of JSON-Schema Draft 7.0>>https://json-schema.org/understanding-json-schema/reference/string.html#built-in-formats||rel="noopener noreferrer" target="_blank"]]. Assuming that my string property only accepts a value of format "email", the openMINDS syntax is the following:
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"##** 
110 110  
111 -{{code language="json"}}
112 -{
113 - "properties": {
114 - "emailProperty": {
115 - "type": "string",
116 - "_formats": [
117 - "email"
118 - ]
119 - }
120 - }
121 -}
122 -{{/code}}
127 +Also very similar to JSON-Schema, additional type-specific keys can be used to set further requirements for the expected value. H
123 123  
124 -(% style="text-align: justify;" %)
125 -Also like JSON-Schema, it is possible to define a customized regular expression pattern for the expected string, supporting the [[ECMA-262 regex-dialect>>https://www.ecma-international.org/publications-and-standards/standards/ecma-262/]]. Assuming that my string property only accepts a Gregorian calendar year, the corresponding openMINDS syntax look like this:
126 126  
127 -{{code language="json"}}
128 -{
129 - "properties": {
130 - "yearProperty": {
131 - "type": "string",
132 - "pattern": "([0-9]{4})"
133 - }
134 - }
135 -}
136 -{{/code}}
137 -
138 -(% style="text-align: justify;" %)
139 -===== Properties expecting a numerical value =====
140 -
141 -(% style="text-align: justify;" %)
142 -(//**coming soon**//)
143 -
144 -(% style="text-align: justify;" %)
145 -===== Properties expecting another object =====
146 -
147 -(% style="text-align: justify;" %)
148 -(//**coming soon**//)
149 -
150 -(% style="text-align: justify;" %)
151 -===== Properties expecting an array of values =====
152 -
153 -(% style="text-align: justify;" %)
154 -(//**coming soon**//)
155 -
156 -
157 157  === The openMINDS integration pipeline ===
158 158  
159 159  (//**coming soon**//)
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openMINDS