added Sor NPI Relation parser

common/common/src/main/java/com/trifork/stamdata/specs/SorRelationsRecordSpecs.java

@@ -0,0 +1,45 @@
+/**
+ * The contents of this file are subject to the Mozilla Public
+ * License Version 1.1 (the "License"); you may not use this file
+ * except in compliance with the License. You may obtain a copy of
+ * the License at http://www.mozilla.org/MPL/
+ *
+ * Software distributed under the License is distributed on an "AS
+ * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
+ * implied. See the License for the specific language governing
+ * rights and limitations under the License.
+ *
+ * Contributor(s): Contributors are attributed in the source code
+ * where applicable.
+ *
+ * The Original Code is "Stamdata".
+ *
+ * The Initial Developer of the Original Code is Trifork Public A/S.
+ *
+ * Portions created for the Original Code are Copyright 2011,
+ * Lægemiddelstyrelsen. All Rights Reserved.
+ *
+ * Portions created for the FMKi Project are Copyright 2011,
+ * National Board of e-Health (NSI). All Rights Reserved.
+ */
+package com.trifork.stamdata.specs;
+
+import static com.trifork.stamdata.persistence.RecordSpecification.field;
+
+import com.trifork.stamdata.persistence.RecordSpecification;
+
+public final class SorRelationsRecordSpecs
+{
+    protected SorRelationsRecordSpecs() {}
+
+    public static final RecordSpecification RELATIONS_RECORD_SPEC = RecordSpecification.createSpecification("SORRelationer", "SORRelationerPID", 
+            field("sor_parent", 100),
+            field("sor_child", 100)
+    );
+
+    public static final RecordSpecification SHAK_YDER_RECORD_SPEC = RecordSpecification.createSpecification("SORYderSHAKRelationer", "SORYderSHAKRelationerPID", 
+            field("shak_yder", 100),
+            field("sor", 100)
+    );
+
+}

dodi/data-manager/src/main/java/com/trifork/stamdata/importer/jobs/sor/relations/SorRelationParser.java

