development adding important changes

pom.xml

@@ -3,11 +3,11 @@
   <modelVersion>4.0.0</modelVersion>
 
   <groupId>text_tox</groupId>
-  <artifactId>ades-rest-api</artifactId>
+  <artifactId>pretox-rest-api</artifactId>
   <version>0.0.1-SNAPSHOT</version>
   <packaging>jar</packaging>
 
-  <name>ades-rest-api</name>
+  <name>pretox-rest-api</name>
   <url>http://maven.apache.org</url>
 	
 	

src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java

@@ -3,11 +3,16 @@ package es.bsc.inb.ades.rest.api.controllers;
 import java.util.List;
 
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 import es.bsc.inb.ades.rest.api.model.Document;
+import es.bsc.inb.ades.rest.api.model.DocumentAnnotations;
 import es.bsc.inb.ades.rest.api.services.DocumentService;
 
 
@@ -24,8 +29,8 @@ public class DocumentController {
     }
 	
 	@RequestMapping("/documents/{id}")
-	public Document find(@PathVariable(value="id") Long id) {
-		return documentService.findByDocumentId(id);
+	public DocumentAnnotations find(@PathVariable(value="id") Long id) {
+		return documentService.findByDocumentAnnotationsByDocumentId(id);
 	}
 	
 //	@RequestMapping("/documents/{id}")
@@ -39,9 +44,30 @@ public class DocumentController {
 		return snippet;
 	}
 	
+	@RequestMapping("/documents/{id}/sentence/{sentenceId}")
+	public String findSentence(@PathVariable(value="id") Long id, @PathVariable(value="sentenceId") Integer sentenceId) {
+		String snippet = documentService.findSentenceById(id, sentenceId);
+		return snippet;
+	}
+	
+	
 	@RequestMapping("/documents/{id}/finding2/{findingId}")
 	public String findFinding2(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId) {
 		String snippet = documentService.findTextSnippetByDocumentIdAndFindingId2(id, findingId);
 		return snippet;
 	}
+	
+	@RequestMapping(value = "/export/{id}")
+    public ResponseEntity<byte[]> generateReport(@PathVariable("id") long documentId){
+    	byte[] content = documentService.exportDocumentAnnotation(documentId);
+    	HttpHeaders head = new HttpHeaders();
+        head.setContentType(MediaType.parseMediaType("text/plain"));
+        head.add("content-disposition", "attachment; filename=ejemple");
+        head.setContentDispositionFormData("ejemple", "ejemple");
+        head.setCacheControl("must-revalidate, post-check=0, pre-check=0");
+        
+    	
+    	return new ResponseEntity<>(content, head,HttpStatus.OK);
+    }
+	
 }
\ No newline at end of file

src/main/java/es/bsc/inb/ades/rest/api/model/Annotation.java

 package es.bsc.inb.ades.rest.api.model;
 
+import java.util.ArrayList;
 import java.util.List;
 
+import org.springframework.data.mongodb.core.mapping.Field;
+
 import es.bsc.inb.ades.rest.api.util.VisualizationHTMLUtil;
 
 /**
@@ -10,7 +13,9 @@ import es.bsc.inb.ades.rest.api.util.VisualizationHTMLUtil;
  *
  */
 public class Annotation implements Comparable<Annotation> {
-
+	@Field("id")
+	private Integer id;
+	
 	private String text;
 	
 	private String value;
@@ -19,10 +24,16 @@ public class Annotation implements Comparable<Annotation> {
 	
 	private Integer endOffset;
 	
-	private List<Feature> features;
+	private ArrayList<Feature> features;
 	
 	private Boolean processed;
 	
+	private List<Finding> findings;
+	
+	public Annotation() {
+		super();
+	}
+
 	public String getText() {
 		return text;
 	}
@@ -47,11 +58,11 @@ public class Annotation implements Comparable<Annotation> {
 		this.endOffset = endOffset;
 	}
 
-	public List<Feature> getFeatures() {
+	public ArrayList<Feature> getFeatures() {
 		return features;
 	}
 
-	public void setFeatures(List<Feature> features) {
+	public void setFeatures(ArrayList<Feature> features) {
 		this.features = features;
 	}
 
@@ -111,6 +122,16 @@ public class Annotation implements Comparable<Annotation> {
 		return null;
 	}
 	
+	
+	
+	public List<Finding> getFindings() {
+		return findings;
+	}
+
+	public void setFindings(List<Finding> findings) {
+		this.findings = findings;
+	}
+
 	/**
 	 * 
 	 * @return
@@ -146,6 +167,14 @@ public class Annotation implements Comparable<Annotation> {
 		return htmlFeatures.toString();
 	}
 
