Merge pull request #113 from PDXFinder/beta

Beta
PDCMFinder · Oct 21, 2019 · 3814acf · 3814acf
2 parents 621fb24 + 0d9d471
commit 3814acf
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Showing 73 changed files with 1,012 additions and 941 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -24,3 +24,12 @@ notifications:
     on_success: always
     on_failure: always
     on_start: never
+
+addons:
+  sonarcloud:
+    organization: "pdxfinder"
+    token:
+      secure: "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"
+
+script:
+  - mvn clean org.jacoco:jacoco-maven-plugin:prepare-agent install sonar:sonar -Dsonar.projectKey=pdxfinder
diff --git a/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html b/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html
@@ -58,6 +58,8 @@ <h3> {{selectedSrc | uppercase}} {{selectedEntityType | uppercase}}
 
 
 
+
+
 <div class="wrapper wrapper-content animated fadeInRight">
     <div class="p-w-md m-t-sm col-lg-10 col-lg-offset-1">
 
@@ -124,7 +126,6 @@ <h3><i class="ti-agenda"></i> <span style="color: #03369D"> {{dataSource | upper
 
                                             <span *ngIf="dataLabel == 'DataSource'" class="clipText overflow-ellipsis"> {{ mapping.mappingValues[dataLabel] | uppercase }} </span>
                                             <span *ngIf="dataLabel != 'DataSource'" class="clipText overflow-ellipsis"> {{ mapping.mappingValues[dataLabel] }} </span>
-
                                         </td>
 
                                         <td><input type="text" name="{{'mappedTermLabel'+i}}" class="editableField"
@@ -180,7 +181,6 @@ <h3><i class="ti-agenda"></i> <span style="color: #03369D"> {{dataSource | upper
                                             « </a>  <!--  href="/{{'curation/'+entityTypeUrl+'/'+dataSource+'/'+data.totaPages}}"  -->
                                     </li>
 
-
                                 </ul>
 
 

diff --git a/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.ts b/admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.ts
@@ -315,7 +315,7 @@ export class DatasourceSpecificComponent implements OnInit {
         //  Auto-Navigate away on page size change
         let newPage = (this.userPage <= 1) ? this.userPage + 1 : 1;
 
-        this.router.navigate([`curation/${this.entityTypeUrl}/${this.dataSource}/${newPage}`])
+        this.router.navigate([`curation/${this.entityTypeUrl}/${this.dataSource}/${this.mappingStatusToGet}-${newPage}`])
 
     }
 

diff --git a/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html b/admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html
@@ -68,7 +68,7 @@ <h3><i class="ti-agenda"></i> {{mapType}} Mapping </h3>
                         <td> {{ summary.DataSource | uppercase }} </td>
 
                         <td class="clickTd" (click)="onSelect(summary.DataSource, 'unmapped')"> {{ summary.Unmapped }} </td>
-                        <td class="clickTd" (click)="onSelect(summary.DataSource, 'mapped')"> {{ summary.Mapped }} </td>
+                        <td class="clickTd" (click)="onSelect(summary.DataSource, 'created,validated')"> {{ summary.Mapped }} </td>
                         <td class="clickTd" (click)="onSelect(summary.DataSource, 'validated')"> {{ summary.Validated }} </td>
                         <td class="clickTd" (click)="onSelect(summary.DataSource, 'created')"> {{ summary.Created }} </td>
                         <td class="clickTd" (click)="onSelect(summary.DataSource, 'orphaned')"> {{ summary.Orphaned }} </td>

diff --git a/admin/src/main/app-ui/src/app/mapping.service.ts b/admin/src/main/app-ui/src/app/mapping.service.ts
@@ -11,7 +11,7 @@ import {SummaryInterface} from "./summary-interface";
 export class MappingService {
 
     private devServer = "http://ves-ebi-bc.ebi.ac.uk:8081";
-    private serverUrl =  "http://localhost:8081"; // this.devServer; //
+    private serverUrl = this.devServer; //"http://localhost:8081"; //
 
     private _summaryUrl = this.serverUrl+"/api/mappings/summary";
     private _mappingsUrl = this.serverUrl+"/api/mappings";
@@ -162,11 +162,6 @@ export class MappingService {
 
 
 
-
-
-
-
-
     connectToDataFlow() {
 
         return fetch('http://localhost:8081/api/mapping/diagnosis?ds=JAX')

diff --git a/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css b/admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css
@@ -1,3 +1,6 @@
+thead tr th {  position: relative;}
+span.ui-column-resizer {  display: block;  position: absolute;  top: 0;  right: 0;  margin: 0;  width: 8px;  height: 100%;  padding: 0;  cursor: col-resize;  border: 1px solid transparent;}
+
 
