add evolution plugin

build.gradle

@@ -17,10 +17,6 @@ buildscript {
 apply plugin: "application"
 apply plugin: "org.biocode.fims-web"
 
-if (!project.hasProperty('fimsEvolutionVersion')) {
-    ext.fimsEvolutionVersion = "1.0.2"
-}
-
 fims {
     maven {
         username mavenUser
@@ -57,6 +53,7 @@ dependencies {
     compile 'com.ibm.icu:icu4j:3.4.4'
 
     compile group: 'org.parboiled', name: 'parboiled-java', version: '1.1.8'
+    compile group: 'com.auth0', name: 'java-jwt', version: '3.8.1'
 
     compile group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.8.11'
     compile group: 'com.fasterxml.jackson.module', name: 'jackson-module-parameter-names', version: '2.9.6'
@@ -80,7 +77,7 @@ dependencies {
     // https://mvnrepository.com/artifact/org.apache.commons/commons-text
     compile group: 'org.apache.commons', name: 'commons-text', version: '1.4'
     compile 'org.apache.commons:commons-lang3:3.8'
-    /compile group: 'commons-collections', name: 'commons-collections', version: '3.2.2'
+    compile group: 'commons-collections', name: 'commons-collections', version: '3.2.2'
 
     compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.2.11'
     compile group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.2.11'
@@ -109,7 +106,6 @@ dependencies {
     compile 'commons-cli:commons-cli:1.4'
 
     compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
-    compile composite.resolveDependency("org.biocode:biocode-fims-evolution:${fimsEvolutionVersion}", ":biocode-fims-evolution")
 
     additionalSources(group: 'org.springframework.data', name: 'spring-data-commons', version: '1.10.1.RELEASE', classifier: 'sources') {
         transitive = false

geome-db.template

@@ -34,3 +34,9 @@ ezidpass = pass
 mailUser = [email protected]
 mailFrom = [email protected]
 mailPassword = mypassword
+
+
+
+############ evolution fims #############
+# The url of the Evolution API
+evolutionApi=http://localhost:3030

settings.gradle

@@ -3,8 +3,3 @@ rootProject.name = 'geome-db'
 if (hasProperty("gradleFimsDir") && file(gradleFimsDir).exists()) {
     includeBuild gradleFimsDir
 }
-
-if (hasProperty("biocodeFimsEvolutionDir")) {
-    include ":biocode-fims-evolution"
-    project(":biocode-fims-evolution").projectDir = file(biocodeFimsEvolutionDir)
-}

src/main/java/biocode/fims/application/config/GeomeAppConfig.java

@@ -24,6 +24,7 @@
 import biocode.fims.ncbi.sra.submission.SubmissionReporter;
 import biocode.fims.ncbi.sra.submission.SubmissionTaskExecuter;
 import biocode.fims.photos.BulkPhotoLoader;
+import biocode.fims.plugins.evolution.application.config.EvolutionAppConfig;
 import biocode.fims.records.FimsRowMapper;
 import biocode.fims.records.GenericRecord;
 import biocode.fims.records.GenericRecordRowMapper;

src/main/java/biocode/fims/plugins/evolution/application/config/EvolutionAppConfig.java

@@ -0,0 +1,51 @@
+package biocode.fims.plugins.evolution.application.config;
+
+import biocode.fims.application.config.FimsProperties;
+import biocode.fims.plugins.evolution.processing.EvolutionTaskExecutor;
+import biocode.fims.plugins.evolution.run.EvolutionDatasetAction;
+import biocode.fims.plugins.evolution.service.EvolutionService;
+import biocode.fims.repositories.EntityIdentifierRepository;
+import biocode.fims.repositories.RecordRepository;
+import biocode.fims.service.ExpeditionService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.PropertySource;
+
+import javax.ws.rs.client.ClientBuilder;
+import java.util.concurrent.Executors;
+
+/**
+ * Configuration class for biocode-fims-evolution application.
+ */
+@Configuration
+@PropertySource(value = "classpath:biocode-fims-evolution.props", ignoreResourceNotFound = true)
+@Import({EvolutionProperties.class})
+public class EvolutionAppConfig {
+    @Autowired
+    FimsProperties fimsProperties;
+    @Autowired
+    EvolutionProperties evolutionProperties;
+
+    @Autowired
+    RecordRepository recordRepository;
+    @Autowired
+    EntityIdentifierRepository entityIdentifierRepository;
+    @Autowired
+    ExpeditionService expeditionService;
+
+    @Bean
+    public EvolutionService evolutionService() {
+        return new EvolutionService(ClientBuilder.newClient(), evolutionProperties);
+    }
+
+    @Bean
+    public EvolutionTaskExecutor evolutionTaskExecutor() {
+        return new EvolutionTaskExecutor(Executors.newFixedThreadPool(1));
+    }
+
+    public EvolutionDatasetAction evolutionDatasetAction() {
+        return new EvolutionDatasetAction(recordRepository, evolutionService(), expeditionService, evolutionTaskExecutor(), entityIdentifierRepository, evolutionProperties, fimsProperties);
+    }
+}

src/main/java/biocode/fims/plugins/evolution/application/config/EvolutionProperties.java