+	public Integer getId() {
+		return id;
+	}
+
+	public void setId(Integer id) {
+		this.id = id;
+	}
+	
 	
 	
 	

src/main/java/es/bsc/inb/ades/rest/api/model/Document.java

@@ -3,11 +3,14 @@ package es.bsc.inb.ades.rest.api.model;
 import java.util.List;
 
 import org.bson.types.ObjectId;
+import org.springframework.data.annotation.Id;
+import org.springframework.data.mongodb.core.mapping.DBRef;
 import org.springframework.data.mongodb.core.mapping.Field;
 
-@org.springframework.data.mongodb.core.mapping.Document(collection="reports")
+@org.springframework.data.mongodb.core.mapping.Document(collection="documents")
 public class Document{
 	@Field("_id")
+	@Id
 	private ObjectId _id;
 	
 	@Field("id")
@@ -17,44 +20,33 @@ public class Document{
 	
 	private String text;
 	
-	//private String textWithAnnotations;
+	private String processDate;
 	
+	private String fileName;
+
 	private List<Finding> findings;
 	
 	public Document() {
 		super();
 	}
 
-	
-
 	public ObjectId get_id() {
 		return _id;
 	}
 
-
-
 	public void set_id(ObjectId _id) {
 		this._id = _id;
 	}
-	
-	
 
 	public Long getDocumentId() {
 		return documentId;
 	}
 
 
-
 	public void setDocumentId(Long documentId) {
 		this.documentId = documentId;
 	}
 
-	
-
-	
-
-
-
 	public String getText() {
 		return text;
 	}
@@ -85,4 +77,25 @@ public class Document{
 
 	
 
+
+
+	public String getProcessDate() {
+		return processDate;
+	}
+
+	public void setProcessDate(String processDate) {
+		this.processDate = processDate;
+	}
+
+	public String getFileName() {
+		return fileName;
+	}
+
+
+
+	public void setFileName(String fileName) {
+		this.fileName = fileName;
+	}
+
+
 }

src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.java

+package es.bsc.inb.ades.rest.api.model;
+
+import java.util.ArrayList;
+
+import org.bson.types.ObjectId;
+import org.springframework.data.annotation.Id;
+import org.springframework.data.annotation.Transient;
+import org.springframework.data.mongodb.core.mapping.Field;
+@org.springframework.data.mongodb.core.mapping.Document(collection="annotations")
+public class DocumentAnnotations {
+
+	@Field("_id")
+	@Id
+	private ObjectId _id;
+	
+	@Field("id")
+	private Long documentId;
+	
+	private String name;
+	
+	@Field("relevant_sentences")
+	private ArrayList<Annotation> relevantSentences;
+	
+	private ArrayList<Finding> findings;
+
+	public DocumentAnnotations() {}
+
+	public ObjectId get_id() {
+		return _id;
+	}
+
+	public void set_id(ObjectId _id) {
+		this._id = _id;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+
+	public Long getDocumentId() {
+		return documentId;
+	}
+
+
+	public ArrayList<Annotation> getRelevantSentences() {
+		return relevantSentences;
+	}
+
+	public void setRelevantSentences(ArrayList<Annotation> relevantSentences) {
+		this.relevantSentences = relevantSentences;
+	}
+
+	public void setDocumentId(Long documentId) {
+		this.documentId = documentId;
+	}
+
+
+
+
+	public ArrayList<Finding> getFindings() {
+		return findings;
+	}
+
+
+
+
+	public void setFindings(ArrayList<Finding> findings) {
+		this.findings = findings;
+	}
+
+	
+	
+}

src/main/java/es/bsc/inb/ades/rest/api/model/Feature.java

@@ -10,6 +10,12 @@ public class Feature {
 	
 	private String value;
 
+	
+	
+	public Feature() {
+		super();
+	}
+
 	public String getName() {
 		return name;
 	}

src/main/java/es/bsc/inb/ades/rest/api/model/Finding.java

@@ -10,7 +10,9 @@ import org.springframework.data.mongodb.core.mapping.Field;
  * @author jcorvi
  *
  */
+
 public class Finding {
+
 	@Field("id")
 	private Integer findingId;
 	

