Merge pull request #51 from PDXFinder/beta

Beta

.gitignore

@@ -14,5 +14,4 @@ hs_err_pid*
 *.iml
 
 node_modules
-
-static
+/admin/src/main/resources/

admin/src/main/java/org/pdxfinder/admin/controllers/AjaxController.java

@@ -1,34 +1,56 @@
 package org.pdxfinder.admin.controllers;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.pdxfinder.admin.pojos.MappingEntity;
+import org.pdxfinder.admin.zooma.ZoomaEntity;
 import org.pdxfinder.services.MappingService;
+import org.pdxfinder.services.UtilityService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.ResponseEntity;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.web.client.RestTemplateBuilder;
+import org.springframework.http.*;
 import org.springframework.web.bind.annotation.*;
+import org.springframework.web.client.RestTemplate;
 
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
+import java.util.*;
+import java.util.concurrent.CompletableFuture;
 
 
 /*
  * Created by csaba on 09/07/2018.
  */
 @RestController
+@RequestMapping("/api")
 public class AjaxController {
 
-    private MappingService mappingService;
     private final static Logger log = LoggerFactory.getLogger(AjaxController.class);
+    private ObjectMapper mapper = new ObjectMapper();
+    private RestTemplate restTemplate;
+
+    private final String ZOOMA_URL = "http://scrappy.ebi.ac.uk:8080/annotations";
+    private String errReport = "";
 
 
     @Autowired
-    public AjaxController(MappingService mappingService) {
+    private UtilityService utilityService;
+    private MappingService mappingService;
+
+    @Autowired
+    public AjaxController(MappingService mappingService, RestTemplateBuilder restTemplateBuilder) {
         this.mappingService = mappingService;
+        this.restTemplate = restTemplateBuilder.build();
     }
 
-    @RequestMapping(value = "/api/missingmapping/diagnosis")
+
+
+                        /****************************************************************
+                         *          INTERACTIONS WITH PDX FINDER KNOWLEDGE BASE         *
+                         ****************************************************************/
+
+
+    @RequestMapping(value = "/missingmapping/diagnosis")
     @ResponseBody
     public Map<String, List<MappingEntity>> getMissingMappings(@RequestParam("ds") Optional<String> dataSource){
 
@@ -41,7 +63,7 @@ public Map<String, List<MappingEntity>> getMissingMappings(@RequestParam("ds") O
     }
 
 
-    @RequestMapping(value = "/api/mapping/diagnosis")
+    @RequestMapping(value = "/mapping/diagnosis")
     @ResponseBody
     public Map<String, List<MappingEntity>>  getDiagnosisMappings(@RequestParam("ds") Optional<String> dataSource){
 
@@ -54,12 +76,102 @@ public Map<String, List<MappingEntity>>  getDiagnosisMappings(@RequestParam("ds"
     }
 
 
-    @PostMapping("/api/diagnosis")
+    @PostMapping("/diagnosis")
     public ResponseEntity<?> createDiagnosisMappings(@RequestBody List<MappingEntity> newMappings){
 
         log.info(newMappings.toString());
         return ResponseEntity.noContent().build();
     }
 
 
+
+
+
+
+                        /****************************************************************
+                         *                   INTERACTIONS WITH ZOOMA                    *
+                         ****************************************************************/
+
+
+    @GetMapping("/zooma/transform")
+    public List<ZoomaEntity> transformAnnotationForZooma(){
+
+        List<ZoomaEntity> zoomaEntities = mappingService.transformMappingsForZooma();
+        return zoomaEntities; //new ResponseEntity<>(result, HttpStatus.OK);
+    }
+
+
+
+    @GetMapping("/zooma")
+    public ResponseEntity<?> writeAllAnnotationsToZooma(){
+
+        Map report = new LinkedHashMap();
+        List<ZoomaEntity> zoomaEntities = mappingService.transformMappingsForZooma();
+
+        int count = 0;
+        List<ZoomaEntity> failedList = new ArrayList<>();
+        for (ZoomaEntity zoomaEntity : zoomaEntities){
+
+            String entity = zoomaEntity.getBiologicalEntities().getBioEntity()+"__"+count++;
+            if (writeToZooma(zoomaEntity)){
+
+                report.put(entity,"SUCCESS WRITE");
+            }else{
+
+                report.put(entity, "THIS ANNOTATION WAS NOT WRITTEN TO ZOOMA");
+                failedList.add(zoomaEntity);
+            }
+        }
+
+        /* LOG FAILED OBJECTS TO FILE */
+        String failedReport = "";
+        try{
+            failedReport = mapper.writeValueAsString(failedList);
+        }catch (Exception e){}
+
+        utilityService.writeToFile(failedReport,(new Date())+"_failed.json");
+        utilityService.writeToFile(this.errReport,(new Date())+"_error.txt");
+
+        return new ResponseEntity<>(report, HttpStatus.OK);
+    }
+
+
+
+
+
+    public Boolean writeToZooma(ZoomaEntity zoomaEntity){
+
+        HttpEntity<String> entity = BuildHttpHeader();
+        HttpEntity<Object> req = new HttpEntity<>(zoomaEntity, entity.getHeaders());
+        Map result =  new HashMap();
+
+        Boolean report = false;
+        try{
+            result = restTemplate.postForObject(ZOOMA_URL, req, Map.class);
+            report = true;
+        }catch (Exception e){
+
+            this.errReport += "\n\n ************************ NEW ERROR LOG "+(new Date())+" *********************** \n"+e;
+        }
+
+        return report;
+    }
+
+
+
+
+
+
+    public HttpEntity<String> BuildHttpHeader(){
+
+        HttpHeaders headers = new HttpHeaders();
+        headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
+        headers.add("Content-Type", "application/json");
+        HttpEntity<String> entity = new HttpEntity<>("parameters", headers);
+
+        return  entity;
+    }
+
+
+
 }

admin/src/main/resources/application.properties

@@ -17,3 +17,5 @@ spring.thymeleaf.cache=false
 server.port=8081
 
 mappings.diagnosis.file = "";
+
+mappings.mappedTermUrl=http://localhost/data/mappings.json

data-model/src/main/java/org/pdxfinder/admin/pojos/MappingEntity.java

@@ -40,9 +40,15 @@ public class MappingEntity {
      * The term that the entity is mapped to. The value of this attribute should be either null (indicating that the
      * entity is not mapped to anything yet) or an existing ontology term.
      */
-    private String mappedTerm;
+    private String mappedTermLabel;
 
 
+    /**
+     * The term url that the entity is mapped to. The value of this attribute should be either null (indicating that the
+     * entity is not mapped to anything yet) or an existing ontology term url.
+     */
+    private String mappedTermUrl;
+
     /**
      * Describes whether the mapping rule is direct or inferred
      */
@@ -64,7 +70,7 @@ public class MappingEntity {
 
 
     /**
-     * A list of entities that are similar to the current entity. This list is empty if the entity's mappedTerm is not null.
+     * A list of entities that are similar to the current entity. This list is empty if the entity's mappedTermLabel is not null.
      */
     private List<MappingEntity> suggestedMappings;
 
@@ -89,7 +95,7 @@ public MappingEntity(Long entityId, String entityType, List<String> mappingLabel
         this.entityType = entityType;
         this.mappingLabels = mappingLabels;
         this.mappingValues = mappingValues;
-        this.mappedTerm = null;
+        this.mappedTermLabel = null;
         this.status = "Created";
         this.suggestedMappings = new ArrayList<>();
         //TODO: get current date, specify date format
@@ -99,14 +105,14 @@ public MappingEntity(Long entityId, String entityType, List<String> mappingLabel
     }
 
     public MappingEntity(Long entityId, String entityType, List<String> mappingLabels, Map<String, String> mappingValues,
-                         String mappedTerm, String status, List<MappingEntity> suggestedMappings, Date dateCreated,
+                         String mappedTermLabel, String status, List<MappingEntity> suggestedMappings, Date dateCreated,
                          Date dateUpdated) {
 
         this.entityId = entityId;
         this.entityType = entityType;
         this.mappingLabels = mappingLabels;
         this.mappingValues = mappingValues;
-        this.mappedTerm = mappedTerm;
+        this.mappedTermLabel = mappedTermLabel;
         this.status = status;
         this.suggestedMappings = suggestedMappings;
         this.dateCreated = dateCreated;
@@ -146,12 +152,12 @@ public void setMappingValues(Map<String, String> mappingValues) {
         this.mappingValues = mappingValues;
     }
 
