EP extensions

[epuzanov]

This PR add following GSRS extensions from https://github.com/epuzanov/gsrs-ep-substance-extension repository.

gsrs.module.substance.exporters.GsrsApiExporterFactory

The GsrsApiExporter can be used for the exporting of the substances directly to anothe GSRS instance.

Dependencies

• org.apache.httpcomponents.httpclient

Configuration

ix.ginas.export.exporterfactories.substances += {
    "exporterFactoryClass": "gsrs.module.substance.exporters.GsrsApiExporterFactory",
    "parameters": {
        "format": {
            "extension": "gsrsapi",
            "displayName": "Send to ..."
        },
        "headers": {
            #"auth-username": "admin",
            #"auth-password": "admin",
            #"AUTHENTICATION_HEADER_NAME_EMAIL": "{{user.email}}",
            "auth-username": "{{user.name}}",
            "auth-key": "{{user.apikey}}"

        },
        "baseUrl": "https://public.gsrs.test/api/v1/substances",
        "timeout": 120000,
        "trustAllCerts": false,
        "allowedRole": "Approver",
        "newAuditor": "admin",
        "changeReason": "{{changeReason}} (Version {{version}})",
        "validate": true
    }
}

gsrs.module.substance.exporters.JmespathSpreadsheetExporterFactory

The JmespathSpreadsheetExporter can to be used for exporting substances to Excel file with custom defined fields. It uses Jmespath expressions to select values from substances json.

Dependencies

• io.burt.jmespath-jackson

Configuration

ix.ginas.export.exporterfactories.substances += {
    "exporterFactoryClass": "gsrs.module.substance.exporters.JmespathSpreadsheetExporterFactory",
    "parameters": {
        "format": {
            "extension": "custom.xlsx",
            "displayName": "Custom Report (xlsx) File"
        },
        "columnExpressions": [
            {"name":"UUID", "expression":"uuid"},
            {"name":"NAME", "expression":"_name"},
            {"name":"APPROVAL_ID", "expression":"_approvalIDDisplay"},
            {"name":"SMILES", "expression":"structure.smiles"},
            {"name":"FORMULA", "expression":"structure.formula"},
            {"name":"SUBSTANCE_TYPE", "expression":"substanceClass"},
            {"name":"STD_INCHIKEY", "expression":"structure.inchikey"},
            {"name":"STD_INCHIKEY_FORMATTED", "expression":"structure.inchikeyf"},
            {"name":"CAS", "expression":"codes[?codeSystem=='CAS'].code","delimiter":"|"},
            {"name":"EC", "expression":"codes[?codeSystem=='ECHA (EC/EINECS)'].code"},
            {"name":"ITIS", "expression":"codes[?codeSystem=='ITIS'].code"},
            {"name":"NCBI", "expression":"codes[?codeSystem=='NCBI TAXONOMY'].code"},
            {"name":"USDA_PLANTS", "expression":"codes[?codeSystem=='USDA PLANTS'].code"},
            {"name":"INN", "expression":"codes[?codeSystem=='INN'].code"},
            {"name":"NCI_THESAURUS", "expression":"codes[?codeSystem=='NCI_THESAURUS'].code"},
            {"name":"RXCUI", "expression":"codes[?codeSystem=='RXCUI'].code"},
            {"name":"PUBCHEM", "expression":"codes[?codeSystem=='PUBCHEM'].code"},
            {"name":"MPNS", "expression":"codes[?codeSystem=='MPNS'].code"},
            {"name":"GRIN", "expression":"codes[?codeSystem=='GRIN'].code"},
            {"name":"INGREDIENT_TYPE", "expression":"relationships[?contains(['IONIC MOIETY', 'MOLECULAR FRAGMENT', 'UNSPECIFIED INGREDIENT', 'SPECIFIED SUBSTANCE'], type)].type || 'INGREDIENT SUBSTANCE'"},
            {"name":"PROTEIN_SEQUENCE", "expression":"protein.subunits[].sequence", "delimiter":"|"},
            {"name":"NUCLEIC_ACID_SEQUENCE", "expression":"nucleicAcid.subunits[].sequence", "delimiter":"|"},
            {"name":"RECORD_ACCESS_GROUPS", "expression":"access", "delimiter":"|"},
            {"name":"LAST_EDITED", "expression":"lastEdited", "datetime":"yyyy-MM-dd HH:mm:ss"}
        ]
    }
}

gsrs.module.substance.indexers.JmespathIndexValueMaker

The JmespathIndexvalueMaker canbe used for creating of the custom indexes. It uses Jmespath expressions to select values from substances json.

Dependencies

• io.burt.jmespath-jackson

Configuration

gsrs.indexers.list += {
    "class" = "ix.ginas.models.v1.Substance",
    "indexer" = "gsrs.module.substance.indexers.JmespathIndexValueMaker",
    "parameters" = {
        "expressions" = [
            {"index":"ATC Level 1", "expression": "codes[?codeSystem=='WHO-ATC' && starts_with(comments, 'ATC|')].comments", "regex":"ATC.([^\\Q|\\E]*).*"},
            {"index":"ATC Level 2", "expression": "codes[?codeSystem=='WHO-ATC' && starts_with(comments, 'ATC|')].comments", "regex":"ATC.[^\\Q|\\E]*.([^\\Q|\\E]*).*"},
            {"index":"ATC Level 3", "expression": "codes[?codeSystem=='WHO-ATC' && starts_with(comments, 'ATC|')].comments", "regex":"ATC.[^\\Q|\\E]*.[^\\Q|\\E]*.([^\\Q|\\E]*).*"},
            {"index":"ATC Level 4", "expression": "codes[?codeSystem=='WHO-ATC' && starts_with(comments, 'ATC|')].comments", "regex":"ATC.[^\\Q|\\E]*.[^\\Q|\\E]*.[^\\Q|\\E]*.([^\\Q|\\E]*).*"},
            {"index":"Naming Orgs", "expression": "names[?type=='of'].nameOrgs[]"},
            {"index":"Name TypeLang", "expression": "names[?type=='of'].languages[].join('_', ['of', @])"},
            {"index":"Name TypeLang", "expression": "names[?type=='sys'].languages[].join('_', ['sys', @])"},
            {"index":"Name TypeLang", "expression": "names[?type=='cn'].languages[].join('_', ['cn', @])"},
            {"index":"Name TypeLang", "expression": "names[?type=='bn'].languages[].join('_', ['bn', @])"},
            {"index":"Name TypeLang", "expression": "names[?type=='cd'].languages[].join('_', ['od', @])"},
            {"index":"Reference Tags", "expression": "references[].tags[]"},
            {"index":"Molecular Weight", "expression": "properties[?starts_with(name, 'MOL_WEIGHT')].floor(value.average)", "ranges": "0 200 400 600 800 1000", "format": "%1$.0f", "sortable":true},
            {"index":"root_structure_mwt", "type": "Double", "expression": "properties[?starts_with(name, 'MOL_WEIGHT')].value.average", "sortable":true},
            {"index":"Deprecated", "expression": "[map(&'Deprecated',[deprecated][?@]),'Not Deprecated'][] | @[0]"}
        ]
    }
}

gsrs.module.substance.processors.CVClassificationsCodeProcessor

The CVClassificationsCodeProcessor can be used for creating the comment string for classification codes.

Configuration

gsrs.entityProcessors += {
    "entityClassName" = "ix.ginas.models.v1.Code",
    "processor" = "gsrs.module.substance.processors.CVClassificationsCodeProcessor",
    "with" = {
        "codeSystem" = "WHO-ATC",
        "prefix" = "ATC",
        "masks" = [1, 3, 4, 5],
        "terms" = {
            "C" = "Cardiovascular system",
            "C01" = "Cardiac therapy",
            "C01E" = "Other cardiac preparations",
            "C01EB" = "Other cardiac preparations",
            "C01EB16" = "Ibuprofen",
            "G" = "Genito urinary system and sex hormones",
            "G02" = "Other gynecologicals",
            "G02C" = "Other gynecologicals",
            "G02CC" = "Antiinflammatory products for vaginal administration",
            "G02CC01" = "Ibuprofen",
            "M" = "Musculo-skeletal system",
            "M01" = "Antiinflammatory and antirheumatic products",
            "M01A" = "Antiinflammatory and antirheumatic products, non-steroids",
            "M01AE" = "Propionic acid derivatives",
            "M01AE01" = "Ibuprofen",
            "M01AE51" = "Ibuprofen, combinations",
            "N" = "Nervous system",
            "N02" = "Analgesics",
            "N02A" = "Opioids",
            "N02AJ" = "Opioids in combination with non-opioid analgesics",
            "N02AJ08" = "Codeine and Ibuprofen",
            "N02AJ19" = "Oxycodone and Ibuprofen",
            "N04" = "Anti-parkinson",
            "N04B" = "Dopaminergic agents",
            "N04BC" = "Dopamine agonists",
            "N04BC05" = "Pramipexole"
        }
    }
}

Alternative Configuration 1

Include Veterinary ATC codes dictionary from JSON file include LEVEL 5 codes.

gsrs.entityProcessors += {
    "entityClassName" = "ix.ginas.models.v1.Code",
    "processor" = "gsrs.module.substance.processors.CVClassificationsCodeProcessor",
    "with" = {
        "codeSystem" = "WHO-VATC",
        "prefix" = "VATC",
        "masks" = [2, 4, 5, 6, 8],
        "terms" = { include "vatcCodes.json" }
    }
}