 .styleFile{ padding:0 0 15px; border-bottom:1px solid rgba(3, 54, 157, 0.9); color:#666; margin:20px 10px 0 0; font-weight: normal; }
 

diff --git a/admin/src/main/java/org/pdxfinder/admin/controllers/MappingController.java b/admin/src/main/java/org/pdxfinder/admin/controllers/MappingController.java
diff --git a/...der/admin/controllers/AjaxController.java → ...pdxfinder/controllers/AjaxController.java b/...der/admin/controllers/AjaxController.java → ...pdxfinder/controllers/AjaxController.java
@@ -1,11 +1,11 @@
-package org.pdxfinder.admin.controllers;
+package org.pdxfinder.controllers;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.csv.CsvMapper;
 import com.fasterxml.jackson.dataformat.csv.CsvSchema;
 import org.pdxfinder.rdbms.dao.MappingEntity;
-import org.pdxfinder.admin.zooma.ZoomaEntity;
+import org.pdxfinder.services.zooma.ZoomaEntity;
 import org.pdxfinder.services.MappingService;
 import org.pdxfinder.services.UtilityService;
 import org.pdxfinder.services.dto.PaginationDTO;

diff --git a/...rg/pdxfinder/admin/controllers/Error.java → ...java/org/pdxfinder/controllers/Error.java b/...rg/pdxfinder/admin/controllers/Error.java → ...java/org/pdxfinder/controllers/Error.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.admin.controllers;
+package org.pdxfinder.controllers;
 
 import org.springframework.http.HttpStatus;
 

diff --git a/...er/admin/controllers/IndexController.java → ...dxfinder/controllers/IndexController.java b/...er/admin/controllers/IndexController.java → ...dxfinder/controllers/IndexController.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.admin.controllers;
+package org.pdxfinder.controllers;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/admin/src/main/java/org/pdxfinder/controllers/ShutDownHook.java b/admin/src/main/java/org/pdxfinder/controllers/ShutDownHook.java
@@ -0,0 +1,26 @@
+package org.pdxfinder.controllers;
+
+import org.springframework.beans.BeansException;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.context.ConfigurableApplicationContext;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+@RestController
+public class ShutDownHook implements ApplicationContextAware {
+
+    private ApplicationContext context;
+
+    @PostMapping("/shutdown")
+    public void shutdownContext() {
+        ((ConfigurableApplicationContext) context).close();
+    }
+
+    @Override
+    public void setApplicationContext(ApplicationContext ctx) throws BeansException {
+        this.context = ctx;
+
+    }
+}
diff --git a/...pdxfinder/controller/TransController.java → ...dxfinder/controllers/TransController.java b/...pdxfinder/controller/TransController.java → ...dxfinder/controllers/TransController.java
@@ -1,14 +1,14 @@
-package org.pdxfinder.controller;
+package org.pdxfinder.controllers;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.commons.collections4.ListUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.pdxfinder.rdbms.dao.MappingEntity;
 import org.pdxfinder.rdbms.repositories.MappingEntityRepository;
 import org.pdxfinder.services.UtilityService;
-import org.pdxfinder.transcommands.DataTransformerService;
-import org.pdxfinder.transdatamodel.PdmrPdxInfo;
-import org.pdxfinder.transdatamodel.PdxInfo;
+import org.pdxfinder.services.TransformerService;
+import org.pdxfinder.rdbms.dao.PdmrPdxInfo;
+import org.pdxfinder.rdbms.dao.PdxInfo;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -19,11 +19,9 @@
 import org.springframework.web.client.RestTemplate;
 
 import java.io.File;
-import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.text.DecimalFormat;
 import java.util.*;
 
 
@@ -36,24 +34,24 @@ public class TransController {
 
     private RestTemplate restTemplate = new RestTemplate();
     private ObjectMapper mapper = new ObjectMapper();
-    private DataTransformerService dataTransformerService;
+    private TransformerService transformerService;
     @Autowired
     private UtilityService utilityService;
     @Autowired
     private MappingEntityRepository mappingEntityRepository;
 
 
 
-    public TransController(DataTransformerService dataTransformerService, RestTemplateBuilder restTemplateBuilder){
-        this.dataTransformerService = dataTransformerService;
+    public TransController(TransformerService transformerService, RestTemplateBuilder restTemplateBuilder){
+        this.transformerService = transformerService;
         this.restTemplate = restTemplateBuilder.build();
     }
 
 
     @GetMapping("/view-data")
     public PdxInfo getAllPdmr()
     {
-        List<PdmrPdxInfo> pdmrPdxInfos = dataTransformerService.getAllPdmr();
+        List<PdmrPdxInfo> pdmrPdxInfos = transformerService.getAllPdmr();
 
