src/hg/instinct/lib/hgHeatmapCustomDb.c 1.2

Index: src/hg/instinct/lib/hgHeatmapCustomDb.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/lib/hgHeatmapCustomDb.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/lib/hgHeatmapCustomDb.c	5 May 2009 22:43:38 -0000	1.1
+++ src/hg/instinct/lib/hgHeatmapCustomDb.c	4 Jun 2009 03:42:49 -0000	1.2
@@ -1,574 +1,578 @@
+/********************************************************************************/
+/* Copyright 2007-2009 -- The Regents of the University of California           */
+/********************************************************************************/
+
 /* hgHeatmapCustomDb.c was originally generated by the autoSql program, which also 
  * generated hgHeatmapCustomDb.h and hgHeatmapCustomDb.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hgHeatmapCustomDb.h"
 
 static char const rcsid[] = "$Id$";
 
 void featuresStaticLoad(char **row, struct features *ret)
 /* Load a row from features table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = sqlUnsigned(row[0]);
 ret->name = row[1];
 ret->shortLabel = row[2];
 ret->longLabel = row[3];
 ret->filterType = row[4];
 ret->priority = sqlDouble(row[5]);
 ret->visibility = row[6];
 }
 
 struct features *featuresLoad(char **row)
 /* Load a features from row fetched with select * from features
  * from database.  Dispose of this with featuresFree(). */
 {
 struct features *ret;
 
 AllocVar(ret);
 ret->id = sqlUnsigned(row[0]);
 ret->name = cloneString(row[1]);
 ret->shortLabel = cloneString(row[2]);
 ret->longLabel = cloneString(row[3]);
 ret->filterType = cloneString(row[4]);
 ret->priority = sqlDouble(row[5]);
 ret->visibility = cloneString(row[6]);
 return ret;
 }
 
 struct features *featuresLoadAll(char *fileName) 
 /* Load all features from a whitespace-separated file.
  * Dispose of this with featuresFreeList(). */
 {
 struct features *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = featuresLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct features *featuresLoadAllByChar(char *fileName, char chopper) 
 /* Load all features from a chopper separated file.
  * Dispose of this with featuresFreeList(). */
 {
 struct features *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = featuresLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct features *featuresLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all features 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 featuresFreeList(). */
 {
 struct features *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = featuresLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void featuresSaveToDb(struct sqlConnection *conn, struct features *el, char *tableName, int updateSize)
 /* Save features 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use featuresSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s','%s',%g,'%s')", 
 	tableName,  el->id,  el->name,  el->shortLabel,  el->longLabel,  el->filterType,  el->priority,  el->visibility);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void featuresSaveToDbEscaped(struct sqlConnection *conn, struct features *el, char *tableName, int updateSize)
 /* Save features 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than featuresSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *name, *shortLabel, *longLabel, *filterType, *visibility;
 name = sqlEscapeString(el->name);
 shortLabel = sqlEscapeString(el->shortLabel);
 longLabel = sqlEscapeString(el->longLabel);
 filterType = sqlEscapeString(el->filterType);
 visibility = sqlEscapeString(el->visibility);
 
 dyStringPrintf(update, "insert into %s values ( %u,'%s','%s','%s','%s',%g,'%s')", 
 	tableName,  el->id,  name,  shortLabel,  longLabel,  filterType,  el->priority,  visibility);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&name);
 freez(&shortLabel);
 freez(&longLabel);
 freez(&filterType);
 freez(&visibility);
 }
 
 struct features *featuresCommaIn(char **pS, struct features *ret)
 /* Create a features out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new features */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->shortLabel = sqlStringComma(&s);
 ret->longLabel = sqlStringComma(&s);
 ret->filterType = sqlStringComma(&s);
 ret->priority = sqlDoubleComma(&s);
 ret->visibility = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void featuresFree(struct features **pEl)
 /* Free a single dynamically allocated features such as created
  * with featuresLoad(). */
 {
 struct features *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->shortLabel);
 freeMem(el->longLabel);
 freeMem(el->filterType);
 freeMem(el->visibility);
 freez(pEl);
 }
 
 void featuresFreeList(struct features **pList)
 /* Free a list of dynamically allocated features's */
 {
 struct features *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     featuresFree(&el);
     }
 *pList = NULL;
 }
 
 void featuresOutput(struct features *el, FILE *f, char sep, char lastSep) 
 /* Print out features.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->shortLabel);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->longLabel);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->filterType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->priority);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->visibility);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void clinicalDataStaticLoad(char **row, struct clinicalData *ret)
 /* Load a row from clinicalData table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->patientId = row[0];
 ret->feature_id = sqlUnsigned(row[1]);
 ret->val = sqlDouble(row[2]);
 ret->code = row[3];
 }
 
 struct clinicalData *clinicalDataLoad(char **row)
 /* Load a clinicalData from row fetched with select * from clinicalData
  * from database.  Dispose of this with clinicalDataFree(). */
 {
 struct clinicalData *ret;
 
