Fixes for mutation step (#31)

Signed-off-by: Zachary Heins <zackheins@gmail.com>

src/main/java/org/cbio/gdcpipeline/JobConfiguration/BatchConfiguration.java

@@ -72,7 +72,7 @@ public Step setUpPipeline() {
                 .tasklet(setUpPipelineTasklet())
                 .build();
     }
-    
+
     @Bean
     public GenomeNexusCache genomeNexusCache() {
         return new GenomeNexusCache();
@@ -131,7 +131,7 @@ public Flow cnaDataFlow() {
                 .next(cnaMetaDataStep)
                 .build();
     }
-    
+
     @Bean
     public Flow expressionDataFlow() {
         return new FlowBuilder<Flow>("expressionDataFlow")
@@ -146,7 +146,7 @@ public Flow gdcAllDatatypesFlow() {
                 .start(clinicalDataFlow())
                 .next(mutationDataFlow())
                 .next(cnaDataFlow())
-                .next(expressionDataFlow())     
+                .next(expressionDataFlow())
                 .build();
     }
 

src/main/java/org/cbio/gdcpipeline/model/ensemblmap/EnsemblMap.java

@@ -0,0 +1,68 @@
+package org.cbio.gdcpipeline.model.ensemblmap;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+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;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({
+    "mappings"
+})
+public class EnsemblMap {
+    @JsonProperty("mappings")
+    private List<Mapping> mappings = new ArrayList<Mapping>();
+    @JsonIgnore
+    private Map<String, Object> additionalProperties = new HashMap<String, Object>();
+
+    /**
+    * No args constructor for use in serialization
+    *
+    */
+    public EnsemblMap() {}
+
+    /**
+    *
+    * @param mappings
+    */
+    public EnsemblMap(List<Mapping> mappings) {
+        super();
+        this.mappings = mappings;
+    }
+
+    @JsonProperty("mappings")
+    public List<Mapping> getMappings() {
+        return mappings;
+    }
+
+    @JsonProperty("mappings")
+    public void setMappings(List<Mapping> mappings) {
+        this.mappings = mappings;
+    }
+
+    public EnsemblMap withMappings(List<Mapping> mappings) {
+        this.mappings = mappings;
+        return this;
+    }
+
+    @JsonAnyGetter
+    public Map<String, Object> getAdditionalProperties() {
+        return this.additionalProperties;
+    }
+
+    @JsonAnySetter
+    public void setAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+    }
+
+    public EnsemblMap withAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+        return this;
+    }
+}

