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Factored out creating of QUDT-formatted activities
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| import groovy.sql.Sql | ||
| import org.openrdf.repository.Repository | ||
| import org.openrdf.repository.sail.SailRepository | ||
| import org.openrdf.sail.memory.MemoryStore | ||
| import org.openrdf.model.vocabulary.RDFS | ||
| import org.openrdf.model.vocabulary.RDF | ||
| import org.openrdf.rio.ntriples.NTriplesWriter | ||
| import com.github.jqudt.Quantity | ||
| import com.github.jqudt.onto.UnitFactory | ||
|
|
||
| // export CLASSPATH=$(JARS=(*.jar); IFS=:; echo "${JARS[*]}") | ||
|
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||
| def props = new Properties() | ||
| new File("vars.properties").withInputStream { stream -> props.load(stream) } | ||
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| def url = "jdbc:mysql://localhost/" + props.dbprefix + props.version | ||
| def sql = Sql.newInstance(url, props.user, props.pwd, "com.mysql.jdbc.Driver") | ||
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||
| allMolregno = "SELECT DISTINCT * FROM activities " + props.limit | ||
|
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| unitMappings = [ | ||
| nM:"http://www.openphacts.org/units/Nanomolar", | ||
| uM:"http://www.openphacts.org/units/Micromolar", | ||
| mM:"http://www.openphacts.org/units/Millimolar", | ||
| pM:"http://www.openphacts.org/units/Picomolar", | ||
| "%":"http://qudt.org/schema/qudt#floatPercentage", | ||
| "ug.mL-1":"http://www.openphacts.org/units/MicrogramPerMilliliter", | ||
| "ug/ml":"http://www.openphacts.org/units/MicrogramPerMilliliter", | ||
| "ug ml-1":"http://www.openphacts.org/units/MicrogramPerMilliliter", | ||
| "pg ml-1":"http://www.openphacts.org/units/PicogramPerMilliliter", | ||
| ] | ||
|
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||
| normalizationMappings = [ | ||
| "IC50" : [ | ||
| nM:"nM", | ||
| uM:"nM", | ||
| mM:"nM", | ||
| pM:"nM", | ||
| "ug.mL-1":"ug/ml", | ||
| "ug/ml":"ug/ml", | ||
| "ug ml-1":"ug/ml", | ||
| "pg ml-1":"ug/ml", | ||
| "%":"%" | ||
| ], | ||
| "Potency" : [ | ||
| M:"uM", | ||
| uM:"uM", | ||
| nM:"uM", | ||
| mM:"uM", | ||
| "%":"%" | ||
| ] | ||
| ] | ||
|
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||
| ACT = props.rooturi + "activity/" | ||
| RES = props.rooturi + "resource/" | ||
| ONTO = "http://rdf.farmbio.uu.se/chembl/onto/#" | ||
| CITO = "http://purl.org/spar/cito/" | ||
| MOL = props.rooturi + "molecule/" | ||
| CHEMBL = props.rooturi + "chemblid/" | ||
| ASS = props.rooturi + "assay/" | ||
| OPS = "http://www.openphacts.org/chembl/onto/#" | ||
|
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| unitFactory = UnitFactory.getInstance(); | ||
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| sql.eachRow(allMolregno) { row -> | ||
| def repos = new SailRepository(new MemoryStore()) | ||
| repos.initialize() | ||
| con = repos.getConnection(); | ||
| factory = repos.getValueFactory(); | ||
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| actURI = factory.createURI(ACT + "a" + row.activity_id) | ||
|
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| if (row.standard_value) { | ||
| type = row.standard_type | ||
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| // now do the units: check if we need to use QUDT and if we normalize | ||
| units = row.standard_units | ||
| if (units != null && unitMappings.containsKey(units)) { | ||
| qudtUnits = unitMappings.get(units) | ||
|
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||
| // first output the value as QUDT | ||
| con.add(actURI, | ||
| factory.createURI(OPS + "standardValue"), | ||
| factory.createLiteral((double)row.standard_value) | ||
| ) | ||
| con.add(actURI, | ||
| factory.createURI(OPS + "standardUnit"), | ||
| factory.createURI(qudtUnits) | ||
| ) | ||
|
|
||
| // now see if I can normalize things | ||
| originalUnit = unitFactory.getUnit(qudtUnits) | ||
| if (originalUnit != null) { | ||
| if (originalUnit.abbreviation == null) originalUnit.abbreviation = units | ||
| quantity = new Quantity(row.standard_value, originalUnit); | ||
|
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||
| if (normalizationMappings.containsKey(type)) { | ||
| // normalize the value, if we know how | ||
| if (normalizationMappings[type] != null && normalizationMappings[type][units] != null) { | ||
| normalizedUnit = unitFactory.getUnit(unitMappings[normalizationMappings[type][units]]) | ||
| if (normalizedUnit != null & normalizedUnit != originalUnit) { | ||
| normalizedQuantity = quantity.convertTo(normalizedUnit) | ||
| con.add(actURI, | ||
| factory.createURI(OPS + "normalisedValue"), | ||
| factory.createLiteral(normalizedQuantity.value) | ||
| ) | ||
| con.add(actURI, | ||
| factory.createURI(OPS + "normalisedUnit"), | ||
| factory.createURI(normalizedUnit.resource.toString()) | ||
| ) | ||
| } | ||
| } else { | ||
| println "# WARN: wanting to normalize $type $units, but no normalization found: " + normalizationMappings[type] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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||
| con.export(new NTriplesWriter(System.out)) | ||
| con.close() | ||
| repos.shutDown() | ||
| } |
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