 AllocVar(ret);
 ret->patientId = cloneString(row[0]);
 ret->feature_id = sqlUnsigned(row[1]);
 ret->val = sqlDouble(row[2]);
 ret->code = cloneString(row[3]);
 return ret;
 }
 
 struct clinicalData *clinicalDataLoadAll(char *fileName) 
 /* Load all clinicalData from a whitespace-separated file.
  * Dispose of this with clinicalDataFreeList(). */
 {
 struct clinicalData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = clinicalDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct clinicalData *clinicalDataLoadAllByChar(char *fileName, char chopper) 
 /* Load all clinicalData from a chopper separated file.
  * Dispose of this with clinicalDataFreeList(). */
 {
 struct clinicalData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = clinicalDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct clinicalData *clinicalDataLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all clinicalData 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 clinicalDataFreeList(). */
 {
 struct clinicalData *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = clinicalDataLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void clinicalDataSaveToDb(struct sqlConnection *conn, struct clinicalData *el, char *tableName, int updateSize)
 /* Save clinicalData 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use clinicalDataSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( '%s',%u,%g,'%s')", 
 	tableName,  el->patientId,  el->feature_id,  el->val,  el->code);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void clinicalDataSaveToDbEscaped(struct sqlConnection *conn, struct clinicalData *el, char *tableName, int updateSize)
 /* Save clinicalData 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than clinicalDataSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *patientId, *code;
 patientId = sqlEscapeString(el->patientId);
 code = sqlEscapeString(el->code);
 
 dyStringPrintf(update, "insert into %s values ( '%s',%u,%g,'%s')", 
 	tableName,  patientId,  el->feature_id,  el->val,  code);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&patientId);
 freez(&code);
 }
 
 struct clinicalData *clinicalDataCommaIn(char **pS, struct clinicalData *ret)
 /* Create a clinicalData out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new clinicalData */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->patientId = sqlStringComma(&s);
 ret->feature_id = sqlUnsignedComma(&s);
 ret->val = sqlDoubleComma(&s);
 ret->code = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void clinicalDataFree(struct clinicalData **pEl)
 /* Free a single dynamically allocated clinicalData such as created
  * with clinicalDataLoad(). */
 {
 struct clinicalData *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->patientId);
 freeMem(el->code);
 freez(pEl);
 }
 
 void clinicalDataFreeList(struct clinicalData **pList)
 /* Free a list of dynamically allocated clinicalData's */
 {
 struct clinicalData *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     clinicalDataFree(&el);
     }
 *pList = NULL;
 }
 
 void clinicalDataOutput(struct clinicalData *el, FILE *f, char sep, char lastSep) 
 /* Print out clinicalData.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->patientId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->feature_id);
 fputc(sep,f);
 fprintf(f, "%g", el->val);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->code);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void labTrackStaticLoad(char **row, struct labTrack *ret)
 /* Load a row from labTrack table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->patientId = row[0];
 ret->trackId = row[1];
 }
 
 struct labTrack *labTrackLoad(char **row)
 /* Load a labTrack from row fetched with select * from labTrack
  * from database.  Dispose of this with labTrackFree(). */
 {
 struct labTrack *ret;
 
 AllocVar(ret);
 ret->patientId = cloneString(row[0]);
 ret->trackId = cloneString(row[1]);
 return ret;
 }
 
 struct labTrack *labTrackLoadAll(char *fileName) 
 /* Load all labTrack from a whitespace-separated file.
  * Dispose of this with labTrackFreeList(). */
 {
 struct labTrack *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 
 while (lineFileRow(lf, row))
     {
     el = labTrackLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct labTrack *labTrackLoadAllByChar(char *fileName, char chopper) 
 /* Load all labTrack from a chopper separated file.
  * Dispose of this with labTrackFreeList(). */
 {
 struct labTrack *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = labTrackLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct labTrack *labTrackLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all labTrack 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 labTrackFreeList(). */
 {
 struct labTrack *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = labTrackLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void labTrackSaveToDb(struct sqlConnection *conn, struct labTrack *el, char *tableName, int updateSize)
 /* Save labTrack 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. Note that strings must be escaped to allow insertion into the database.
  * For example "autosql's features include" --> "autosql\'s features include" 
  * If worried about this use labTrackSaveToDbEscaped() */
 {
 struct dyString *update = newDyString(updateSize);
 dyStringPrintf(update, "insert into %s values ( '%s','%s')", 
 	tableName,  el->patientId,  el->trackId);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 void labTrackSaveToDbEscaped(struct sqlConnection *conn, struct labTrack *el, char *tableName, int updateSize)
 /* Save labTrack 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. Automatically 
  * escapes all simple strings (not arrays of string) but may be slower than labTrackSaveToDb().
  * For example automatically copies and converts: 
  * "autosql's features include" --> "autosql\'s features include" 
  * before inserting into database. */ 
 {
 struct dyString *update = newDyString(updateSize);
 char  *patientId, *trackId;
 patientId = sqlEscapeString(el->patientId);
 trackId = sqlEscapeString(el->trackId);
 
 dyStringPrintf(update, "insert into %s values ( '%s','%s')", 
 	tableName,  patientId,  trackId);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&patientId);
 freez(&trackId);
 }
 
 struct labTrack *labTrackCommaIn(char **pS, struct labTrack *ret)
 /* Create a labTrack out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new labTrack */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->patientId = sqlStringComma(&s);
 ret->trackId = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void labTrackFree(struct labTrack **pEl)
 /* Free a single dynamically allocated labTrack such as created
  * with labTrackLoad(). */
 {
 struct labTrack *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->patientId);
 freeMem(el->trackId);
 freez(pEl);
 }
 
 void labTrackFreeList(struct labTrack **pList)
 /* Free a list of dynamically allocated labTrack's */
 {
 struct labTrack *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     labTrackFree(&el);
     }
 *pList = NULL;
 }
 
 void labTrackOutput(struct labTrack *el, FILE *f, char sep, char lastSep) 
 /* Print out labTrack.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->patientId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->trackId);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */