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Merge pull request genome-nexus#825 from leexgh/transcript-subversion
Add transcript subversions
2 parents 3e270b4 + 9b687c4 commit fb3b400

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12 files changed

+125
-14
lines changed

12 files changed

+125
-14
lines changed

‎model/src/main/java/org/cbioportal/genome_nexus/model/AggregatedHotspots.java‎

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,7 @@ public class AggregatedHotspots
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private GenomicLocation genomicLocation;
88
private String variant;
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private String transcriptId;
10+
private String transcriptIdVersion;
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private ProteinLocation proteinLocation;
1112
private List<Hotspot> hotspots;
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@@ -49,4 +50,12 @@ public String getTranscriptId() {
4950
public void setTranscriptId(String transcriptId) {
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this.transcriptId = transcriptId;
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}
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54+
public String getTranscriptIdVersion() {
55+
return transcriptIdVersion;
56+
}
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58+
public void setTranscriptIdVersion(String transcriptIdVersion) {
59+
this.transcriptIdVersion = transcriptIdVersion;
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}
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}

‎model/src/main/java/org/cbioportal/genome_nexus/model/EnsemblCanonical.java‎

Lines changed: 41 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,14 @@ public class EnsemblCanonical
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private String uniprotCanonicalTranscriptId;
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@Field(value="mskcc_canonical_transcript")
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private String mskccCanonicalTranscriptId;
26+
@Field(value="ensembl_canonical_transcript_version")
27+
private String ensemblCanonicalTranscriptVersion;
28+
@Field(value="genome_nexus_canonical_transcript_version")
29+
private String genomeNexusCanonicalTranscriptVersion;
30+
@Field(value="uniprot_canonical_transcript_version")
31+
private String uniprotCanonicalTranscriptVersion;
32+
@Field(value="mskcc_canonical_transcript_version")
33+
private String mskccCanonicalTranscriptVersion;
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@Field(value="hgnc_id")
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private String hgncId;
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@Field(value="approved_name")
@@ -138,4 +146,36 @@ public String getHgncId() {
138146
public void setHgncId(String hgncId) {
139147
this.hgncId = hgncId;
140148
}
141-
}
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150+
public String getEnsemblCanonicalTranscriptVersion() {
151+
return this.ensemblCanonicalTranscriptVersion;
152+
}
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154+
public void setEnsemblCanonicalTranscriptVersion(String ensemblCanonicalTranscriptVersion) {
155+
this.ensemblCanonicalTranscriptVersion = ensemblCanonicalTranscriptVersion;
156+
}
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158+
public String getGenomeNexusCanonicalTranscriptVersion() {
159+
return this.genomeNexusCanonicalTranscriptVersion;
160+
}
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162+
public void setGenomeNexusCanonicalTranscriptVersion(String genomeNexusCanonicalTranscriptVersion) {
163+
this.genomeNexusCanonicalTranscriptVersion = genomeNexusCanonicalTranscriptVersion;
164+
}
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166+
public String getUniprotCanonicalTranscriptVersion() {
167+
return this.uniprotCanonicalTranscriptVersion;
168+
}
169+
170+
public void setUniprotCanonicalTranscriptVersion(String uniprotCanonicalTranscriptVersion) {
171+
this.uniprotCanonicalTranscriptVersion = uniprotCanonicalTranscriptVersion;
172+
}
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174+
public String getMskccCanonicalTranscriptVersion() {
175+
return this.mskccCanonicalTranscriptVersion;
176+
}
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178+
public void setMskccCanonicalTranscriptVersion(String mskccCanonicalTranscriptVersion) {
179+
this.mskccCanonicalTranscriptVersion = mskccCanonicalTranscriptVersion;
180+
}
181+
}

