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Added support for version 90 of the Ensembl schema
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The status column has been removed from the Ensembl Core
schema for the gene able and the transcript table.
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@thibauthourlier
thibauthourlier committed Jul 24, 2017
1 parent caf66e6 commit 7b0502f
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Showing 6 changed files with 30 additions and 75 deletions.
43 changes: 18 additions & 25 deletions src/DataAdaptors/GeneAdaptor.c
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Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,6 @@ char *Gene_cols[] = {
"g.biotype",
"g.display_xref_id",
"g.description",
"g.status",
"g.source",
"g.is_current",
"g.canonical_transcript_id",
Expand Down Expand Up @@ -1428,7 +1427,6 @@ IDType GeneAdaptor_store(GeneAdaptor *ga, Gene *gene, int ignoreRelease) {
"biotype = '%s',"
"description = %%s,"
"source = %%s,"
"status = %%s,"
//"description = '%s',"
//"source = '%s',"
//"status = '%s',"
Expand All @@ -1451,10 +1449,7 @@ IDType GeneAdaptor_store(GeneAdaptor *ga, Gene *gene, int ignoreRelease) {
char sourceQStr[1024];
Gene_getSource(gene) ? sprintf(sourceQStr,"'%s'", Gene_getSource(gene)) : sprintf(sourceQStr, "NULL");

char statusQStr[1024];
Gene_getStatus(gene) ? sprintf(statusQStr,"'%s'", Gene_getStatus(gene)) : sprintf(statusQStr, "NULL");

sprintf(qStr, fmtStr, descQStr, sourceQStr, statusQStr);
sprintf(qStr, fmtStr, descQStr, sourceQStr);

if (Gene_getStableId(gene)) {
/* Use FROM_UNIXTIME for now
Expand Down Expand Up @@ -1899,26 +1894,25 @@ Vector *GeneAdaptor_objectsFromStatementHandle(GeneAdaptor *ga,
char *biotype = row->getStringAt(row,6);
IDType displayXrefId = row->getLongLongAt(row,7);
char *geneDescription = row->getStringAt(row,8);
char *status = row->getStringAt(row,9);
char *source = row->getStringAt(row,10);
int isCurrent = row->getIntAt(row,11);
IDType canonicalTranscriptId = row->getLongLongAt(row,12);
char *stableId = row->getStringAt(row,13);
int version = row->getIntAt(row,14);
int createdDate = row->getIntAt(row,15);
int modifiedDate = row->getIntAt(row,16);
char *source = row->getStringAt(row,9);
int isCurrent = row->getIntAt(row,10);
IDType canonicalTranscriptId = row->getLongLongAt(row,11);
char *stableId = row->getStringAt(row,12);
int version = row->getIntAt(row,13);
int createdDate = row->getIntAt(row,14);
int modifiedDate = row->getIntAt(row,15);
// Changed from perl xrefDisplayId to xrefDisplayLabel to match Transcript version
char *xrefDisplayLabel = row->getStringAt(row,17);
char *xrefPrimaryAcc = row->getStringAt(row,18);
char *xrefDesc = row->getStringAt(row,19);
char *xrefVersion = row->getStringAt(row,20);
char *externalDb = row->getStringAt(row,21);
char *externalStatus = row->getStringAt(row,22);
char *externalRelease = row->getStringAt(row,23);
char *externalDbName = row->getStringAt(row,24);
char *xrefDisplayLabel = row->getStringAt(row,16);
char *xrefPrimaryAcc = row->getStringAt(row,17);
char *xrefDesc = row->getStringAt(row,18);
char *xrefVersion = row->getStringAt(row,19);
char *externalDb = row->getStringAt(row,20);
char *externalStatus = row->getStringAt(row,21);
char *externalRelease = row->getStringAt(row,22);
char *externalDbName = row->getStringAt(row,23);
// Added xref prefix to info* var names to match Transcript version
char *xrefInfoType = row->getStringAt(row,25);
char *xrefInfoText = row->getStringAt(row,26);
char *xrefInfoType = row->getStringAt(row,24);
char *xrefInfoText = row->getStringAt(row,25);

// get the analysis object
Analysis *analysis = AnalysisAdaptor_fetchByDbID(aa, analysisId);
Expand Down Expand Up @@ -2115,7 +2109,6 @@ Vector *GeneAdaptor_objectsFromStatementHandle(GeneAdaptor *ga,
Gene_setExternalDb (gene, externalDb);
Gene_setExternalStatus(gene, externalStatus);
Gene_setDisplayXref (gene, displayXref);
Gene_setStatus (gene, status);
Gene_setSource (gene, source);
Gene_setIsCurrent (gene, isCurrent);
Gene_setCanonicalTranscriptId(gene, canonicalTranscriptId);
Expand Down
34 changes: 12 additions & 22 deletions src/DataAdaptors/TranscriptAdaptor.c
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,6 @@ char *Transcript_cols[] = {
"UNIX_TIMESTAMP(t.modified_date)",
"t.description",
"t.biotype",
"t.status",
"exdb.db_name",
"exdb.status",
"exdb.db_display_name",
Expand Down Expand Up @@ -1051,7 +1050,6 @@ IDType TranscriptAdaptor_store(TranscriptAdaptor *ta, Transcript *transcript, ID
"seq_region_end = %ld, "
"seq_region_strand = %d, "
"biotype = %%s, "
"status = %%s, "
"description = %%s, "
//"biotype = '%s', "
//"status = '%s', "
Expand All @@ -1075,20 +1073,14 @@ IDType TranscriptAdaptor_store(TranscriptAdaptor *ta, Transcript *transcript, ID
} else {
sprintf(bioTypeQStr, "NULL");
}
char statusQStr[1024];
if (Transcript_getStatus(transcript)) {
sprintf(statusQStr,"'%s'", Transcript_getStatus(transcript));
} else {
sprintf(statusQStr, "NULL");
}
char descQStr[1024];
if (Transcript_getDescription(transcript)) {
sprintf(descQStr,"'%s'", Transcript_getDescription(transcript));
} else {
sprintf(descQStr, "NULL");
}

sprintf(qStr, fmtStr, bioTypeQStr, statusQStr, descQStr);
sprintf(qStr, fmtStr, bioTypeQStr, descQStr);

if (Transcript_getStableId(transcript)) {
/* Use FROM_UNIXTIME for now
Expand Down Expand Up @@ -1822,21 +1814,20 @@ Vector *TranscriptAdaptor_objectsFromStatementHandle(TranscriptAdaptor *ta,
int modifiedDate = row->getIntAt(row,11);
char *description = row->getStringAt(row,12);
char *biotype = row->getStringAt(row,13);
char *status = row->getStringAt(row,14);
char *externalDb = row->getStringAt(row,15);
char *externalStatus = row->getStringAt(row,16);
char *externalDbName = row->getStringAt(row,17);
char *externalDb = row->getStringAt(row,14);
char *externalStatus = row->getStringAt(row,15);
char *externalDbName = row->getStringAt(row,16);
// Note changed from xrefId to displayXrefId to match GeneAdaptor version of this code
IDType displayXrefId = row->getLongLongAt(row,18);
char *xrefDisplayLabel = row->getStringAt(row,19);
char *xrefPrimaryAcc = row->getStringAt(row,20);
char *xrefVersion = row->getStringAt(row,21);
IDType displayXrefId = row->getLongLongAt(row,17);
char *xrefDisplayLabel = row->getStringAt(row,18);
char *xrefPrimaryAcc = row->getStringAt(row,19);
char *xrefVersion = row->getStringAt(row,20);
// Note changed from xrefDescription to xrefDesc to match GeneAdaptor version of this code
char *xrefDesc = row->getStringAt(row,22);
char *xrefInfoType = row->getStringAt(row,23);
char *xrefInfoText = row->getStringAt(row,24);
char *xrefDesc = row->getStringAt(row,21);
char *xrefInfoType = row->getStringAt(row,22);
char *xrefInfoText = row->getStringAt(row,23);
// Added externalRelease to be consistent with Gene version
char *externalRelease = row->getStringAt(row,25);
char *externalRelease = row->getStringAt(row,24);

Analysis *analysis = AnalysisAdaptor_fetchByDbID(aa, analysisId);

Expand Down Expand Up @@ -2058,7 +2049,6 @@ Vector *TranscriptAdaptor_objectsFromStatementHandle(TranscriptAdaptor *ta,
Transcript_setExternalDb (transcript, externalDb);
Transcript_setExternalStatus(transcript, externalStatus);
Transcript_setDisplayXref (transcript, displayXref);
Transcript_setStatus (transcript, status);
Transcript_setIsCurrent (transcript, isCurrent);
Transcript_setEditsEnabled (transcript, 1);

Expand Down
11 changes: 0 additions & 11 deletions src/DataModel/Gene.c
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Original file line number Diff line number Diff line change
Expand Up @@ -315,17 +315,6 @@ ECOSTRING Gene_setBiotype(Gene *g, char *biotype) {
return g->biotype;
}

ECOSTRING Gene_setStatus(Gene *g, char *status) {
EcoString_copyStr(ecoSTable, &(g->status),status,0);

if (g->status == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for status\n");
return NULL;
}

return g->status;
}

ECOSTRING Gene_setSource(Gene *g, char *source) {
EcoString_copyStr(ecoSTable, &(g->source),source,0);

Expand Down
3 changes: 0 additions & 3 deletions src/DataModel/Gene.h
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Original file line number Diff line number Diff line change
Expand Up @@ -95,9 +95,6 @@ ECOSTRING Gene_setExternalDb(Gene *gene, char *externalDb);
#define Gene_getExternalDb(gene) (gene)->externalDb


ECOSTRING Gene_setStatus(Gene *gene, char *status);
#define Gene_getStatus(gene) (gene)->status

ECOSTRING Gene_setSource(Gene *gene, char *source);
#define Gene_getSource(gene) (gene)->source

Expand Down
11 changes: 0 additions & 11 deletions src/DataModel/Transcript.c
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Original file line number Diff line number Diff line change
Expand Up @@ -487,17 +487,6 @@ ECOSTRING Transcript_getBiotype(Transcript *t) {
}
}

ECOSTRING Transcript_setStatus(Transcript *t, char *status) {
EcoString_copyStr(ecoSTable, &(t->status),status,0);

if (t->status == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for status\n");
return NULL;
}

return t->status;
}

char *Transcript_setDescription(Transcript *t, char *description) {
if ((t->description = (char *)malloc(strlen(description)+1)) == NULL) {
fprintf(stderr,"ERROR: Failed allocating space for description\n");
Expand Down
3 changes: 0 additions & 3 deletions src/DataModel/Transcript.h
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Original file line number Diff line number Diff line change
Expand Up @@ -167,9 +167,6 @@ Translation *Transcript_getTranslation(Transcript *trans);
char *Transcript_setDescription(Transcript *t, char *description);
#define Transcript_getDescription(transcript) (transcript)->description

ECOSTRING Transcript_setStatus(Transcript *t, char *status);
#define Transcript_getStatus(transcript) (transcript)->status

ECOSTRING Transcript_setExternalDb(Transcript *t, char *externalDb);
ECOSTRING Transcript_setExternalStatus(Transcript *t, char *externalStatus);
char *Transcript_setExternalName(Transcript *t, char *externalName);
Expand Down

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