src/main/java/org/cbio/gdcpipeline/model/ensemblmap/Mapped.java

@@ -0,0 +1,166 @@
+package org.cbio.gdcpipeline.model.ensemblmap;
+
+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;
+import java.util.HashMap;
+import java.util.Map;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({
+    "end",
+    "assembly",
+    "coord_system",
+    "strand",
+    "start",
+    "seq_region_name"
+})
+public class Mapped {
+    @JsonProperty("end")
+    private Integer end;
+    @JsonProperty("assembly")
+    private String assembly;
+    @JsonProperty("coord_system")
+    private String coordSystem;
+    @JsonProperty("strand")
+    private Integer strand;
+    @JsonProperty("start")
+    private Integer start;
+    @JsonProperty("seq_region_name")
+    private String seqRegionName;
+    @JsonIgnore
+    private Map<String, Object> additionalProperties = new HashMap<String, Object>();
+
+    /**
+    * No args constructor for use in serialization
+    *
+    */
+    public Mapped() {}
+
+    /**
+    *
+    * @param start
+    * @param assembly
+    * @param strand
+    * @param seqRegionName
+    * @param coordSystem
+    * @param end
+    */
+    public Mapped(Integer end, String assembly, String coordSystem, Integer strand, Integer start, String seqRegionName) {
+        super();
+        this.end = end;
+        this.assembly = assembly;
+        this.coordSystem = coordSystem;
+        this.strand = strand;
+        this.start = start;
+        this.seqRegionName = seqRegionName;
+    }
+
+    @JsonProperty("end")
+    public Integer getEnd() {
+        return end;
+    }
+
+    @JsonProperty("end")
+    public void setEnd(Integer end) {
+        this.end = end;
+    }
+
+    public Mapped withEnd(Integer end) {
+        this.end = end;
+        return this;
+    }
+
+    @JsonProperty("assembly")
+    public String getAssembly() {
+        return assembly;
+    }
+
+    @JsonProperty("assembly")
+    public void setAssembly(String assembly) {
+        this.assembly = assembly;
+    }
+
+    public Mapped withAssembly(String assembly) {
+        this.assembly = assembly;
+        return this;
+    }
+
+    @JsonProperty("coord_system")
+    public String getCoordSystem() {
+        return coordSystem;
+    }
+
+    @JsonProperty("coord_system")
+    public void setCoordSystem(String coordSystem) {
+        this.coordSystem = coordSystem;
+    }
+
+    public Mapped withCoordSystem(String coordSystem) {
+        this.coordSystem = coordSystem;
+        return this;
+    }
+
+    @JsonProperty("strand")
+    public Integer getStrand() {
+        return strand;
+    }
+
+    @JsonProperty("strand")
+    public void setStrand(Integer strand) {
+        this.strand = strand;
+    }
+
+    public Mapped withStrand(Integer strand) {
+        this.strand = strand;
+        return this;
+    }
+
+    @JsonProperty("start")
+    public Integer getStart() {
+        return start;
+    }
+
+    @JsonProperty("start")
+    public void setStart(Integer start) {
+        this.start = start;
+    }
+
+    public Mapped withStart(Integer start) {
+        this.start = start;
+        return this;
+    }
+
+    @JsonProperty("seq_region_name")
+    public String getSeqRegionName() {
+        return seqRegionName;
+    }
+
+    @JsonProperty("seq_region_name")
+    public void setSeqRegionName(String seqRegionName) {
+        this.seqRegionName = seqRegionName;
+    }
+
+    public Mapped withSeqRegionName(String seqRegionName) {
+        this.seqRegionName = seqRegionName;
+        return this;
+    }
+
+    @JsonAnyGetter
+    public Map<String, Object> getAdditionalProperties() {
+        return this.additionalProperties;
+    }
+
+    @JsonAnySetter
+    public void setAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+    }
+
+    public Mapped withAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+        return this;
+    }
+}

src/main/java/org/cbio/gdcpipeline/model/ensemblmap/Mapping.java

@@ -0,0 +1,87 @@
+package org.cbio.gdcpipeline.model.ensemblmap;
+
+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;
+import java.util.HashMap;
+import java.util.Map;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@JsonPropertyOrder({
+    "original",
+    "mapped"
+})
+public class Mapping {
+
+    @JsonProperty("original")
+    private Original original;
+    @JsonProperty("mapped")
+    private Mapped mapped;
+    @JsonIgnore
+    private Map<String, Object> additionalProperties = new HashMap<String, Object>();
+
+    /**
+    * No args constructor for use in serialization
+    *
+    */
+    public Mapping() {}
+
+    /**
+    *
+    * @param original
+    * @param mapped
+    */
+    public Mapping(Original original, Mapped mapped) {
+        super();
+        this.original = original;
+        this.mapped = mapped;
+    }
+
+    @JsonProperty("original")
+    public Original getOriginal() {
+        return original;
+    }
+
+    @JsonProperty("original")
+    public void setOriginal(Original original) {
+        this.original = original;
+    }
+
+    public Mapping withOriginal(Original original) {
+    this.original = original;
+        return this;
+    }
+
+    @JsonProperty("mapped")
+    public Mapped getMapped() {
+        return mapped;
+    }
+
+    @JsonProperty("mapped")
+    public void setMapped(Mapped mapped) {
+        this.mapped = mapped;
+    }
+
+    public Mapping withMapped(Mapped mapped) {
+        this.mapped = mapped;
+        return this;
+    }
+
+    @JsonAnyGetter
+    public Map<String, Object> getAdditionalProperties() {
+        return this.additionalProperties;
+    }
+
+    @JsonAnySetter
+    public void setAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+    }
+
+    public Mapping withAdditionalProperty(String name, Object value) {
+        this.additionalProperties.put(name, value);
+        return this;
+    }
+}