c88b8a093cac2bc72ca4b4e3ff1fc2d1aea17f55 hiram Sat Feb 3 13:59:52 2024 -0800 the NULL specification confused autoSql for numbers that should be zero refs #23589 diff --git src/hg/lib/asmSummary.c src/hg/lib/asmSummary.c index 01a54fd..47f0847 100644 --- src/hg/lib/asmSummary.c +++ src/hg/lib/asmSummary.c @@ -1,858 +1,785 @@ /* asmSummary.c was originally generated by the autoSql program, which also * generated asmSummary.h and asmSummary.sql. This module links the database and * the RAM representation of objects. */ #include "common.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "asmSummary.h" char *asmSummaryCommaSepFieldNames = "assemblyAccession,bioproject,biosample,wgsMaster,refseqCategory,taxId,speciesTaxid,organismName,infraspecificName,isolate,versionStatus,assemblyLevel,releaseType,genomeRep,seqRelDate,asmName,asmSubmitter,gbrsPairedAsm,pairedAsmComp,ftpPath,excludedFromRefseq,relationToTypeMaterial,assemblyType,phyloGroup,genomeSize,genomeSizeUngapped,gcPercent,repliconCount,scaffoldCount,contigCount,annotationProvider,annotationName,annotationDate,totalGeneCount,proteinCodingGeneCount,nonCodingGeneCount,pubmedId"; void asmSummaryStaticLoadWithNull(char **row, struct asmSummary *ret) /* Load a row from asmSummary table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->assemblyAccession = row[0]; ret->bioproject = row[1]; ret->biosample = row[2]; ret->wgsMaster = row[3]; ret->refseqCategory = row[4]; +ret->taxId = 0; +ret->speciesTaxid = 0; if (row[5] != NULL) { - ret->taxId = needMem(sizeof(*(ret->taxId))); - *(ret->taxId) = sqlUnsigned(row[5]); - } -else - { - ret->taxId = NULL; + ret->taxId = sqlUnsigned(row[5]); } if (row[6] != NULL) { - ret->speciesTaxid = needMem(sizeof(*(ret->speciesTaxid))); - *(ret->speciesTaxid) = sqlUnsigned(row[6]); - } -else - { - ret->speciesTaxid = NULL; + ret->speciesTaxid = sqlUnsigned(row[6]); } ret->organismName = row[7]; ret->infraspecificName = row[8]; ret->isolate = row[9]; ret->versionStatus = row[10]; ret->assemblyLevel = row[11]; ret->releaseType = row[12]; ret->genomeRep = row[13]; ret->seqRelDate = row[14]; ret->asmName = row[15]; ret->asmSubmitter = row[16]; ret->gbrsPairedAsm = row[17]; ret->pairedAsmComp = row[18]; ret->ftpPath = row[19]; ret->excludedFromRefseq = row[20]; ret->relationToTypeMaterial = row[21]; ret->assemblyType = row[22]; ret->phyloGroup = row[23]; +ret->genomeSize = 0; +ret->genomeSizeUngapped = 0; +ret->gcPercent = 0.0; +ret->repliconCount = 0; +ret->scaffoldCount = 0; +ret->contigCount = 0; +ret->proteinCodingGeneCount = 0; if (row[24] != NULL) { - ret->genomeSize = needMem(sizeof(*(ret->genomeSize))); - *(ret->genomeSize) = sqlLongLong(row[24]); - } -else - { - ret->genomeSize = NULL; + ret->genomeSize = sqlLongLong(row[24]); } if (row[25] != NULL) { - ret->genomeSizeUngapped = needMem(sizeof(*(ret->genomeSizeUngapped))); - *(ret->genomeSizeUngapped) = sqlLongLong(row[25]); - } -else - { - ret->genomeSizeUngapped = NULL; + ret->genomeSizeUngapped = sqlLongLong(row[25]); } if (row[26] != NULL) { - ret->gcPercent = needMem(sizeof(float)); - *(ret->gcPercent) = sqlFloat(row[26]); + ret->gcPercent = sqlFloat(row[26]); } if (row[27] != NULL) { - ret->repliconCount = needMem(sizeof(*(ret->repliconCount))); - *(ret->repliconCount) = sqlUnsigned(row[27]); - } -else - { - ret->repliconCount = NULL; + ret->repliconCount = sqlUnsigned(row[27]); } if (row[28] != NULL) { - ret->scaffoldCount = needMem(sizeof(*(ret->scaffoldCount))); - *(ret->scaffoldCount) = sqlUnsigned(row[28]); - } -else - { - ret->scaffoldCount = NULL; + ret->scaffoldCount = sqlUnsigned(row[28]); } if (row[29] != NULL) { - ret->contigCount = needMem(sizeof(*(ret->contigCount))); - *(ret->contigCount) = sqlUnsigned(row[29]); - } -else - { - ret->contigCount = NULL; + ret->contigCount = sqlUnsigned(row[29]); } ret->annotationProvider = row[30]; ret->annotationName = row[31]; ret->annotationDate = row[32]; ret->totalGeneCount = row[33]; if (row[34] != NULL) { - ret->proteinCodingGeneCount = needMem(sizeof(*(ret->proteinCodingGeneCount))); - *(ret->proteinCodingGeneCount) = sqlUnsigned(row[34]); - } -else - { - ret->proteinCodingGeneCount = NULL; + ret->proteinCodingGeneCount = sqlUnsigned(row[34]); } ret->nonCodingGeneCount = row[35]; ret->pubmedId = row[36]; } struct asmSummary *asmSummaryLoadByQuery(struct sqlConnection *conn, char *query) /* Load all asmSummary from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with asmSummaryFreeList(). */ { struct asmSummary *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = asmSummaryLoadWithNull(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void asmSummarySaveToDb(struct sqlConnection *conn, struct asmSummary *el, char *tableName, int updateSize) /* Save asmSummary as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ { struct dyString *update = dyStringNew(updateSize); sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%u,%u,'%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s','%s',%lld,%lld,%g,%u,%u,%u,'%s','%s','%s','%s',%u,'%s','%s')", - tableName, el->assemblyAccession, el->bioproject, el->biosample, el->wgsMaster, el->refseqCategory, *(el->taxId), *(el->speciesTaxid), el->organismName, el->infraspecificName, el->isolate, el->versionStatus, el->assemblyLevel, el->releaseType, el->genomeRep, el->seqRelDate, el->asmName, el->asmSubmitter, el->gbrsPairedAsm, el->pairedAsmComp, el->ftpPath, el->excludedFromRefseq, el->relationToTypeMaterial, el->assemblyType, el->phyloGroup, *(el->genomeSize), *(el->genomeSizeUngapped), *(el->gcPercent), *(el->repliconCount), *(el->scaffoldCount), *(el->contigCount), el->annotationProvider, el->annotationName, el->annotationDate, el->totalGeneCount, *(el->proteinCodingGeneCount), el->nonCodingGeneCount, el->pubmedId); + tableName, el->assemblyAccession, el->bioproject, el->biosample, el->wgsMaster, el->refseqCategory, el->taxId, el->speciesTaxid, el->organismName, el->infraspecificName, el->isolate, el->versionStatus, el->assemblyLevel, el->releaseType, el->genomeRep, el->seqRelDate, el->asmName, el->asmSubmitter, el->gbrsPairedAsm, el->pairedAsmComp, el->ftpPath, el->excludedFromRefseq, el->relationToTypeMaterial, el->assemblyType, el->phyloGroup, el->genomeSize, el->genomeSizeUngapped, el->gcPercent, el->repliconCount, el->scaffoldCount, el->contigCount, el->annotationProvider, el->annotationName, el->annotationDate, el->totalGeneCount, el->proteinCodingGeneCount, el->nonCodingGeneCount, el->pubmedId); sqlUpdate(conn, update->string); dyStringFree(&update); } struct asmSummary *asmSummaryLoadWithNull(char **row) /* Load a asmSummary from row fetched with select * from asmSummary * from database. Dispose of this with asmSummaryFree(). */ { struct asmSummary *ret; AllocVar(ret); ret->assemblyAccession = cloneString(row[0]); ret->bioproject = cloneString(row[1]); ret->biosample = cloneString(row[2]); ret->wgsMaster = cloneString(row[3]); ret->refseqCategory = cloneString(row[4]); +ret->taxId = 0; +ret->speciesTaxid = 0; if (row[5] != NULL) { - ret->taxId = needMem(sizeof(*(ret->taxId))); - *(ret->taxId) = sqlUnsigned(row[5]); - } -else - { - ret->taxId = NULL; + ret->taxId = sqlUnsigned(row[5]); } if (row[6] != NULL) { - ret->speciesTaxid = needMem(sizeof(*(ret->speciesTaxid))); - *(ret->speciesTaxid) = sqlUnsigned(row[6]); - } -else - { - ret->speciesTaxid = NULL; + ret->speciesTaxid = sqlUnsigned(row[6]); } ret->organismName = cloneString(row[7]); ret->infraspecificName = cloneString(row[8]); ret->isolate = cloneString(row[9]); ret->versionStatus = cloneString(row[10]); ret->assemblyLevel = cloneString(row[11]); ret->releaseType = cloneString(row[12]); ret->genomeRep = cloneString(row[13]); ret->seqRelDate = cloneString(row[14]); ret->asmName = cloneString(row[15]); ret->asmSubmitter = cloneString(row[16]); ret->gbrsPairedAsm = cloneString(row[17]); ret->pairedAsmComp = cloneString(row[18]); ret->ftpPath = cloneString(row[19]); ret->excludedFromRefseq = cloneString(row[20]); ret->relationToTypeMaterial = cloneString(row[21]); ret->assemblyType = cloneString(row[22]); ret->phyloGroup = cloneString(row[23]); +ret->genomeSize = 0; +ret->genomeSizeUngapped = 0; +ret->gcPercent = 0.0; +ret->repliconCount = 0; +ret->scaffoldCount = 0; +ret->contigCount = 0; +ret->proteinCodingGeneCount = 0; if (row[24] != NULL) { - ret->genomeSize = needMem(sizeof(*(ret->genomeSize))); - *(ret->genomeSize) = sqlLongLong(row[24]); - } -else - { - ret->genomeSize = NULL; + ret->genomeSize = sqlLongLong(row[24]); } if (row[25] != NULL) { - ret->genomeSizeUngapped = needMem(sizeof(*(ret->genomeSizeUngapped))); - *(ret->genomeSizeUngapped) = sqlLongLong(row[25]); - } -else - { - ret->genomeSizeUngapped = NULL; + ret->genomeSizeUngapped = sqlLongLong(row[25]); } if (row[26] != NULL) { - ret->gcPercent = needMem(sizeof(float)); - *(ret->gcPercent) = sqlFloat(row[26]); + ret->gcPercent = sqlFloat(row[26]); } if (row[27] != NULL) { - ret->repliconCount = needMem(sizeof(*(ret->repliconCount))); - *(ret->repliconCount) = sqlUnsigned(row[27]); - } -else - { - ret->repliconCount = NULL; + ret->repliconCount = sqlUnsigned(row[27]); } if (row[28] != NULL) { - ret->scaffoldCount = needMem(sizeof(*(ret->scaffoldCount))); - *(ret->scaffoldCount) = sqlUnsigned(row[28]); - } -else - { - ret->scaffoldCount = NULL; + ret->scaffoldCount = sqlUnsigned(row[28]); } if (row[29] != NULL) { - ret->contigCount = needMem(sizeof(*(ret->contigCount))); - *(ret->contigCount) = sqlUnsigned(row[29]); - } -else - { - ret->contigCount = NULL; + ret->contigCount = sqlUnsigned(row[29]); } ret->annotationProvider = cloneString(row[30]); ret->annotationName = cloneString(row[31]); ret->annotationDate = cloneString(row[32]); ret->totalGeneCount = cloneString(row[33]); if (row[34] != NULL) { - ret->proteinCodingGeneCount = needMem(sizeof(*(ret->proteinCodingGeneCount))); - *(ret->proteinCodingGeneCount) = sqlUnsigned(row[34]); - } -else - { - ret->proteinCodingGeneCount = NULL; + ret->proteinCodingGeneCount = sqlUnsigned(row[34]); } ret->nonCodingGeneCount = cloneString(row[35]); ret->pubmedId = cloneString(row[36]); return ret; } struct asmSummary *asmSummaryLoadAll(char *fileName) /* Load all asmSummary from a whitespace-separated file. * Dispose of this with asmSummaryFreeList(). */ { struct asmSummary *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[37]; while (lineFileRow(lf, row)) { el = asmSummaryLoadWithNull(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct asmSummary *asmSummaryLoadAllByChar(char *fileName, char chopper) /* Load all asmSummary from a chopper separated file. * Dispose of this with asmSummaryFreeList(). */ { struct asmSummary *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[37]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = asmSummaryLoadWithNull(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct asmSummary *asmSummaryCommaIn(char **pS, struct asmSummary *ret) /* Create a asmSummary out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new asmSummary */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->assemblyAccession = sqlStringComma(&s); ret->bioproject = sqlStringComma(&s); ret->biosample = sqlStringComma(&s); ret->wgsMaster = sqlStringComma(&s); ret->refseqCategory = sqlStringComma(&s); -ret->taxId = needMem(sizeof(unsigned)); -*(ret->taxId) = sqlUnsignedComma(&s); -ret->speciesTaxid = needMem(sizeof(unsigned)); -*(ret->speciesTaxid) = sqlUnsignedComma(&s); +ret->taxId = sqlUnsignedComma(&s); +ret->speciesTaxid = sqlUnsignedComma(&s); ret->organismName = sqlStringComma(&s); ret->infraspecificName = sqlStringComma(&s); ret->isolate = sqlStringComma(&s); ret->versionStatus = sqlStringComma(&s); ret->assemblyLevel = sqlStringComma(&s); ret->releaseType = sqlStringComma(&s); ret->genomeRep = sqlStringComma(&s); ret->seqRelDate = sqlStringComma(&s); ret->asmName = sqlStringComma(&s); ret->asmSubmitter = sqlStringComma(&s); ret->gbrsPairedAsm = sqlStringComma(&s); ret->pairedAsmComp = sqlStringComma(&s); ret->ftpPath = sqlStringComma(&s); ret->excludedFromRefseq = sqlStringComma(&s); ret->relationToTypeMaterial = sqlStringComma(&s); ret->assemblyType = sqlStringComma(&s); ret->phyloGroup = sqlStringComma(&s); -ret->genomeSize = needMem(sizeof(*(ret->genomeSize))); -*(ret->genomeSize) = sqlLongLongComma(&s); -ret->genomeSizeUngapped = needMem(sizeof(*(ret->genomeSizeUngapped))); -*(ret->genomeSizeUngapped) = sqlLongLongComma(&s); -ret->gcPercent = needMem(sizeof(*(ret->gcPercent))); -*(ret->gcPercent) = sqlFloatComma(&s); -ret->repliconCount = needMem(sizeof(unsigned)); -*(ret->repliconCount) = sqlUnsignedComma(&s); -ret->scaffoldCount = needMem(sizeof(unsigned)); -*(ret->scaffoldCount) = sqlUnsignedComma(&s); -ret->contigCount = needMem(sizeof(unsigned)); -*(ret->contigCount) = sqlUnsignedComma(&s); +ret->genomeSize = sqlLongLongComma(&s); +ret->genomeSizeUngapped = sqlLongLongComma(&s); +ret->gcPercent = sqlFloatComma(&s); +ret->repliconCount = sqlUnsignedComma(&s); +ret->scaffoldCount = sqlUnsignedComma(&s); +ret->contigCount = sqlUnsignedComma(&s); ret->annotationProvider = sqlStringComma(&s); ret->annotationName = sqlStringComma(&s); ret->annotationDate = sqlStringComma(&s); ret->totalGeneCount = sqlStringComma(&s); -ret->proteinCodingGeneCount = needMem(sizeof(unsigned)); -*(ret->proteinCodingGeneCount) = sqlUnsignedComma(&s); +ret->proteinCodingGeneCount = sqlUnsignedComma(&s); ret->nonCodingGeneCount = sqlStringComma(&s); ret->pubmedId = sqlStringComma(&s); *pS = s; return ret; } void asmSummaryFree(struct asmSummary **pEl) /* Free a single dynamically allocated asmSummary such as created * with asmSummaryLoad(). */ { struct asmSummary *el; if ((el = *pEl) == NULL) return; freeMem(el->assemblyAccession); freeMem(el->bioproject); freeMem(el->biosample); freeMem(el->wgsMaster); freeMem(el->refseqCategory); freeMem(el->organismName); freeMem(el->infraspecificName); freeMem(el->isolate); freeMem(el->versionStatus); freeMem(el->assemblyLevel); freeMem(el->releaseType); freeMem(el->genomeRep); freeMem(el->seqRelDate); freeMem(el->asmName); freeMem(el->asmSubmitter); freeMem(el->gbrsPairedAsm); freeMem(el->pairedAsmComp); freeMem(el->ftpPath); freeMem(el->excludedFromRefseq); freeMem(el->relationToTypeMaterial); freeMem(el->assemblyType); freeMem(el->phyloGroup); freeMem(el->annotationProvider); freeMem(el->annotationName); freeMem(el->annotationDate); freeMem(el->totalGeneCount); freeMem(el->nonCodingGeneCount); freeMem(el->pubmedId); freez(pEl); } void asmSummaryFreeList(struct asmSummary **pList) /* Free a list of dynamically allocated asmSummary's */ { struct asmSummary *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; asmSummaryFree(&el); } *pList = NULL; } void asmSummaryOutput(struct asmSummary *el, FILE *f, char sep, char lastSep) /* Print out asmSummary. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->assemblyAccession); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->bioproject); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->biosample); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->wgsMaster); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->refseqCategory); if (sep == ',') fputc('"',f); fputc(sep,f); -fprintf(f, "%u", *(el->taxId)); +fprintf(f, "%u", el->taxId); fputc(sep,f); -fprintf(f, "%u", *(el->speciesTaxid)); +fprintf(f, "%u", el->speciesTaxid); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->organismName); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->infraspecificName); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->isolate); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->versionStatus); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->assemblyLevel); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->releaseType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->genomeRep); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->seqRelDate); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->asmName); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->asmSubmitter); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->gbrsPairedAsm); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->pairedAsmComp); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->ftpPath); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->excludedFromRefseq); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->relationToTypeMaterial); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->assemblyType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->phyloGroup); if (sep == ',') fputc('"',f); fputc(sep,f); -fprintf(f, "%lld", *(el->genomeSize)); +fprintf(f, "%lld", el->genomeSize); fputc(sep,f); -fprintf(f, "%lld", *(el->genomeSizeUngapped)); +fprintf(f, "%lld", el->genomeSizeUngapped); fputc(sep,f); -fprintf(f, "%g", *(el->gcPercent)); +fprintf(f, "%g", el->gcPercent); fputc(sep,f); -fprintf(f, "%u", *(el->repliconCount)); +fprintf(f, "%u", el->repliconCount); fputc(sep,f); -fprintf(f, "%u", *(el->scaffoldCount)); +fprintf(f, "%u", el->scaffoldCount); fputc(sep,f); -fprintf(f, "%u", *(el->contigCount)); +fprintf(f, "%u", el->contigCount); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->annotationProvider); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->annotationName); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->annotationDate); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->totalGeneCount); if (sep == ',') fputc('"',f); fputc(sep,f); -fprintf(f, "%u", *(el->proteinCodingGeneCount)); +fprintf(f, "%u", el->proteinCodingGeneCount); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->nonCodingGeneCount); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->pubmedId); if (sep == ',') fputc('"',f); fputc(lastSep,f); } void asmSummaryJsonOutput(struct asmSummary *el, FILE *f) /* Print out asmSummary in JSON format. */ { fputc('{',f); fputc('"',f); fprintf(f,"assemblyAccession"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->assemblyAccession); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"bioproject"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->bioproject); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"biosample"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->biosample); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"wgsMaster"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->wgsMaster); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"refseqCategory"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->refseqCategory); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"taxId"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->taxId)); +fprintf(f, "%u", el->taxId); fputc(',',f); fputc('"',f); fprintf(f,"speciesTaxid"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->speciesTaxid)); +fprintf(f, "%u", el->speciesTaxid); fputc(',',f); fputc('"',f); fprintf(f,"organismName"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->organismName); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"infraspecificName"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->infraspecificName); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"isolate"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->isolate); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"versionStatus"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->versionStatus); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"assemblyLevel"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->assemblyLevel); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"releaseType"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->releaseType); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"genomeRep"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->genomeRep); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"seqRelDate"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->seqRelDate); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"asmName"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->asmName); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"asmSubmitter"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->asmSubmitter); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"gbrsPairedAsm"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->gbrsPairedAsm); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"pairedAsmComp"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->pairedAsmComp); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"ftpPath"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->ftpPath); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"excludedFromRefseq"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->excludedFromRefseq); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"relationToTypeMaterial"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->relationToTypeMaterial); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"assemblyType"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->assemblyType); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"phyloGroup"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->phyloGroup); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"genomeSize"); fputc('"',f); fputc(':',f); -fprintf(f, "%lld", *(el->genomeSize)); +fprintf(f, "%lld", el->genomeSize); fputc(',',f); fputc('"',f); fprintf(f,"genomeSizeUngapped"); fputc('"',f); fputc(':',f); -fprintf(f, "%lld", *(el->genomeSizeUngapped)); +fprintf(f, "%lld", el->genomeSizeUngapped); fputc(',',f); fputc('"',f); fprintf(f,"gcPercent"); fputc('"',f); fputc(':',f); -fprintf(f, "%g", *(el->gcPercent)); +fprintf(f, "%g", el->gcPercent); fputc(',',f); fputc('"',f); fprintf(f,"repliconCount"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->repliconCount)); +fprintf(f, "%u", el->repliconCount); fputc(',',f); fputc('"',f); fprintf(f,"scaffoldCount"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->scaffoldCount)); +fprintf(f, "%u", el->scaffoldCount); fputc(',',f); fputc('"',f); fprintf(f,"contigCount"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->contigCount)); +fprintf(f, "%u", el->contigCount); fputc(',',f); fputc('"',f); fprintf(f,"annotationProvider"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->annotationProvider); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"annotationName"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->annotationName); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"annotationDate"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->annotationDate); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"totalGeneCount"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->totalGeneCount); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"proteinCodingGeneCount"); fputc('"',f); fputc(':',f); -fprintf(f, "%u", *(el->proteinCodingGeneCount)); +fprintf(f, "%u", el->proteinCodingGeneCount); fputc(',',f); fputc('"',f); fprintf(f,"nonCodingGeneCount"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->nonCodingGeneCount); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"pubmedId"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->pubmedId); fputc('"',f); fputc('}',f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct asmSummary *asmSummaryFullText(struct sqlConnection *conn, char *words, long long rowLimit, long long *totalMatch) /* perform a FULLTEXT search on the asmSummary table with the list * of words string (may be only a single word) * return is a list of items found up to rowLimit, or NULL if none found * also returning totalMatch to understand if it is more than the rowLimit */ { char query[4096]; sqlSafef(query, sizeof(query), "SELECT count(*) FROM asmSummary WHERE MATCH (bioproject, biosample, organismName, isolate, asmName, asmSubmitter, annotationProvider, annotationName) AGAINST (\"%s\")", words); *totalMatch = (long long) sqlQuickNum(conn, query); sqlSafef(query, sizeof(query), "SELECT * FROM asmSummary WHERE MATCH (bioproject, biosample, organismName, isolate, asmName, asmSubmitter, annotationProvider, annotationName) AGAINST (\"%s\") LIMIT %lld", words, rowLimit); struct asmSummary *list = asmSummaryLoadByQuery(conn, query); return list; }