@@ -0,0 +1,304 @@
+/**
+ * The contents of this file are subject to the Mozilla Public
+ * License Version 1.1 (the "License"); you may not use this file
+ * except in compliance with the License. You may obtain a copy of
+ * the License at http://www.mozilla.org/MPL/
+ *
+ * Software distributed under the License is distributed on an "AS
+ * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
+ * implied. See the License for the specific language governing
+ * rights and limitations under the License.
+ *
+ * Contributor(s): Contributors are attributed in the source code
+ * where applicable.
+ *
+ * The Original Code is "Stamdata".
+ *
+ * The Initial Developer of the Original Code is Trifork Public A/S.
+ *
+ * Portions created for the Original Code are Copyright 2011,
+ * Lægemiddelstyrelsen. All Rights Reserved.
+ *
+ * Portions created for the FMKi Project are Copyright 2011,
+ * National Board of e-Health (NSI). All Rights Reserved.
+ */
+package com.trifork.stamdata.importer.jobs.sor.relations;
+
+import static com.trifork.stamdata.Preconditions.checkNotNull;
+import static com.trifork.stamdata.importer.tools.SLALoggerHolder.getSLALogger;
+
+import java.io.File;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.inject.Inject;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+import oio.sundhedsstyrelsen.organisation._1_0.HealthInstitutionEntityType;
+import oio.sundhedsstyrelsen.organisation._1_0.HealthInstitutionType;
+import oio.sundhedsstyrelsen.organisation._1_0.InstitutionOwnerEntityType;
+import oio.sundhedsstyrelsen.organisation._1_0.InstitutionOwnerType;
+import oio.sundhedsstyrelsen.organisation._1_0.OrganizationalUnitEntityType;
+import oio.sundhedsstyrelsen.organisation._1_0.OrganizationalUnitType;
+import oio.sundhedsstyrelsen.organisation._1_0.SorStatusType;
+import oio.sundhedsstyrelsen.organisation._1_0.SorTreeType;
+
+import org.apache.log4j.Logger;
+import org.apache.log4j.MDC;
+import org.joda.time.DateTime;
+import org.mortbay.log.Log;
+
+import com.trifork.stamdata.importer.config.KeyValueStore;
+import com.trifork.stamdata.importer.parsers.Parser;
+import com.trifork.stamdata.importer.parsers.annotations.ParserInformation;
+import com.trifork.stamdata.importer.parsers.exceptions.OutOfSequenceException;
+import com.trifork.stamdata.importer.parsers.exceptions.ParserException;
+import com.trifork.stamdata.persistence.RecordBuilder;
+import com.trifork.stamdata.persistence.RecordPersister;
+import com.trifork.stamdata.persistence.RecordSpecification;
+import com.trifork.stamdata.specs.SorRelationsRecordSpecs;
+
+import dk.sdsd.nsp.slalog.api.SLALogItem;
+
+@ParserInformation(id = "sorRelation", name = "SorRelation")
+public class SorRelationParser implements Parser {
+
+    private final RecordSpecification recordSpecification;
+    private final RecordSpecification shakYderSpecification;
+    private final KeyValueStore keyValueStore;
+    private static Logger logger = Logger.getLogger(SorRelationParser.class);
+    private Map<String, String> selfRelationsMap;
+    private Map<String, HashSet<String>> shakYderMap;
+    private DateTime snapshotDate;
+
+    @Inject
+    SorRelationParser(KeyValueStore keyValueStore) {
+        this.keyValueStore = keyValueStore;
+        this.recordSpecification = SorRelationsRecordSpecs.RELATIONS_RECORD_SPEC;
+        this.shakYderSpecification = SorRelationsRecordSpecs.SHAK_YDER_RECORD_SPEC;
+    }
+
+    @Override
+    public void process(File dataSet, RecordPersister persister) throws OutOfSequenceException, ParserException,
+            Exception {
+
+        SLALogItem slaLogItem = getSLALogger().createLogItem("SorRelationParser", "dataSet");
+        try {
+            File files = checkRequiredFiles(dataSet);
+
+            List<InstitutionOwnerEntityType> list = unmarshallFile(files);
+            selfRelationsMap = new HashMap<String, String>();
+            shakYderMap = new HashMap<String, HashSet<String>>();
+            for (InstitutionOwnerEntityType institutions : list) {
+                persistInstitutionRelations(institutions, persister);
+            }
+            // persist institutions relations with self
+            Set<String> keys = selfRelationsMap.keySet();
+            for (String sorSelfRelationId : keys) {
+                persistNode(sorSelfRelationId, sorSelfRelationId, persister);
+            }
+
+            // persist collected shak/yder numbers
+            Set<String> syKeys = shakYderMap.keySet();
+            for (String shakYderKey : syKeys) {
+                persistShakYder(shakYderKey, shakYderMap.get(shakYderKey), persister);
+            }
+
+            slaLogItem.setCallResultOk();
+            slaLogItem.store();
+        } catch (Exception e) {
+            slaLogItem.setCallResultError("SorRelationParser Failed - Cause: " + e.getMessage());
+            slaLogItem.store();
+            throw e;
+        } finally {
+            selfRelationsMap = null;
+            shakYderMap = null;
+        }
+
+    }
+
+    private void persistInstitutionRelations(InstitutionOwnerEntityType institution, RecordPersister persister) throws SQLException {
+
+        InstitutionOwnerType owner = institution.getInstitutionOwner();
+        String ownerId = ""+owner.getSorIdentifier();
+        if(!hasValidPeriod(owner.getSorStatus())) {
+            Log.debug("Institution with SOR id:" +ownerId+"  is is no longer valid, toDate: "+owner.getSorStatus().getToDate());
+            return;
+        }
+
+        List<HealthInstitutionEntityType> childInstitutions = institution.getHealthInstitutionEntity();
+
+        selfRelationsMap.put(ownerId, "");
+
+        for (HealthInstitutionEntityType hiChild : childInstitutions) {
+            String childId = ""+hiChild.getHealthInstitution().getSorIdentifier();
+            persistNode(ownerId, childId, persister);
+
+            List<OrganizationalUnitEntityType> organizationalUnitEntity = hiChild.getOrganizationalUnitEntity();
+            for (OrganizationalUnitEntityType ouChild : organizationalUnitEntity) {
+                traverseOrganizationalUnitEntity(ownerId, ouChild, persister);
+            }
+            traverseHealthInstitutionChild(hiChild, persister);
+        }
+    }
+
+    private void traverseHealthInstitutionChild(HealthInstitutionEntityType child, RecordPersister persister) throws SQLException {
+        HealthInstitutionType healthInstitution = child.getHealthInstitution();
+
+        String hiChildId = ""+healthInstitution.getSorIdentifier();
+        if(!hasValidPeriod(healthInstitution.getSorStatus())) {
+            Log.debug("Institution with SOR id:" +hiChildId+" is no longer valid, toDate: "+healthInstitution.getSorStatus().getToDate());
+            return;
+        }
+
+        selfRelationsMap.put(hiChildId, "");
+
+        String shakIdentifier = healthInstitution.getShakIdentifier();
+        if(shakIdentifier != null && shakIdentifier.trim().length() > 0) {
+            putValueInShakYderMap("SHAK="+shakIdentifier, hiChildId);
+        }
+
+        List<OrganizationalUnitEntityType> organizationalUnitEntity = child.getOrganizationalUnitEntity();
+        for (OrganizationalUnitEntityType ouChild : organizationalUnitEntity) {
+            traverseOrganizationalUnitEntity(hiChildId, ouChild, persister);
+        }
+    }
+
+    private void traverseOrganizationalUnitEntity(String parentId, OrganizationalUnitEntityType ouChild, RecordPersister persister) throws SQLException {
+        OrganizationalUnitType ou = ouChild.getOrganizationalUnit();
+        String childId = ""+ou.getSorIdentifier();
+
+        if(!hasValidPeriod(ou.getSorStatus())) {
+            Log.debug("Institution with SOR id:" +ou+" is no longer valid, toDate: "+ou.getSorStatus().getToDate());
+            return;
+        }
+
+        // persist relation with owner and with self
+        persistNode(parentId, childId, persister);
+        selfRelationsMap.put(childId, "");
+
+        String shakIdentifier = ou.getShakIdentifier();
+        if(shakIdentifier != null && shakIdentifier.trim().length() > 0) {
+            putValueInShakYderMap("SHAK="+shakIdentifier, childId);
+        }
+        String yderIdentifier = ou.getProviderIdentifier();
+        if(yderIdentifier != null && yderIdentifier.trim().length() > 0) {
+            putValueInShakYderMap("Yder="+yderIdentifier, childId);
+        }
+
+        if(ouChild.getOrganizationalUnitEntity() != null) {
+            // first persist any existing childs with parent relation
+            List<OrganizationalUnitEntityType> subChilds = ouChild.getOrganizationalUnitEntity();
+            for (OrganizationalUnitEntityType subChild : subChilds) {
+                traverseOrganizationalUnitEntity(parentId, subChild, persister);
+            }
+            // then traverse recursively through childs;
+            List<OrganizationalUnitEntityType> subChilds2 = ouChild.getOrganizationalUnitEntity();
+            for (OrganizationalUnitEntityType subChild : subChilds2) {
+                String ouChildId = ""+ouChild.getOrganizationalUnit().getSorIdentifier();
+                traverseOrganizationalUnitEntity(ouChildId, subChild, persister);
+            }
+        }
+    }
+
+    private void persistNode(String parent, String child, RecordPersister persister) throws SQLException {
+        RecordBuilder OwnerRecord = new RecordBuilder(recordSpecification);
+        OwnerRecord.field("sor_parent", parent);
+        OwnerRecord.field("sor_child", child);
+        persister.persist(OwnerRecord.build(), recordSpecification);
+    }
+
+    private void persistShakYder(String shakYder, HashSet<String> sorSet, RecordPersister persister) throws SQLException {
+
+        if(shakYder == null) {
+            throw new IllegalArgumentException("SHAK or YDER must be set");
+        }
+
+        for (String sor : sorSet) {
+            RecordBuilder OwnerRecord = new RecordBuilder(shakYderSpecification);
+            OwnerRecord.field("shak_yder", shakYder);
+            OwnerRecord.field("sor", sor);
+            persister.persist(OwnerRecord.build(), shakYderSpecification);
+        }
+    }
+
+    private void putValueInShakYderMap(String shakYder, String sor) {
+
+        HashSet<String> sorSet = shakYderMap.get(shakYder);
+        if(sorSet == null) {
+            sorSet = new HashSet<String>();
+        }
+        sorSet.add(sor);
+        shakYderMap.put(shakYder, sorSet);
+    }
+
+
+    private boolean hasValidPeriod(SorStatusType sorStatus) {
+        if(sorStatus != null) {
+            XMLGregorianCalendar toDate = sorStatus.getToDate();
+            if(toDate != null) {
+                DateTime toDateTime = new DateTime(toDate.toGregorianCalendar().getTime());
+                if(snapshotDate.isAfter(toDateTime)) {
+                    return false;
+                }
+            }
+        }
+        // if toDate of sorStatus cannot be found assume entity is valid.
+        return true;
+    }
+
+    private List<InstitutionOwnerEntityType> unmarshallFile(File dataSet) {
+        List<InstitutionOwnerEntityType> list = new ArrayList<InstitutionOwnerEntityType>();
+
+        try {
+            JAXBContext jaxbContext = JAXBContext.newInstance(SorTreeType.class.getPackage().getName());
+            Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
+            File[] input = null;
+            if(dataSet.isDirectory()) {
+                 input = dataSet.listFiles();
+            } else {
+                input = new File[] {dataSet};
+            }
+
+            for (int i = 0; i < input.length; i++) {
+                JAXBElement<SorTreeType> jaxbSOR = (JAXBElement<SorTreeType>) jaxbUnmarshaller.unmarshal(input[i]);
+                SorTreeType sor = jaxbSOR.getValue();
+                snapshotDate = new DateTime(sor.getSnapshotDate().toGregorianCalendar().getTime());
+                List<InstitutionOwnerEntityType> institutionOwnerEntity = sor.getInstitutionOwnerEntity();
+                list.addAll(institutionOwnerEntity);
+            }
+        } catch (JAXBException e) {
+            logger.error("", e);
+        }
+        return list;
+    }
+
+    private File checkRequiredFiles(File dataSet) {
+
+       checkNotNull(dataSet);
+
+       File[] input = null;
+       if(dataSet.isDirectory()) {
+            input = dataSet.listFiles();
+       } else {
+           input = new File[] {dataSet};
+       }
+
+       for (int i = 0; i < input.length; i++) {
+           String fileName = input[i].getName();
+           MDC.put("filename", fileName);
+       }
+
+       return dataSet;
+    }
+
+}