src/main/java/es/bsc/inb/ades/rest/api/model/RelevantSentence.java

+package es.bsc.inb.ades.rest.api.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.springframework.data.mongodb.core.mapping.Field;
+
+/**
+ * 
+ * @author jcorvi
+ *
+ */
+public class RelevantSentence {
+	@Field("id")
+	private Integer findingId;
+	
+	private Annotation finding_field;
+
+	@Field("FINDING")
+	private Annotation finding;
+	
+	@Field("SPECIMEN")
+	private Annotation specimen;
+	
+	@Field("SEX")
+	private Annotation sex;
+	
+	@Field("MANIFESTATION_FINDING")
+	private Annotation manifestation_finding;
+
+	@Field("GROUP")
+	private Annotation group;
+	
+	@Field("DOSE")
+	private Annotation dose;
+	
+	@Field("STUDY_TESTCD")
+	private Annotation study_testcd;
+	
+	@Field("STUDY_DOMAIN")
+	private Annotation study_domain;
+	
+	@Field("IS_TREATMENT_RELATED")
+	private Annotation is_treatment_related;
+	
+	@Field("RISK_LEVEL")
+	private Annotation risk_level;
+	
+	@Field("ROUTE_OF_AMINISTRATION")
+	private Annotation route_of_administration;
+	
+//	@Field("DOSE_QUANTITY")
+//	private Annotation dose_quantity;
+//	
+//	@Field("DOSE_FREQUENCY")
+//	private Annotation dose_frequency;
+//	
+//	@Field("DOSE_DURATION")
+//	private Annotation dose_duration;
+	
+	@Field("STATISTICAL_SIGNIFICANCE")
+	private Annotation statistical_significance;
+	
+	@Field("OBSERVATION_QUALIFICATION")
+	private Annotation observation_qualification;
+	
+	@Field("RELEVANT_TEXT")
+	private Annotation relevant_text;
+	
+	public RelevantSentence() {}
+	
+	
+	public Integer getFindingId() {
+		return findingId;
+	}
+
+	public void setFindingId(Integer findingId) {
+		this.findingId = findingId;
+	}
+
+
+
+
+	public Annotation getFinding_field() {
+		return finding_field;
+	}
+
+
+
+
+	public void setFinding_field(Annotation finding_field) {
+		this.finding_field = finding_field;
+	}
+
+
+
+
+	public Annotation getFinding() {
+		return finding;
+	}
+
+
+
+
+	public void setFinding(Annotation finding) {
+		this.finding = finding;
+	}
+
+
+
+
+	public Annotation getSpecimen() {
+		return specimen;
+	}
+
+
+
+
+	public void setSpecimen(Annotation specimen) {
+		this.specimen = specimen;
+	}
+
+
+
+
+	public Annotation getSex() {
+		return sex;
+	}
+
+
+
+
+	public void setSex(Annotation sex) {
+		this.sex = sex;
+	}
+
+
+
+
+	public Annotation getManifestation_finding() {
+		return manifestation_finding;
+	}
+
+
+
+
+	public void setManifestation_finding(Annotation manifestation_finding) {
+		this.manifestation_finding = manifestation_finding;
+	}
+
+
+
+
+	public Annotation getGroup() {
+		return group;
+	}
+
+
+
+
+	public void setGroup(Annotation group) {
+		this.group = group;
+	}
+
+
+
+
+	public Annotation getStudy_testcd() {
+		return study_testcd;
+	}
+
+
+
+
+	public void setStudy_testcd(Annotation study_testcd) {
+		this.study_testcd = study_testcd;
+	}
+
+
+
+
+	public Annotation getStudy_domain() {
+		return study_domain;
+	}
+
+
+
+
+	public void setStudy_domain(Annotation study_domain) {
+		this.study_domain = study_domain;
+	}
+
+	public Annotation getRelevant_text() {
+		return relevant_text;
+	}
+
+
+	public void setRelevant_text(Annotation relevant_text) {
+		this.relevant_text = relevant_text;
+	}
+
+
+	public Annotation getIs_treatment_related() {
+		return is_treatment_related;
+	}
+
+
+	public void setIs_treatment_related(Annotation is_treatment_related) {
+		this.is_treatment_related = is_treatment_related;
+	}
+
+
+	public Annotation getRisk_level() {
+		return risk_level;
+	}
+
+	public void setRisk_level(Annotation risk_level) {
+		this.risk_level = risk_level;
+	}
+
+	public Annotation getRoute_of_administration() {
+		return route_of_administration;
+	}
+
+	public void setRoute_of_administration(Annotation route_of_administration) {
+		this.route_of_administration = route_of_administration;
+	}
+
+//	public Annotation getDose_quantity() {
+//		return dose_quantity;
+//	}
+//
+//	public void setDose_quantity(Annotation dose_quantity) {
+//		this.dose_quantity = dose_quantity;
+//	}
+//
+//	public Annotation getDose_frequency() {
+//		return dose_frequency;
+//	}
+//
+//
+//	public void setDose_frequency(Annotation dose_frequency) {
+//		this.dose_frequency = dose_frequency;
+//	}
+//
+//	public Annotation getDose_duration() {
+//		return dose_duration;
+//	}
+//
+//	public void setDose_duration(Annotation dose_duration) {
+//		this.dose_duration = dose_duration;
+//	}
+
+	public Annotation getDose() {
+		return dose;