         PdxInfo pdxInfo = new PdxInfo();
         pdxInfo.setPdxInfo(pdmrPdxInfos);
@@ -65,13 +63,13 @@ public PdxInfo getAllPdmr()
     @GetMapping("/drugs")
     public String getAllPdmrDrugs()
     {
-        List<PdmrPdxInfo> pdmrPdxInfos = dataTransformerService.getAllPdmr();
+        List<PdmrPdxInfo> pdmrPdxInfos = transformerService.getAllPdmr();
 
         String drugList = "";
 
         for (PdmrPdxInfo pdmrPdxInfo : pdmrPdxInfos){
 
-            drugList += dataTransformerService.getDrugs(pdmrPdxInfo);
+            drugList += transformerService.getDrugs(pdmrPdxInfo);
         }
 
         return drugList;
@@ -80,9 +78,9 @@ public String getAllPdmrDrugs()
 
 
     @GetMapping("/transform-pdmr-data")
-    public List<Map> connectPdmr(){
+    public Object connectPdmr(){
 
-        List<Map> mappingList = dataTransformerService.transformDataAndSave();
+        List<Map<String, String>> mappingList = transformerService.transformDataAndSave();
         return mappingList;
 
     }
@@ -129,11 +127,12 @@ public List<MappingEntity> getMapping(){
     }
 
 
-    private String omicFile= System.getProperty("user.home") + "/Downloads/NGS-LOADER/ncicancergenepaneldata_MARCH2019.csv";
 
     @RequestMapping("/rewrite-pdmr-omic-data")
     public Object downloads() {
 
+        String omicFile= System.getProperty("user.home") + "/Downloads/NGS-LOADER/ncicancergenepaneldata_MARCH2019.csv";
+
         List<Map<String, String>> dataList = utilityService.serializeCSVToMaps(omicFile);
 
 
@@ -145,7 +144,7 @@ public Object downloads() {
                 String modelID = data.get("Model_ID");
                 String sampleID = data.get("Sample_ID");
 
-                String passage = dataTransformerService.getPassageByModelIDAndSampleID(modelID, sampleID);
+                String passage = transformerService.getPassageByModelIDAndSampleID(modelID, sampleID);
 
                 data.put("Passage", passage);
 
@@ -237,39 +236,6 @@ public Object irccTransformJson() {
         }
 
 
-        /*
-
-            "datasource": "IRCC-CRC",
-            "Model_ID": "CRC0112LM",                                Model ID
-            "Sample_ID": "CRC0112LMH0000000000D01000",              Sample ID
-            "sample_origin": "patient tumor",                       modelId+"H" [patient Tumor] , modelId+"X" [Xenograft]
-            "Passage": "",                                          null
-            "host_strain_name": "",                                 "" *****
-            "hgnc_symbol": "A2M",                                   Gene
-            "amino_acid_change": "R823W",                           Protein
-            "nucleotide_change": "",                                "" *****
-            "consequence": "Missense_Mutation",                     Effect
-            "read_depth": "",                                       "" *****
-            "Allele_frequency": "",                                 VAF
-            "chromosome": "12",                                     Chrom
-            "seq_start_position": "9243799",                        Pos *****
-            "ref_allele": "",                                       Ref
-            "alt_allele": "",                                       Alt
-            "ucsc_gene_id": "",                                     "" *****
-            "ncbi_gene_id": "2",                                    "" *****
-            "ensembl_gene_id": "",                                  "" *****
-            "ensembl_transcript_id": "",                            "" *****
-            "rs_id_Variant": "",                                    avsnp147
-            "genome_assembly": "37",
-            "Platform": "whole exome sequencing                     TargetedNGS_MUT   ... platformURL.get("targetedNgsPlatformURL")
-
-
-
-            ma.setCdsChange(variation.getString("CDS"));
-            ma.setType(type);
-
-        */
-
 
         // Get Exome Template
         String exomeFile = System.getProperty("user.home") + "/PDXFinder/data/IRCC-CRC/exome_IRCC-CRC template.xlsx";

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java b/data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
@@ -44,6 +44,7 @@ public class MarkerAssociation {
     private String readDepth;
     private String alleleFrequency;
     private String genomeAssembly; //NCBI_build in ircc
+    private String zscore;
 
     private String seqStartPosition;
     private String seqEndPosition;
@@ -262,6 +263,14 @@ public void setGenomeAssembly(String genomeAssembly) {
         this.genomeAssembly = genomeAssembly;
     }
 
