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opal rest /datasources --opal httphttps://opal-demo.obiba.org:8080 --user administrator --password password --json |
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where the URL is changed to your install location and the 'administrator/password' bits are changed accordingly. Assuming you get something sensible back you have installed the opal client correctly and know all your credentials!
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Once you have a project you want to add a table to it. The first step is to make a JSON file and save it as e.g. my_table.json. The entityType seems to be entirely arbitrary, so call it something relevant to you.
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{'entityType': 'Book', 'name': 'Hamlet'}
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Now we can push this JSON file into the opal.
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opal rest -o http://opal_url --user administrator --password password -m POST -ct "application/json" /datasource/my_project/tables < my_table.json |
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The table will not have any variables associated with it at this stage. We can add them in a similar way to above, first off build a JSON file and save it as e.g. my_variables.json
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[
{
"name": "content",
"entityType": "Book",
"valueType": "text",
"isRepeatable": False,
"index": 1,
},
{
"name": "clean_content",
"entityType": "Book",
"valueType": "text",
"isRepeatable": False,
"index": 2,
}
] |
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Here name is the variable name, entityType matches that defined in the table above, valueType is what the variable actually is (allowed types are: text/integer/decimal/.....), isRepeatable is ??? and index is the order the columns are displayed in.
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opal rest -o http://opal_address --user administrator --password password -m POST -ct "application/json" /datasource/my_project/table/hamlet/variables < my_variables.json |
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Variables can have quite complex definitions - attributes, categories etc can be added to them, see e.g. below.
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[
{
"name": "VAR1",
"entityType": "Participant",
"valueType": "text",
"unit": "",
"isRepeatable": false,
"referencedEntityType": "",
"mimeType": "",
"occurrenceGroup": "",
"index": 1,
"attributes": [
{
"name": "label",
"value": "Which language do you speak?",
"locale": "en"
},
{
"name": "label",
"value": "Quelles langues parlez-vous?",
"locale": "fr"
}
]
},
{
"name": "VAR2",
"entityType": "Participant",
"valueType": "integer",
"mimeType": "",
"isRepeatable": false,
"occurrenceGroup": "",
"unit": "",
"referencedEntityType": "",
"index": 2,
"attributes": [
{
"name": "label",
"value": "Do you like that?"
}
],
"categories": [
{
"name": "1",
"isMissing": false,
"attributes": [
{
"name": "label",
"value": "yes"
}
]
},
{
"name": "2",
"isMissing": false,
"attributes": [
{
"name": "label",
"value": "no"
}
]
},
{
"name": "9",
"isMissing": true,
"attributes": [
{
"name": "label",
"value": "do not know"
}
]
}
]
}
] |
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Adding some data
Now to import some data. The general work flow here is to make a CSV file elsewhere, upload it to opal, then tell opal to use the uploaded file.
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Opal may take a few minutes to process all the data, it also will try to index it too. You can follow the process from the web interface.