config.json

{
   "name": "Pedigree Editor Module",
   "namespace": "AEHRC\\PedigreeEditorExternalModule", 
   "description": "This module will allow the use of a pedigree editor to build a pedigree diagram, saving the diagram into a field with the tag @PEDIGREE_EDITOR",
   "authors": [
       {
            "name": "David Conlan",
            "email": "david.conlan@csiro.au",
            "institution": "Commonwealth Science & Industrial Research Organisation"
        },
   	 	{
            "name": "Maryam Mehdizadeh",
            "email": "maryam.mehdizadeh@csiro.au",
            "institution": "Commonwealth Science & Industrial Research Organisation"
        }           
    ],
    "permissions": [
        "redcap_data_entry_form", "redcap_survey_page"
    ],
    "system-settings" : [
		{
			"key" : "action_tag_info",
			"name" : "Three action tags will be enabled for notes<ul><li><b>'@PEDIGREE_HPO'</b> - A pedigree diagram using HPO and OMIM coding systems</li><li><b>'@PEDIGREE_SCT'</b> - A pedigree diagram using SNOMED-CT coding system</li><li><b>'@PEDIGREE'</b> - A pedigree diagram using the project configured default coding systems.</li></ul>The default 'Hide Text' flag can be overriden in the action tag by appending <ul><li><b>=HIDE_TEXT</b> - Hide the text area.</li><li><b>=SHOW_TEXT</b> - Show the text area.</li></ul>An action tag of <b>@PEDIGREE_HPO=HIDE_TEXT</b> will use the HPO code system and hide the text area for the field.",
			"type" : "descriptive"
		},
		{
			"key" : "hide_text_info",
			"name" : "The Hide Text flag indicates if the text area containing the FHIR representation of the diagram should be hidden.<br>The default 'Hide Text' flag can be overriden in the action tag by appending <ul><li><b>=HIDE_TEXT</b> - Hide the text area.</li><li><b>=SHOW_TEXT</b> - Show the text area.</li></ul>An action tag of <b>@PEDIGREE_HPO=HIDE_TEXT</b> will use the HPO code system and hide the text area for the field.",
			"type" : "descriptive"
		},
		{
			"key" : "hide_text",
			"name" : "Hide Text",
			"type" : "checkbox"
		},
		{
			"key" : "system_allow_edit",
			"name" : "Allow manual entry",
			"type" : "checkbox"
		},
		{
			"key" : "system_format_info",
			"name" : "The original version of this plugin used a custom FHIR format, in version 0.3 this was changed to a format defined by GA4GH. The format field allows the format to be selected, <i><b>fhir_v1</b></i> is the old format, while <i><b>GA4GH</b></i> is the new format. If <i><b>GA4GH</b></i> is selected it will still read the old format. The new format is recommended and has better round tripping. In version 0.4 five new formats were added, <i><b>PED</b></i>, <i><b>PEDX</b></i>, <i><b>DADA2</b></i>, <i><b>DADA2X</b></i> and <i><b>internal</b></i>. <i><b>PED</b></i> is a very simple format that only captures the base structure of the pedigree, but could be used to default the value of the field based on other fields in the instrument. <i><b>PEDX</b></i> is an extension to this that wraps the <i><b>PED</b></i> format in an XML document to allow the resulting SVG image produced to also be stored. <i><b>DADA2</b></i> and <i><b>DADA2X</b></i> are a customization of the PED format for use at DADA2.org. It includes an extra field for life status. Finally <i><b>internal</b></i> uses the openpedigree internal json model which is not documented and may not be compatible with future versions of the external module but should allow the best round tripping. This format and PED do not include a svg version of the pedigree diagram so will not show the diagram except when the diagram is saved into the system.",
			"type" : "descriptive"
		},
		{
			"key" : "system_format",
			"name" : "Storage Format",
			"type": "dropdown",
			"choices": [
				{ "value": "fhir_v1", "name": "fhir_v1 - Legacy FHIR Format"},
				{ "value": "GA4GH", "name": "GA4GH - Recommended FHIR Format"},
				{ "value": "PED", "name": "PED Format"},
				{ "value": "PEDX", "name": "PEDX - XML format PED and possible SVG Image"},
				{ "value": "DADA2", "name": "DADA2 Format"},
				{ "value": "DADA2X", "name": "DADA2X - XML format DADA2 and possible SVG Image"},
				{ "value": "internal", "name": "Open-pedigree internal format - may break with new version of EM"}
			]
		},
		{
			"key" : "compression_info",
			"name" : "A complicated pedigree may be large, the compress data setting indicates if the data should be compressed.<br>The default 'Compress Data' value can be overridden in the action tag by appending <ul><li><b>=NEVER_COMPRESS</b> - Never Compress.</li><li><b>=COMPRESS_LARGE</b> - Compress Large Diagrams >65K.</li><li><b>=ALWAYS_COMPRESS</b> - Always Compress</li></ul>An action tag of <b>@PEDIGREE_HPO=ALWAYS_COMPRESS</b> will always compress the data in the field.",
			"type" : "descriptive"
		},
		{
			"key" : "system_compression",