‎model/src/main/java/org/cbioportal/genome_nexus/model/EnsemblTranscript.java‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -19,6 +19,9 @@ public class EnsemblTranscript
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@Field(value=EnsemblTranscript.TRANSCRIPT_ID_FIELD_NAME)
2020
private String transcriptId;
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22+
@Field(value="transcript_id_version")
23+
private String transcriptIdVersion;
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@Field(value="gene_stable_id")
2326
private String geneId;
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@@ -57,6 +60,14 @@ public void setTranscriptId(String transcriptId) {
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this.transcriptId = transcriptId;
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}
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63+
public String getTranscriptIdVersion() {
64+
return transcriptIdVersion;
65+
}
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67+
public void setTranscriptIdVersion(String transcriptIdVersion) {
68+
this.transcriptIdVersion = transcriptIdVersion;
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}
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public String getGeneId() {
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return geneId;
6273
}

‎model/src/main/java/org/cbioportal/genome_nexus/model/Hotspot.java‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -52,6 +52,9 @@ public class Hotspot
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@Field(value="transcript_id")
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private String transcriptId;
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55+
@Field(value="transcript_id_version")
56+
private String transcriptIdVersion;
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@Field(value="residue")
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private String residue;
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@@ -89,6 +92,14 @@ public void setTranscriptId(String transcriptId) {
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this.transcriptId = transcriptId;
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}
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95+
public String getTranscriptIdVersion() {
96+
return this.transcriptIdVersion;
97+
}
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99+
public void setTranscriptIdVersion(String transcriptIdVersion) {
100+
this.transcriptIdVersion = transcriptIdVersion;
101+
}
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92103
public String getResidue() {
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return residue;
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}

‎model/src/main/java/org/cbioportal/genome_nexus/model/TranscriptConsequence.java‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,6 +44,7 @@
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public class TranscriptConsequence
4545
{
4646
private String transcriptId;
47+
private String transcriptIdVersion;
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4849
private String hgvsp;
4950
private String hgvsc;
@@ -103,6 +104,17 @@ public void setTranscriptId(String transcriptId)
103104
this.transcriptId = transcriptId;
104105
}
105106

107+
@Field(value="transcript_id_version")
108+
public String getTranscriptIdVersion()
109+
{
110+
return transcriptIdVersion;
111+
}
112+
113+
public void setTranscriptIdVersion(String transcriptIdVersion)
114+
{
115+
this.transcriptIdVersion = transcriptIdVersion;
116+
}
117+
106118
@Field(value="hgvsp")
107119
public String getHgvsp()
108120
{

‎model/src/main/java/org/cbioportal/genome_nexus/model/TranscriptConsequenceSummary.java‎

Lines changed: 13 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
public class TranscriptConsequenceSummary
33
{
44
private String transcriptId;
5+
private String transcriptIdVersion;
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private String codonChange;
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private String aminoAcids;
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private String aminoAcidRef;
@@ -36,6 +37,18 @@ public String getTranscriptId() {
3637
return transcriptId;
3738
}
3839

40+
public void setTranscriptId(String transcriptId) {
41+
this.transcriptId = transcriptId;
42+
}
43+
44+
public String getTranscriptIdVersion() {
45+
return transcriptIdVersion;
46+
}
47+
48+
public void setTranscriptIdVersion(String transcriptIdVersion) {
49+
this.transcriptIdVersion = transcriptIdVersion;
50+
}
51+
3952
public String getAminoAcidAlt() {
4053
return aminoAcidAlt;
4154
}
@@ -52,10 +65,6 @@ public void setAminoAcidRef(String aminoAcidRef) {
5265
this.aminoAcidRef = aminoAcidRef;
5366
}
5467

55-
public void setTranscriptId(String transcriptId) {
56-
this.transcriptId = transcriptId;
57-
}
58-
5968
public String getCodonChange() {
6069
return codonChange;
6170
}

‎service/src/main/java/org/cbioportal/genome_nexus/service/mixin/TranscriptConsequenceMixin.java‎

