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/gwasCatalog.c src/hg/cgilib/gwasCatalog.c
new file mode 100644
index 0000000..1e2959a
--- /dev/null
+++ src/hg/cgilib/gwasCatalog.c
@@ -0,0 +1,280 @@
+/* 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 -------------------------------- */
+