Alternative Configuration 2

Use the GSRS CV for storing ATC Classification information. And initially populate the CV from the JSON file if the cvVersion is greater then the version of the CV Domain.

gsrs.entityProcessors += {
    "entityClassName" = "ix.ginas.models.v1.Code",
    "processor" = "gsrs.module.substance.processors.CVClassificationsCodeProcessor",
    "with" = {
        "codeSystem" = "WHO-ATC",
        "prefix" = "ATC",
        "masks" = [1, 3, 4, 5],
        "cvDomain": "CLASSIFICATION_WHO_ATC",
        "cvVersion": 2,
        "terms" = { include "atcCodes.json" }
    }
}

gsrs.module.substance.processors.DBClassificationsCodeProcessor

The DBClassificationsCodeProcessor can be used for creating the comment string for classification codes using SQL database as the source. The query must return 4 fields.
The first field contains COMMENTS text, the second field contains URL, the third field contains DOC_TYPE of the Reference and the fourth field contains CITATION of the Reference.
The second, third and fourth fields can return NULL values.

Configuration

gsrs.entityProcessors += {
    "entityClassName" = "ix.ginas.models.v1.Code",
    "processor" = "gsrs.module.substance.processors.DBClassificationsCodeProcessor",
    "with" = {
        "codeSystem" = "PV",
        "query" = """SELECT
'ROOT|' || SUB_CATEGORY || '|' || CLASSIFICATION,
URL,
REF_DOC_TYPE,
REF_CITATION
FROM CLASSIFICATIONS
WHERE CODE = ?
""",
        "datasource" = {
            "url" = "jdbc:oracle:thin:@//db-server:1521/CLASSIFICATIONS",
            "username" = "gsrs",
            "password" = "somepassword"
        }
    }
}

gsrs.module.substance.processors.SetAccessCodeProcessor

The SetAccessCodeProcessor can be used to force the access value for the specific code system.

Configuration

gsrs.entityProcessors += {
    "class":"ix.ginas.models.v1.Code",
    "processor":"gsrs.module.substance.processors.SetAccessCodeProcessor",
    "with":{
        "codeSystemAccess": {
            "BDNUM": ["protected"],
            "*": []
        }
    }
}

gsrs.module.substance.tasks.UpdateEntityTaskInitializer

The UpdateEntityTaskInitializer task can be used for updating attributes from any Entity class in the GSRS
The optional parameter "query" can be used for granular selection of the objects.
The optional parameter "resetFields" can be used to nullify specified fields before invoking the "preUpdate" method.

Configuration

gsrs.scheduled-tasks.list+= {
    "scheduledTaskClass" : "gsrs.module.substance.tasks.UpdateEntityTaskInitializer",
    "parameters" : {
        "entityClass": "ix.ginas.models.v1.Code",
        "query": "select uuid from Code where codeSystem = 'CAS'",
        "resetFields": ["url"],
        "autorun": false
    }
}

ix.ginas.utils.validation.validators.JmespathValidator

The JmespathValidator can to be used for creating the custom GSRS validations rules. It uses Jmespath expressions to validate the substances json.

Dependencies

• io.burt.jmespath-jackson

Configuration

gsrs.validators.substances += {
    "validatorClass" = "ix.ginas.utils.validation.validators.JmespathValidator",
    "newObjClass" = "ix.ginas.models.v1.Substance",
    "configClass" = "SubstanceValidatorConfig",
    "parameters"= {
        "expressions" = [
            {"messageType": "ERROR", "messageTemplate": "Only single %s Code allowed.", "expression": "new.codes[?type=='PRIMARY' && codeSystem=='MyCodeSystem'].codeSystem | [1]"},
            {"messageType": "ERROR", "messageTemplate": "The MyCodeSystem Code can not be changed.", "expression": "values(@)[*].codes[?type=='PRIMARY' && codeSystem=='MyCodeSystem'].code | [] | [0] != [1] && [1] != `null`"},
            {"messageType": "ERROR", "messageTemplate": "More then One Note with Public Reference is not allowed.", "expression": "new.notes[?length(references[? publicDomain==`true` && contains(tags, 'PUBLIC_DOMAIN_RELEASE') && length(access) == `0`]) > `0`].note | [1]"}.
            {"messageType": "ERROR", "messageTemplate": "Non Public records must have a PUBLIC DOMAIN reference without a '%s' tag", "expression": "to_array(new)[?length(access) > `0`].references[] | [? publicDomain==`true` && contains(tags, 'PUBLIC_DOMAIN_RELEASE') && length(access) == `0`].tags[0]"}
        ]
    }
}