-    public String getMappedTerm() {
-        return mappedTerm;
+    public String getMappedTermLabel() {
+        return mappedTermLabel;
     }
 
-    public void setMappedTerm(String mappedTerm) {
-        this.mappedTerm = mappedTerm;
+    public void setMappedTermLabel(String mappedTermLabel) {
+        this.mappedTermLabel = mappedTermLabel;
     }
 
     public String getMapType() {
@@ -202,4 +208,11 @@ public void setDateUpdated(Date dateUpdated) {
         this.dateUpdated = dateUpdated;
     }
 
+    public String getMappedTermUrl() {
+        return mappedTermUrl;
+    }
+
+    public void setMappedTermUrl(String mappedTermUrl) {
+        this.mappedTermUrl = mappedTermUrl;
+    }
 }

data-model/src/main/java/org/pdxfinder/admin/zooma/BiologicalEntities.java

@@ -0,0 +1,58 @@
+package org.pdxfinder.admin.zooma;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonPropertyOrder({
+        "bioEntity",
+        "studies",
+        "bioEntityUri"
+})
+public class BiologicalEntities {
+
+    private String bioEntity;
+    private Studies studies;
+    private Object bioEntityUri;
+
+
+    public BiologicalEntities() {
+    }
+
+    public BiologicalEntities(String bioEntity, Studies studies, Object bioEntityUri) {
+        this.bioEntity = bioEntity;
+        this.studies = studies;
+        this.bioEntityUri = bioEntityUri;
+    }
+
+    @JsonProperty("bioEntity")
+    public String getBioEntity() {
+        return bioEntity;
+    }
+
+    @JsonProperty("bioEntity")
+    public void setBioEntity(String bioEntity) {
+        this.bioEntity = bioEntity;
+    }
+
+    @JsonProperty("studies")
+    public Studies getStudies() {
+        return studies;
+    }
+
+    @JsonProperty("studies")
+    public void setStudies(Studies studies) {
+        this.studies = studies;
+    }
+
+    @JsonProperty("bioEntityUri")
+    public Object getBioEntityUri() {
+        return bioEntityUri;
+    }
+
+    @JsonProperty("bioEntityUri")
+    public void setBioEntityUri(Object bioEntityUri) {
+        this.bioEntityUri = bioEntityUri;
+    }
+
+}

data-model/src/main/java/org/pdxfinder/admin/zooma/Property.java

@@ -0,0 +1,49 @@
+package org.pdxfinder.admin.zooma;
+
+import java.util.HashMap;
+import java.util.Map;
+import com.fasterxml.jackson.annotation.JsonAnyGetter;
+import com.fasterxml.jackson.annotation.JsonAnySetter;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonPropertyOrder;
+
+@JsonPropertyOrder({
+        "propertyType",
+        "propertyValue"
+})
+public class Property {
+
+    private String propertyType;
+    private String propertyValue;
+
+    public Property() {
+    }
+
+    public Property(String propertyType, String propertyValue) {
+        this.propertyType = propertyType;
+        this.propertyValue = propertyValue;
+    }
+
+    @JsonProperty("propertyType")
+    public String getPropertyType() {
+        return propertyType;
+    }
+
+    @JsonProperty("propertyType")
+    public void setPropertyType(String propertyType) {
+        this.propertyType = propertyType;
+    }
+
+    @JsonProperty("propertyValue")
+    public String getPropertyValue() {
+        return propertyValue;
+    }
+
+    @JsonProperty("propertyValue")
+    public void setPropertyValue(String propertyValue) {
+        this.propertyValue = propertyValue;
+    }
+
+}