+    public String getZscore() {
+        return zscore;
+    }
+
+    public void setZscore(String zscore) {
+        this.zscore = zscore;
+    }
+
     public String getSeqStartPosition() {
         return seqStartPosition;
     }

diff --git a/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java b/data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java
@@ -16,6 +16,7 @@ public class Platform {
     private Long id;
     private String name;
     private String url;
+    private String type;
 
     @Relationship(type = "GROUP", direction = Relationship.INCOMING)
     private Group group;
@@ -61,4 +62,12 @@ public Group getGroup() {
     public void setGroup(Group group) {
         this.group = group;
     }
+
+    public String getType() {
+        return type;
+    }
+
+    public void setType(String type) {
+        this.type = type;
+    }
 }
diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
@@ -203,7 +203,8 @@ Integer countMarkerAssociationBySourcePdxId(@Param("sourcePdxId") String sourceP
             "WITH model, spr, sp, hsr, hs, psamp, ir " +
             "OPTIONAL MATCH (sp)-[sfr:SAMPLED_FROM]-(s:Sample) " +
             "OPTIONAL MATCH (s)-[cbr:CHARACTERIZED_BY]-(mc:MolecularCharacterization)-[pur:PLATFORM_USED]-(pl:Platform) " +
-            "RETURN model, spr, sp, hsr, hs, sfr, s, psamp, ir, cbr, mc, pur, pl")
+            "OPTIONAL MATCH (psamp)-[cbr2:CHARACTERIZED_BY]-(mc2:MolecularCharacterization)-[pur2:PLATFORM_USED]-(pl2:Platform) " +
+            "RETURN model, spr, sp, hsr, hs, sfr, s, psamp, ir, cbr, mc, pur, pl, cbr2, mc2, pur2, pl2")
     ModelCreation findBySourcePdxIdAndDataSourceWithSamplesAndSpecimensAndHostStrain(@Param("modelId") String modelId, @Param("dataSource") String dataSource);
 
     @Query("CREATE INDEX ON :ModelCreation(dataSource, sourcePdxId)")

diff --git a/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformRepository.java b/data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformRepository.java
@@ -18,11 +18,11 @@ public interface PlatformRepository extends PagingAndSortingRepository<Platform,
 
     Platform findByName(@Param("name") String name);
 
-    @Query("MATCH (p:Platform)-[]-(g:Group) where p.name = {name} and g.name={dataSource} and g.type='Provider' return p")
-    Platform findByNameAndDataSource(@Param("name") String name, @Param("dataSource") String dataSource);
+    @Query("MATCH (p:Platform)-[]-(g:Group) where p.name = {name} and p.type = {type} and g.name={dataSource} and g.type='Provider' return p")
+    Platform findByNameAndTypeAndDataSource(@Param("name") String name, @Param("type") String type, @Param("dataSource") String dataSource);
 
-    @Query("MATCH (p:Platform)-[]-(g:Group) where p.name = {name} and g.name={dataSource} and g.type='Provider' and p.url = {url} return p")
-    Platform findByNameAndDataSourceAndUrl(@Param("name") String name, @Param("dataSource") String dataSource, @Param("url") String url);
+    @Query("MATCH (p:Platform)-[]-(g:Group) where p.name = {name} and p.type = {type} and g.name={dataSource} and g.type='Provider' and p.url = {url} return p")
+    Platform findByNameAndTypeAndDataSourceAndUrl(@Param("name") String name, @Param("type") String type, @Param("dataSource") String dataSource, @Param("url") String url);
 
 
 

diff --git a/...pdxfinder/transdatamodel/PdmrPdxInfo.java → .../org/pdxfinder/rdbms/dao/PdmrPdxInfo.java b/...pdxfinder/transdatamodel/PdmrPdxInfo.java → .../org/pdxfinder/rdbms/dao/PdmrPdxInfo.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.transdatamodel;
+package org.pdxfinder.rdbms.dao;
 
 
 import com.fasterxml.jackson.annotation.*;

diff --git a/...org/pdxfinder/transdatamodel/PdxInfo.java → ...java/org/pdxfinder/rdbms/dao/PdxInfo.java b/...org/pdxfinder/transdatamodel/PdxInfo.java → ...java/org/pdxfinder/rdbms/dao/PdxInfo.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.transdatamodel;
+package org.pdxfinder.rdbms.dao;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;

diff --git a/.../org/pdxfinder/transdatamodel/Sample.java → .../java/org/pdxfinder/rdbms/dao/Sample.java b/.../org/pdxfinder/transdatamodel/Sample.java → .../java/org/pdxfinder/rdbms/dao/Sample.java
@@ -1,4 +1,4 @@
-package org.pdxfinder.transdatamodel;
+package org.pdxfinder.rdbms.dao;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;