			"name" : "Compress Data",
			"type": "dropdown",
			"choices": [
				{ "value": "never", "name": "Never Compress"},
				{ "value": "large", "name": "Compress Large Diagrams >65K"},
				{ "value": "always", "name": "Always Compress"}
			]
		},
		{
			"key" : "system_ontology_server_info",
			"name" : "The Ontology Server URL setting indicates the server to use to lookup disorders and phenotypes, leaving blank will result in the default value of <b>'https://r4.ontoserver.csiro.au/fhir'</b>",
			"type" : "descriptive"
		},
		{
			"key" : "system_ontology_server",
			"name" : "Ontology Server URL",
			"type" : "text"
		},
		{
			"key": "authentication_type_info",
			"name": "The fhir server may require some form of authentication, currently only OAuth2 Client Credentials is supported. Communication with the FHIR server is made by the redcap server, not the users browser.",
			"type": "descriptive"
		},
		{
			"key": "authentication_type",
			"name": "Authentication Type",
			"required": true,
			"type": "dropdown",
			"choices": [
				{
					"value": "none",
					"name": "No Authentication Required"
				},
				{
					"value": "cc",
					"name": "OAuth2 Client Credentials"
				}
			]
		},
		{
			"key": "cc_token_endpoint",
			"name": "OAuth2 token endpoint",
			"type": "text",
			"branchingLogic": {
				"field": "authentication_type",
				"value": "cc"
			}
		},
		{
			"key": "cc_client_id",
			"name": "Client Id",
			"type": "text",
			"branchingLogic": {
				"field": "authentication_type",
				"value": "cc"
			}
		},
		{
			"key": "cc_client_secret",
			"name": "Client Secret",
			"type": "text",
			"branchingLogic": {
				"field": "authentication_type",
				"value": "cc"
			}
		},
		{
			"key" : "terminology_info",
			"name" : "FHIR valuesets to use for disorders, phenotypes and genes to use for @PEDIGREE tag.",
			"type" : "descriptive"
		},
		{
			"key": "system_def_terminology",
			"name": "Default Terminology",
			"required": true,
			"type": "dropdown",
			"choices": [
				{
					"value": "SCT",
					"name": "SnomedCT"
				},
				{
					"value": "HPO",
					"name": "HPO + omim"
				},
				{
					"value": "CUSTOM",
					"name": "Custom"
				}
			]
		},
		{
			"key" : "system_custom_terminology_info",
			"name" : "Custom terminology requires a code system, valueset and valid code regular expression to be defined for disorders, phenotypes and genes.<br/>A regular expression of '.+' should be used if the code systems values are not regular.<br/>The following values are used for HPO and SCT tags:<br/><table><tr><th>Entry</th><th>Code System</th><th>Valueset</th><th>Regex</th></tr><tr><td>OMIM (HPO Disorder)</td><td>http://www.omim.org</td><td>http://www.omim.org?vs</td><td>[0-9]+</td></tr><tr><td>HPO (HPO Phenotype)</td><td>http://purl.obolibrary.org/obo/hp.fhir</td><td>http://purl.obolibrary.org/obo/hp.fhir?vs</td><td>^(http:\\/\\/)|(HP:)</td></tr><tr><td>Gene</td><td>http://www.genenames.org/geneId</td><td>http://www.genenames.org/geneId?vs</td><td>^HGNC:</td></tr><tr><td>SnomedCT (SCT Disorder)</td><td>http://snomed.info/sct</td><td>http://snomed.info/sct?fhir_vs=refset/32570581000036105</td><td>[0-9]+</td></tr><tr><td>SnomedCT (SCT Phenotype)</td><td>http://snomed.info/sct</td><td>http://ga4gh.org/fhir/ValueSet/phenotype</td><td>[0-9]+</td></tr></table>",
			"type" : "descriptive",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_disorder_system",
			"name": "Disorder Code System",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_disorder_valueset",
			"name": "Disorder Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_disorder_regex",
			"name": "Disorder Regex",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_phenotype_system",
			"name": "Phenotype Code System",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_phenotype_valueset",
			"name": "Phenotype Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_phenotype_regex",
			"name": "Phenotype Regex",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_gene_system",
			"name": "Gene Code System",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_gene_valueset",
			"name": "Gene Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "system_gene_regex",
			"name": "Gene Regex",
			"type": "text",
			"branchingLogic": {
				"field": "system_def_terminology",
				"value": "CUSTOM"
			}
		}
	],
	"project-settings" : [
		{
			"key" : "project_allow_edit",
			"name" : "Allow manual entry",
			"type" : "checkbox"
		},
		{
			"key" : "project_format_info",
