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 -------------------------------- */
+