@@ -0,0 +1,50 @@
+package biocode.fims.plugins.evolution.application.config;
+
+import biocode.fims.fimsExceptions.FimsRuntimeException;
+import org.postgresql.util.Base64;
+import org.springframework.core.env.Environment;
+
+import java.security.KeyFactory;
+import java.security.interfaces.ECPrivateKey;
+import java.security.spec.PKCS8EncodedKeySpec;
+
+/**
+ * @author rjewing
+ */
+public class EvolutionProperties {
+    private final Environment env;
+
+    public EvolutionProperties(Environment env) {
+        this.env = env;
+    }
+
+    public String api() {
+        return env.getRequiredProperty("evolutionApi");
+    }
+
+    public String resolverEndpoint() {
+        String url = env.getRequiredProperty("evolutionRecordResolverEndpoint");
+
+        if (!url.endsWith("/")) {
+            url += "/";
+        }
+
+        return url;
+    }
+
+    public String clientId() {
+        return env.getRequiredProperty("evolutionClientID");
+    }
+
+    public ECPrivateKey clientSK() {
+        String pemKey = env.getRequiredProperty("evolutionClientSK");
+
+        try {
+            PKCS8EncodedKeySpec keySpec = new PKCS8EncodedKeySpec(Base64.decode(pemKey));
+            KeyFactory kf = KeyFactory.getInstance("EC");
+            return (ECPrivateKey) kf.generatePrivate(keySpec);
+        } catch (Exception e) {
+            throw new FimsRuntimeException("Failed to load evolutionClientSK", 500, e);
+        }
+    }
+}

src/main/java/biocode/fims/plugins/evolution/models/EvolutionRecord.java

@@ -0,0 +1,29 @@
+package biocode.fims.plugins.evolution.models;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+
+import java.util.Map;
+
+/**
+ * @author rjewing
+ */
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class EvolutionRecord {
+    public String guid;
+    public String url;
+    public Map<String, Object> data;
+    public String recordDependency;
+    public String eventId;
+    public String userId;
+
+    public EvolutionRecord(String guid, String url, String recordDependency, Map<String, Object> data, String eventId, String userId) {
+        this.guid = guid;
+        this.url = url;
+        this.recordDependency = recordDependency;
+        this.data = data;
+        this.eventId = eventId;
+        this.userId = userId;
+    }
+}

src/main/java/biocode/fims/plugins/evolution/models/EvolutionRecordReference.java

@@ -0,0 +1,21 @@
+package biocode.fims.plugins.evolution.models;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonInclude;
+
+/**
+ * @author rjewing
+ */
+@JsonIgnoreProperties(ignoreUnknown = true)
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class EvolutionRecordReference {
+    public String recordGuid;
+    public String eventId;
+    public String userId;
+
+    public EvolutionRecordReference(String recordGuid, String eventId, String userId) {
+        this.recordGuid = recordGuid;
+        this.eventId = eventId;
+        this.userId = userId;
+    }
+}

src/main/java/biocode/fims/plugins/evolution/processing/EvolutionDiscoveryTask.java

@@ -0,0 +1,29 @@
+package biocode.fims.plugins.evolution.processing;
+
+import biocode.fims.plugins.evolution.models.EvolutionRecordReference;
+import biocode.fims.plugins.evolution.service.EvolutionService;
+import org.apache.commons.collections4.ListUtils;
+
+import java.util.List;
+
+
+/**
+ * @author rjewing
+ */
+public class EvolutionDiscoveryTask implements Runnable {
+
+    private final EvolutionService evolutionService;
+    private final List<EvolutionRecordReference> references;
+
+    public EvolutionDiscoveryTask(EvolutionService evolutionService, List<EvolutionRecordReference> references) {
+        this.evolutionService = evolutionService;
+        this.references = references;
+    }
+
+    @Override
+    public void run() {
+        ListUtils.partition(references, 10000).forEach(evolutionService::discovery);
+    }
+
+}
+

src/main/java/biocode/fims/plugins/evolution/processing/EvolutionRetrievalTask.java

@@ -0,0 +1,28 @@
+package biocode.fims.plugins.evolution.processing;
+
+import biocode.fims.plugins.evolution.models.EvolutionRecordReference;
+import biocode.fims.plugins.evolution.service.EvolutionService;
+import org.apache.commons.collections4.ListUtils;
+
+import java.util.List;
+
+/**
+ * @author rjewing
+ */
+public class EvolutionRetrievalTask implements Runnable {
+
+    private final EvolutionService evolutionService;
+    private final List<EvolutionRecordReference> references;
+
+    public EvolutionRetrievalTask(EvolutionService evolutionService, List<EvolutionRecordReference> references) {
+        this.evolutionService = evolutionService;
+        this.references = references;
+    }
+
+    @Override
+    public void run() {
+        ListUtils.partition(references, 10000).forEach(evolutionService::retrieval);
+    }
+
+}
+

src/main/java/biocode/fims/plugins/evolution/processing/EvolutionTaskExecutor.java

@@ -0,0 +1,31 @@
+package biocode.fims.plugins.evolution.processing;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.concurrent.ExecutorService;
+
+/**
+ * @author rjewing
+ */
+public class EvolutionTaskExecutor {
+    private static final Logger logger = LoggerFactory.getLogger(EvolutionTaskExecutor.class);
+
+    private ExecutorService executorService;
+
+    public EvolutionTaskExecutor(ExecutorService executorService) {
+        this.executorService = executorService;
+    }
+
+    // TODO maybe need to set a timeout? https://geowarin.github.io/completable-futures-with-spring-async.html
+    public void addTask(Runnable task) {
+//        CompletableFuture.runAsync(task, executorService)
+//                .whenComplete((v, err) -> {
+//                    if (err != null) {
+//                        logger.error(err.getMessage(), err);
+//                    }
+                    // TODO log the results here?
+//                });
+
+    }
+}