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/lib/dbRIP.c src/hg/lib/dbRIP.c deleted file mode 100644 index 034f943..0000000 --- src/hg/lib/dbRIP.c +++ /dev/null @@ -1,304 +0,0 @@ -/* 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 -------------------------------- */ -