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Original file line numberDiff line numberDiff line change
@@ -12,6 +12,9 @@ public class TranscriptConsequenceMixin
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@JsonProperty(value="transcript_id", required = true)
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private String transcriptId;
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15+
@JsonProperty(value="transcript_id_version", required = true)
16+
private String transcriptIdVersion;
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1518
@JsonProperty(value="hgvsp", required = true)
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private String hgvsp;
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‎web/src/main/java/org/cbioportal/genome_nexus/web/mixin/EnsemblTranscriptMixin.java‎

Lines changed: 12 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -10,30 +10,33 @@ public class EnsemblTranscriptMixin {
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@ApiModelProperty(value = "Ensembl transcript id", position=1, required = true)
1111
private String transcriptId;
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13-
@ApiModelProperty(value = "Ensembl gene id", position=2, required = true)
13+
@ApiModelProperty(value = "Ensembl transcript id version", position=2)
14+
private String transcriptIdVersion;
15+
16+
@ApiModelProperty(value = "Ensembl gene id", position=3, required = true)
1417
private String geneId;
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16-
@ApiModelProperty(value = "Ensembl protein id", position=3, required = true)
19+
@ApiModelProperty(value = "Ensembl protein id", position=4, required = true)
1720
private String proteinId;
1821

19-
@ApiModelProperty(value = "Length of protein", position=4)
22+
@ApiModelProperty(value = "Length of protein", position=5)
2023
private Integer proteinLength;
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22-
@ApiModelProperty(value = "Pfam domains", position=5, dataType="List")
25+
@ApiModelProperty(value = "Pfam domains", position=6, dataType="List")
2326
private List<PfamDomainRangeMixin> pfamDomains;
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25-
@ApiModelProperty(value = "Hugo symbols", position=6, dataType="List")
28+
@ApiModelProperty(value = "Hugo symbols", position=7, dataType="List")
2629
private List<String> hugoSymbols;
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28-
@ApiModelProperty(value = "RefSeq mRNA ID", position=7)
31+
@ApiModelProperty(value = "RefSeq mRNA ID", position=8)
2932
private String refseqMrnaId;
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31-
@ApiModelProperty(value = "Consensus CDS (CCDS) ID", position=8)
34+
@ApiModelProperty(value = "Consensus CDS (CCDS) ID", position=9)
3235
private String ccdsId;
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34-
@ApiModelProperty(value = "Exon information", position=9, dataType="List")
37+
@ApiModelProperty(value = "Exon information", position=10, dataType="List")
3538
private List<ExonMixin> exons;
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37-
@ApiModelProperty(value = "UTR information", position=10, dataType="List")
40+
@ApiModelProperty(value = "UTR information", position=11, dataType="List")
3841
private List<UntranslatedRegionMixin> utrs;
3942
}

‎web/src/main/java/org/cbioportal/genome_nexus/web/mixin/HotspotMixin.java‎

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Original file line numberDiff line numberDiff line change
@@ -16,6 +16,9 @@ public class HotspotMixin
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@ApiModelProperty(value = "Ensembl Transcript Id")
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private String transcriptId;
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19+
@ApiModelProperty(value = "Ensembl Transcript Id Version")
20+
private String transcriptIdVersion;
21+
1922
@ApiModelProperty(value = "Hotspot residue")
2023
private String residue;
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‎web/src/main/java/org/cbioportal/genome_nexus/web/mixin/TranscriptConsequenceMixin.java‎

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Original file line numberDiff line numberDiff line change
@@ -13,6 +13,10 @@ public class TranscriptConsequenceMixin
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@ApiModelProperty(value = "Ensembl transcript id", required = true)
1414
private String transcriptId;
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16+
@JsonProperty(value="transcript_id_version", required = true)
17+
@ApiModelProperty(value = "Ensembl transcript id version", required = false)
18+
private String transcriptIdVersion;
19+
1620
@JsonProperty(value="hgvsp", required = true)
1721
@ApiModelProperty(value = "HGVSp", required = false)
1822
private String hgvsp;

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