			"name" : "The original version of this plugin used a custom FHIR format, in version 0.3 this was changed to a format defined by GA4GH. The format field allows the format to be selected, <i><b>fhir_v1</b></i> is the old format, while <i><b>GA4GH</b></i> is the new format. If <i><b>GA4GH</b></i> is selected it will still read the old format. The new format is recommended and has better round tripping. In version 0.4 five new formats were added, <i><b>PED</b></i>, <i><b>PEDX</b></i>, <i><b>DADA2</b></i>, <i><b>DADA2X</b></i> and <i><b>internal</b></i>. <i><b>PED</b></i> is a very simple format that only captures the base structure of the pedigree, but could be used to default the value of the field based on other fields in the instrument. <i><b>PEDX</b></i> is an extension to this that wraps the <i><b>PED</b></i> format in an XML document to allow the resulting SVG image produced to also be stored. <i><b>DADA2</b></i> and <i><b>DADA2X</b></i> are a customization of the PED format for use at DADA2.org. It includes an extra field for life status. Finally <i><b>internal</b></i> uses the openpedigree internal json model which is not documented and may not be compatible with future versions of the external module but should allow the best round tripping. This format and PED do not include a svg version of the pedigree diagram so will not show the diagram except when the diagram is saved into the system.",
			"type" : "descriptive"
		},
		{
			"key" : "project_format",
			"name" : "Storage Format",
			"type": "dropdown",
			"choices": [
				{ "value": "fhir_v1", "name": "fhir_v1 - Legacy Format"},
				{ "value": "GA4GH", "name": "GA4GH - Recommended Format"},
				{ "value": "PED", "name": "PED Format"},
				{ "value": "PEDX", "name": "PEDX - XML format PED and possible SVG Image"},
				{ "value": "DADA2", "name": "DADA2 Format"},
				{ "value": "DADA2X", "name": "DADA2X - XML format DADA2 and possible SVG Image"},
				{ "value": "internal", "name": "Open-pedigree internal format"}
			]
		},
		{
			"key" : "project_compression",
			"name" : "Compress Data",
			"type": "dropdown",
			"choices": [
				{ "value": "never", "name": "Never compress"},
				{ "value": "large", "name": "Compress Large Diagrams >65K"},
				{ "value": "always", "name": "Always compress"}
			]
		},
		{
			"key" : "project_terminology_info",
			"name" : "FHIR valuesets to use for disorders, phenotypes and genes to use for @PEDIGREE tag.",
			"type" : "descriptive"
		},
		{
			"key": "project_def_terminology",
			"name": "Default Terminology",
			"type": "dropdown",
			"choices": [
				{
					"value": "SYSTEM",
					"name": "System Default"
				},
				{
					"value": "SCT",
					"name": "SnomedCT"
				},
				{
					"value": "HPO",
					"name": "HPO + omim"
				},
				{
					"value": "CUSTOM",
					"name": "Custom"
				}
			]
		},
		{
			"key" : "project_custom_terminology_info",
			"name" : "Custom terminology requires a code system, valueset and valid code regular expression to be defined for disorders, phenotypes and genes.<br/>A regular expression of '.+' should be used if the code systems values are not regular.<br/>The following values are used for HPO and SCT tags:<br/><table><tr><th>Entry</th><th>Code System</th><th>Valueset</th><th>Regex</th></tr><tr><td>OMIM (HPO Disorder)</td><td>http://www.omim.org</td><td>http://www.omim.org?vs</td><td>[0-9]+</td></tr><tr><td>HPO (HPO Phenotype)</td><td>http://purl.obolibrary.org/obo/hp.fhir</td><td>http://purl.obolibrary.org/obo/hp.fhir?vs</td><td>^(http:\\/\\/)|(HP:)</td></tr><tr><td>Gene</td><td>http://www.genenames.org/geneId</td><td>http://www.genenames.org/geneId?vs</td><td>^HGNC:</td></tr><tr><td>SnomedCT (SCT Disorder)</td><td>http://snomed.info/sct</td><td>http://snomed.info/sct?fhir_vs=refset/32570581000036105</td><td>[0-9]+</td></tr><tr><td>SnomedCT (SCT Phenotype)</td><td>http://snomed.info/sct</td><td>http://ga4gh.org/fhir/ValueSet/phenotype</td><td>[0-9]+</td></tr></table>",
			"type" : "descriptive",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_disorder_system",
			"name": "Disorder Code System",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_disorder_valueset",
			"name": "Disorder Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_disorder_regex",
			"name": "Disorder Regex",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_phenotype_system",
			"name": "Phenotype Code System",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_phenotype_valueset",
			"name": "Phenotype Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_phenotype_regex",
			"name": "Phenotype Regex",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_gene_system",
			"name": "Gene Code System",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_gene_valueset",
			"name": "Gene Value Set",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		},
		{
			"key": "project_gene_regex",
			"name": "Gene Regex",
			"type": "text",
			"branchingLogic": {
				"field": "project_def_terminology",
				"value": "CUSTOM"
			}
		}
	],
	"no-auth-pages": [
		"TerminologyService"
	],

  "compatibility": {
    "php-version-min" : "5.4.0",
    "redcap-version-min": "8.8.1",
    "framework-version": 1
  }
}