dodi/data-manager/src/main/resources/com/trifork/stamdata/importer/jobs/sor/relations/jaxb.index

@@ -0,0 +1,3 @@
+SorTree
+InstitutionOwnerEntity
+InstitutionOwner

dodi/data-manager/src/main/resources/sorschema/ActivityAddressInformation.xsd

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8"?>
+<xs:schema xmlns="urn:oio:sundhedsstyrelsen:organisation:1.0.0" 
+           xmlns:xs="http://www.w3.org/2001/XMLSchema" 
+           targetNamespace="urn:oio:sundhedsstyrelsen:organisation:1.0.0" 
+           elementFormDefault="qualified" 
+           attributeFormDefault="unqualified" 
+           xml:lang="EN" >
+	<xs:include schemaLocation="AddressInformation.xsd"/>
+
+  <xs:element name="ActivityAddressInformation" type="AddressInformationType"/>
+</xs:schema>

dodi/data-manager/src/main/resources/sorschema/ActivityAddressInformation.xsd.meta.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Metadata xmlns="http://rep.oio.dk/infostructurebase/schemas/2004/09/13/">
+  <Title>ActivityAddressInformation</Title>
+  <DescriptionStructure>
+    <DescriptionEnglish />
+    <DescriptionDanish>Oplysninger om enhedens aktivitetsadresse. Aktivitetsadressen kan angives som værende den samme som enhedens besøgsadresse. Obligatorisk oplysning.</DescriptionDanish>
+  </DescriptionStructure>
+  <Author>Sundhedsstyrelsen, SOR</Author>
+  <LabelStructure>
+    <LabelDanish>Aktivitetsadresse</LabelDanish>
+  </LabelStructure>
+  <ObjectTerm>Adresse</ObjectTerm>
+  <PropertyTerm></PropertyTerm>
+  <RepresentationTerm></RepresentationTerm>
+  <Version>1.0.0</Version>
+</Metadata>
+