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/gwasCatalog.c src/hg/lib/gwasCatalog.c deleted file mode 100644 index 1e2959a..0000000 --- src/hg/lib/gwasCatalog.c +++ /dev/null @@ -1,280 +0,0 @@ -/* gwasCatalog.c was originally generated by the autoSql program, which also - * generated gwasCatalog.h and gwasCatalog.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 "gwasCatalog.h" - - -/* definitions for cnv column */ -static char *values_cnv[] = {"Y", "N", NULL}; -static struct hash *valhash_cnv = NULL; - -void gwasCatalogStaticLoad(char **row, struct gwasCatalog *ret) -/* Load a row from gwasCatalog 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->pubMedID = sqlUnsigned(row[4]); -ret->author = row[5]; -ret->pubDate = row[6]; -ret->journal = row[7]; -ret->title = row[8]; -ret->trait = row[9]; -ret->initSample = row[10]; -ret->replSample = row[11]; -ret->region = row[12]; -ret->genes = row[13]; -ret->riskAllele = row[14]; -ret->riskAlFreq = row[15]; -ret->pValue = row[16]; -ret->pValueDesc = row[17]; -ret->orOrBeta = row[18]; -ret->ci95 = row[19]; -ret->platform = row[20]; -ret->cnv = sqlEnumParse(row[21], values_cnv, &valhash_cnv); -} - -struct gwasCatalog *gwasCatalogLoad(char **row) -/* Load a gwasCatalog from row fetched with select * from gwasCatalog - * from database. Dispose of this with gwasCatalogFree(). */ -{ -struct gwasCatalog *ret; - -AllocVar(ret); -ret->chrom = cloneString(row[0]); -ret->chromStart = sqlUnsigned(row[1]); -ret->chromEnd = sqlUnsigned(row[2]); -ret->name = cloneString(row[3]); -ret->pubMedID = sqlUnsigned(row[4]); -ret->author = cloneString(row[5]); -ret->pubDate = cloneString(row[6]); -ret->journal = cloneString(row[7]); -ret->title = cloneString(row[8]); -ret->trait = cloneString(row[9]); -ret->initSample = cloneString(row[10]); -ret->replSample = cloneString(row[11]); -ret->region = cloneString(row[12]); -ret->genes = cloneString(row[13]); -ret->riskAllele = cloneString(row[14]); -ret->riskAlFreq = cloneString(row[15]); -ret->pValue = cloneString(row[16]); -ret->pValueDesc = cloneString(row[17]); -ret->orOrBeta = cloneString(row[18]); -ret->ci95 = cloneString(row[19]); -ret->platform = cloneString(row[20]); -ret->cnv = sqlEnumParse(row[21], values_cnv, &valhash_cnv); -return ret; -} - -struct gwasCatalog *gwasCatalogLoadAll(char *fileName) -/* Load all gwasCatalog from a whitespace-separated file. - * Dispose of this with gwasCatalogFreeList(). */ -{ -struct gwasCatalog *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[22]; - -while (lineFileRow(lf, row)) - { - el = gwasCatalogLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct gwasCatalog *gwasCatalogLoadAllByChar(char *fileName, char chopper) -/* Load all gwasCatalog from a chopper separated file. - * Dispose of this with gwasCatalogFreeList(). */ -{ -struct gwasCatalog *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[22]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = gwasCatalogLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct gwasCatalog *gwasCatalogCommaIn(char **pS, struct gwasCatalog *ret) -/* Create a gwasCatalog out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new gwasCatalog */ -{ -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->pubMedID = sqlUnsignedComma(&s); -ret->author = sqlStringComma(&s); -ret->pubDate = sqlStringComma(&s); -ret->journal = sqlStringComma(&s); -ret->title = sqlStringComma(&s); -ret->trait = sqlStringComma(&s); -ret->initSample = sqlStringComma(&s); -ret->replSample = sqlStringComma(&s); -ret->region = sqlStringComma(&s); -ret->genes = sqlStringComma(&s); -ret->riskAllele = sqlStringComma(&s); -ret->riskAlFreq = sqlStringComma(&s); -ret->pValue = sqlStringComma(&s); -ret->pValueDesc = sqlStringComma(&s); -ret->orOrBeta = sqlStringComma(&s); -ret->ci95 = sqlStringComma(&s); -ret->platform = sqlStringComma(&s); -ret->cnv = sqlEnumComma(&s, values_cnv, &valhash_cnv); -*pS = s; -return ret; -} - -void gwasCatalogFree(struct gwasCatalog **pEl) -/* Free a single dynamically allocated gwasCatalog such as created - * with gwasCatalogLoad(). */ -{ -struct gwasCatalog *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->chrom); -freeMem(el->name); -freeMem(el->author); -freeMem(el->pubDate); -freeMem(el->journal); -freeMem(el->title); -freeMem(el->trait); -freeMem(el->initSample); -freeMem(el->replSample); -freeMem(el->region); -freeMem(el->genes); -freeMem(el->riskAllele); -freeMem(el->riskAlFreq); -freeMem(el->pValue); -freeMem(el->pValueDesc); -freeMem(el->orOrBeta); -freeMem(el->ci95); -freeMem(el->platform); -freez(pEl); -} - -void gwasCatalogFreeList(struct gwasCatalog **pList) -/* Free a list of dynamically allocated gwasCatalog's */ -{ -struct gwasCatalog *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - gwasCatalogFree(&el); - } -*pList = NULL; -} - -void gwasCatalogOutput(struct gwasCatalog *el, FILE *f, char sep, char lastSep) -/* Print out gwasCatalog. 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->pubMedID); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->author); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->pubDate); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->journal); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->title); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->trait); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->initSample); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->replSample); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->region); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->genes); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->riskAllele); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->riskAlFreq); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->pValue); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->pValueDesc); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->orOrBeta); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->ci95); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->platform); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -sqlEnumPrint(f, el->cnv, values_cnv); -if (sep == ',') fputc('"',f); -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ -