OHDSI/AchillesWeb

Name: AchillesWeb

Owner: Observational Health Data Sciences and Informatics

Description: Interactive web site for reviewing the results of the Achilles R package.

Created: 2014-05-28 16:35:15.0

Updated: 2017-10-22 23:46:55.0

Pushed: 2017-12-06 01:16:30.0

Homepage: null

Size: 745

Language: JavaScript

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README

AchillesWeb

Interactive web site for reviewing the results of the Achilles R package.

Getting Started

There are a few configuration steps required to setup AchillesWeb. These steps assume that you have already run the Achilles R package to populate the statistics on your CDM instance.

1. Download AchillesWeb (e.g by clicking “Download ZIP” on the right side of this page), and extract to a folder accessible through a web server.

2. Create a 'data' directory in the root of your AchillesWeb folder and run the Achilles R package exportToJSON method specifying the output path to a subdirectory for the data source that you want to view through AchillesWeb. For example:

   rtToJson(connectionDetails,"CDM_SCHEMA", "RESULTS_SCHEMA", "C:/AchillesWeb/data/SAMPLE", cdmVersion = "cdm version")
   

   The “cdm version” can either be 4 or 5. The exportToJSON method will take a very long time if you haven't added the minimum recommended set of indexes to your cdm.

3. Create a file in the AchillesWeb 'data' directory named 'datasources.json' with the following structure where the name is a caption for the data source and the folder is the name of the subdirectory under data. You will have to update the datasources.json file whenever you add a new data source subfolder to the data directory. Note: cdmVersion property should be set to the version of the CDM datasource from the Achilles analysis. Valid values are 4 and 5. If the value is not found, it assumes cdmVersion = 4.

   datasources":[ { "name":"My Sample Database", "folder":"SAMPLE", "cdmVersion": 5 } ] } 
   

3: Access the AchillesWeb 'index.html' as a web page (i.e., via http:// rather than file://) and your data should load.

For more information see the Achilles wiki

Datasource Structure

In order to improve usability with other applications and file structures, var datasourcepath can be changed in index.html to the location of the file. Default is data/datasource.json but it can be changed to anything (including REST service) as long as it returns a json with a valid structure.

Datasource file structure also allows configurations with different parameters like url and map (and parentUrl).

Example

"datasources":  [ 
{ "name":"My Sample Folder", "folder":"SAMPLE", "cdmVersion": 4 },
{ "name":"My Sample URL", "url":"http://my-sample-server.com/SAMPLE", "cdmVersion": 5 },
{ "name":"My Sample Parent URL","parentUrl":"http://my-sample-server.com", "url":"SAMPLE" },
{ "name":"My Sample Map", "parentUrl":"http://my-sample-server.com/rest",
    "map": {
        "achillesheel" : {
            "type"  : "service",
            "url"   : "achillesheel/"
                },
        "condition_treemap" : {
            "type"  : "service",
            "url"   : "condition_treemap/"
        },
        "conditionera_treemap" : {
            "type"  : "service",
            "url"   : "conditionera_treemap/"
        },
        "drug_treemap" : {
            "type"  : "service",
            "url"   : "drug_treemap/"
        },
        "drugera_treemap" : {
            "type"  : "service",
            "url"   : "drugera_treemap/"
        },
        "observation_treemap" : {
            "type"  : "service",
            "url"   : "observation_treemap/"
        },
        "visit_treemap" : {
            "type"  : "service",
            "url"   : "visit_treemap/"
        },
        "procedure_treemap" : {
            "type"  : "service",
            "url"   : "procedure_treemap/"
        },
        "dashboard" : {
            "type"  : "service",
            "url"   : "dashboard/"
        },
        "datadensity" : {
            "type"  : "service",
            "url"   : "datadensity/"
        },
        "death" : {
            "type"  : "service",
            "url"   : "death/"
        },
        "person" : {
            "type"  : "service",
            "url"   : "person/"
        },
        "observationperiod" : {
            "type"  : "service",
            "url"   : "observationperiod/"
        },
        "conditioneras" : {
            "type"  : "collection",
            "url"   : "conditioneras/{id}/"
        },
        "conditions"    : {
            "type"  : "collection",
            "url"   : "conditions/{id}/"
        },
        "drugeras"      : {
            "type"  : "collection",
            "url"   : "drugeras/{id}/"
        },
        "drugs"         : {
            "type"  : "collection",
            "url"   : "drugs/{id}/"
        },
        "observations"  : {
            "type"  : "collection",
            "url"   : "observations/{id}/"
        },
        "procedures"    : {
            "type"  : "collection",
            "url"   : "procedures/{id}/"
        },
        "visits"        : {
            "type"  : "collection",
            "url"   : "visits/{id}/"
        }
    }
}

Different datasources behave differently but the expected json always follow the same structure.

• url and folder behave similarly but url allows the file structure not to be available on the data/ directory, allowing more flexibility.
• parentUrl is always prepended to url and map datasources. (Along with trailing / ).

Example:

|parentUrl | url | becames| |—|—|—| | | http://my-url.com/data | http://my-url.com/data/achillesheel.json | |http://my-url.com | data2 | http://my-url.com/data2/achillesheel.json |

• mapattribute allows the definition of different paths to different locations, including REST services.
  • each object in map has the location of each resource needed to build each report.
  • each object in map has two attributes, type and url:
    • type can be one of folder, collection, service or file
    • url allows patterns in folder or collection like {id} that will be replaced id of the each sample.

Example:

|parentUrl|type|url|becames| |—|—|—|—| |http://my-url.com/data|file|achillesheel.json| http://my-url.com/data/achillesheel.json | |http://my-url.com/rest|service| person/ | http://my-url.com/rest/person/| |http://my-url.com/data|folder| condition_{id}.json | http://my-url.com/data/condition_123.json| |http://my-url.com/rest|collection| drugs/{id}/ | http://my-url.com/rest/drugs/123|

License

Achilles is licensed under Apache License 2.0