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/dbSnpRs.c src/hg/cgilib/dbSnpRs.c new file mode 100644 index 0000000..e56a76d --- /dev/null +++ src/hg/cgilib/dbSnpRs.c @@ -0,0 +1,213 @@ +/* dbSnpRs.c was originally generated by the autoSql program, which also + * generated dbSnpRs.h and dbSnpRs.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 "dbSnpRs.h" + + +void dbSnpRsStaticLoad(char **row, struct dbSnpRs *ret) +/* Load a row from dbSnpRs table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->rsId = row[0]; +ret->avHet = atof(row[1]); +ret->avHetSE = atof(row[2]); +ret->valid = row[3]; +ret->allele1 = row[4]; +ret->allele2 = row[5]; +ret->assembly = row[6]; +ret->alternate = row[7]; +ret->func = row[8]; +} + +struct dbSnpRs *dbSnpRsLoad(char **row) +/* Load a dbSnpRs from row fetched with select * from dbSnpRs + * from database. Dispose of this with dbSnpRsFree(). */ +{ +struct dbSnpRs *ret; + +AllocVar(ret); +ret->rsId = cloneString(row[0]); +ret->avHet = atof(row[1]); +ret->avHetSE = atof(row[2]); +ret->valid = cloneString(row[3]); +ret->allele1 = cloneString(row[4]); +ret->allele2 = cloneString(row[5]); +ret->assembly = cloneString(row[6]); +ret->alternate = cloneString(row[7]); +ret->func = cloneString(row[8]); +return ret; +} + +struct dbSnpRs *dbSnpRsLoadAll(char *fileName) +/* Load all dbSnpRs from a whitespace-separated file. + * Dispose of this with dbSnpRsFreeList(). */ +{ +struct dbSnpRs *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[9]; + +while (lineFileRow(lf, row)) + { + el = dbSnpRsLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dbSnpRs *dbSnpRsLoadAllByChar(char *fileName, char chopper) +/* Load all dbSnpRs from a chopper separated file. + * Dispose of this with dbSnpRsFreeList(). */ +{ +struct dbSnpRs *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[9]; + +while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) + { + el = dbSnpRsLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct dbSnpRs *dbSnpRsLoadByQuery(struct sqlConnection *conn, char *query) +/* Load all dbSnpRs 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 dbSnpRsFreeList(). */ +{ +struct dbSnpRs *list = NULL, *el; +struct sqlResult *sr; +char **row; + +sr = sqlGetResult(conn, query); +while ((row = sqlNextRow(sr)) != NULL) + { + el = dbSnpRsLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +return list; +} + +void dbSnpRsSaveToDb(struct sqlConnection *conn, struct dbSnpRs *el, char *tableName, int updateSize) +/* Save dbSnpRs 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',%f,%f,'%s','%s','%s','%s','%s','%s')", + tableName, el->rsId, el->avHet, el->avHetSE, el->valid, el->allele1, el->allele2, el->assembly, el->alternate, el->func); +sqlUpdate(conn, update->string); +freeDyString(&update); +} + + +struct dbSnpRs *dbSnpRsCommaIn(char **pS, struct dbSnpRs *ret) +/* Create a dbSnpRs out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new dbSnpRs */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +ret->rsId = sqlStringComma(&s); +ret->avHet = sqlFloatComma(&s); +ret->avHetSE = sqlFloatComma(&s); +ret->valid = sqlStringComma(&s); +ret->allele1 = sqlStringComma(&s); +ret->allele2 = sqlStringComma(&s); +ret->assembly = sqlStringComma(&s); +ret->alternate = sqlStringComma(&s); +ret->func = sqlStringComma(&s); +*pS = s; +return ret; +} + +void dbSnpRsFree(struct dbSnpRs **pEl) +/* Free a single dynamically allocated dbSnpRs such as created + * with dbSnpRsLoad(). */ +{ +struct dbSnpRs *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->rsId); +freeMem(el->valid); +freeMem(el->allele1); +freeMem(el->allele2); +freeMem(el->assembly); +freeMem(el->alternate); +freeMem(el->func); +freez(pEl); +} + +void dbSnpRsFreeList(struct dbSnpRs **pList) +/* Free a list of dynamically allocated dbSnpRs's */ +{ +struct dbSnpRs *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + dbSnpRsFree(&el); + } +*pList = NULL; +} + +void dbSnpRsOutput(struct dbSnpRs *el, FILE *f, char sep, char lastSep) +/* Print out dbSnpRs. Separate fields with sep. Follow last field with lastSep. */ +{ +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->rsId); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%f", el->avHet); +fputc(sep,f); +fprintf(f, "%f", el->avHetSE); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->valid); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->allele1); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->allele2); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->assembly); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->alternate); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->func); +if (sep == ',') fputc('"',f); +fputc(lastSep,f); +} + +/* -------------------------------- End autoSql Generated Code -------------------------------- */ +