533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/cgilib/dbRIP.c src/hg/cgilib/dbRIP.c new file mode 100644 index 0000000..034f943 --- /dev/null +++ src/hg/cgilib/dbRIP.c @@ -0,0 +1,304 @@ +/* dbRIP.c was originally generated by the autoSql program, which also + * generated dbRIP.h and dbRIP.sql. This module links the database and + * the RAM representation of objects. */ + +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + +#include "common.h" +#include "linefile.h" +#include "dystring.h" +#include "jksql.h" +#include "dbRIP.h" + + +void dbRIPStaticLoad(char **row, struct dbRIP *ret) +/* Load a row from dbRIP table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = row[3]; +ret->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->originalId = row[6]; +ret->forwardPrimer = row[7]; +ret->reversePrimer = row[8]; +ret->polyClass = row[9]; +ret->polyFamily = row[10]; +ret->polySubfamily = row[11]; +ret->polySeq = row[12]; +ret->polySource = row[13]; +ret->reference = row[14]; +ret->ascertainingMethod = row[15]; +ret->remarks = row[16]; +ret->tm = atof(row[17]); +ret->filledSize = sqlSigned(row[18]); +ret->emptySize = sqlSigned(row[19]); +ret->disease = row[20]; +ret->genoRegion = row[21]; +} + +struct dbRIP *dbRIPLoad(char **row) +/* Load a dbRIP from row fetched with select * from dbRIP + * from database. Dispose of this with dbRIPFree(). */ +{ +struct dbRIP *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->originalId = cloneString(row[6]); +ret->forwardPrimer = cloneString(row[7]); +ret->reversePrimer = cloneString(row[8]); +ret->polyClass = cloneString(row[9]); +ret->polyFamily = cloneString(row[10]); +ret->polySubfamily = cloneString(row[11]); +ret->polySeq = cloneString(row[12]); +ret->polySource = cloneString(row[13]); +ret->reference = cloneString(row[14]); +ret->ascertainingMethod = cloneString(row[15]); +ret->remarks = cloneString(row[16]); +ret->tm = atof(row[17]); +ret->filledSize = sqlSigned(row[18]); +ret->emptySize = sqlSigned(row[19]); +ret->disease = cloneString(row[20]); +ret->genoRegion = cloneString(row[21]); +return ret; +} + +struct dbRIP *dbRIPLoadAll(char *fileName) +/* Load all dbRIP from a whitespace-separated file. + * Dispose of this with dbRIPFreeList(). */ +{ +struct dbRIP *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[22]; + +while (lineFileRow(lf, row)) + { + el = dbRIPLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dbRIP *dbRIPLoadAllByChar(char *fileName, char chopper) +/* Load all dbRIP from a chopper separated file. + * Dispose of this with dbRIPFreeList(). */ +{ +struct dbRIP *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[22]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = dbRIPLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dbRIP *dbRIPLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all dbRIP 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 dbRIPFreeList(). */ +{ +struct dbRIP *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = dbRIPLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void dbRIPSaveToDb(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize) +/* Save dbRIP 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. Strings are automatically escaped to allow insertion into the database. */ +{ +struct dyString *update = newDyString(updateSize); +sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')", + tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand, el->originalId, el->forwardPrimer, el->reversePrimer, el->polyClass, el->polyFamily, el->polySubfamily, el->polySeq, el->polySource, el->reference, el->ascertainingMethod, el->remarks, el->tm, el->filledSize, el->emptySize, el->disease, el->genoRegion); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct dbRIP *dbRIPCommaIn(char **pS, struct dbRIP *ret) +/* Create a dbRIP out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new dbRIP */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->chrom = sqlStringComma(&s); +ret->chromStart = sqlUnsignedComma(&s); +ret->chromEnd = sqlUnsignedComma(&s); +ret->name = sqlStringComma(&s); +ret->score = sqlUnsignedComma(&s); +sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); +ret->originalId = sqlStringComma(&s); +ret->forwardPrimer = sqlStringComma(&s); +ret->reversePrimer = sqlStringComma(&s); +ret->polyClass = sqlStringComma(&s); +ret->polyFamily = sqlStringComma(&s); +ret->polySubfamily = sqlStringComma(&s); +ret->polySeq = sqlStringComma(&s); +ret->polySource = sqlStringComma(&s); +ret->reference = sqlStringComma(&s); +ret->ascertainingMethod = sqlStringComma(&s); +ret->remarks = sqlStringComma(&s); +ret->tm = sqlFloatComma(&s); +ret->filledSize = sqlSignedComma(&s); +ret->emptySize = sqlSignedComma(&s); +ret->disease = sqlStringComma(&s); +ret->genoRegion = sqlStringComma(&s); +*pS = s; +return ret; +} + +void dbRIPFree(struct dbRIP **pEl) +/* Free a single dynamically allocated dbRIP such as created + * with dbRIPLoad(). */ +{ +struct dbRIP *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->originalId); +freeMem(el->forwardPrimer); +freeMem(el->reversePrimer); +freeMem(el->polyClass); +freeMem(el->polyFamily); +freeMem(el->polySubfamily); +freeMem(el->polySeq); +freeMem(el->polySource); +freeMem(el->reference); +freeMem(el->ascertainingMethod); +freeMem(el->remarks); +freeMem(el->disease); +freeMem(el->genoRegion); +freez(pEl); +} + +void dbRIPFreeList(struct dbRIP **pList) +/* Free a list of dynamically allocated dbRIP's */ +{ +struct dbRIP *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + dbRIPFree(&el); + } +*pList = NULL; +} + +void dbRIPOutput(struct dbRIP *el, FILE *f, char sep, char lastSep) +/* Print out dbRIP. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->chromStart); +fputc(sep,f); +fprintf(f, "%u", el->chromEnd); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->name); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->score); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->strand); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->originalId); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->forwardPrimer); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->reversePrimer); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->polyClass); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->polyFamily); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->polySubfamily); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->polySeq); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->polySource); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->reference); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->ascertainingMethod); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->remarks); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%g", el->tm); +fputc(sep,f); +fprintf(f, "%d", el->filledSize); +fputc(sep,f); +fprintf(f, "%d", el->emptySize); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->disease); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->genoRegion); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +