4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/cgilib/oreganno.c src/hg/cgilib/oreganno.c
index 7644e15..6124496 100644
--- src/hg/cgilib/oreganno.c
+++ src/hg/cgilib/oreganno.c
@@ -1,531 +1,531 @@
 /* oreganno.c was originally generated by the autoSql program, which also 
  * generated oreganno.h and oreganno.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. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "oreganno.h"
 
 
 void oregannoStaticLoad(char **row, struct oreganno *ret)
 /* Load a row from oreganno table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = row[1];
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->id = row[4];
 strcpy(ret->strand, row[5]);
 ret->name = row[6];
 }
 
 struct oreganno *oregannoLoad(char **row)
 /* Load a oreganno from row fetched with select * from oreganno
  * from database.  Dispose of this with oregannoFree(). */
 {
 struct oreganno *ret;
 
 AllocVar(ret);
 ret->bin = sqlUnsigned(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->chromStart = sqlUnsigned(row[2]);
 ret->chromEnd = sqlUnsigned(row[3]);
 ret->id = cloneString(row[4]);
 strcpy(ret->strand, row[5]);
 ret->name = cloneString(row[6]);
 return ret;
 }
 
 struct oreganno *oregannoLoadAll(char *fileName) 
 /* Load all oreganno from a whitespace-separated file.
  * Dispose of this with oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oreganno *oregannoLoadAllByChar(char *fileName, char chopper) 
 /* Load all oreganno from a chopper separated file.
  * Dispose of this with oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oreganno *oregannoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oreganno 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 oregannoFreeList(). */
 {
 struct oreganno *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoSaveToDb(struct sqlConnection *conn, struct oreganno *el, char *tableName, int updateSize)
 /* Save oreganno 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 ( %u,'%s',%u,%u,'%s','%s','%s')", 
 	tableName,  el->bin,  el->chrom,  el->chromStart,  el->chromEnd,  el->id,  el->strand,  el->name);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct oreganno *oregannoCommaIn(char **pS, struct oreganno *ret)
 /* Create a oreganno out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oreganno */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->bin = sqlUnsignedComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->id = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->name = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoFree(struct oreganno **pEl)
 /* Free a single dynamically allocated oreganno such as created
  * with oregannoLoad(). */
 {
 struct oreganno *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->id);
 freeMem(el->name);
 freez(pEl);
 }
 
 void oregannoFreeList(struct oreganno **pList)
 /* Free a list of dynamically allocated oreganno's */
 {
 struct oreganno *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoOutput(struct oreganno *el, FILE *f, char sep, char lastSep) 
 /* Print out oreganno.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->bin);
 fputc(sep,f);
 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->id);
 if (sep == ',') fputc('"',f);
 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->name);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void oregannoAttrStaticLoad(char **row, struct oregannoAttr *ret)
 /* Load a row from oregannoAttr table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attribute = row[1];
 ret->attrVal = row[2];
 }
 
 struct oregannoAttr *oregannoAttrLoad(char **row)
 /* Load a oregannoAttr from row fetched with select * from oregannoAttr
  * from database.  Dispose of this with oregannoAttrFree(). */
 {
 struct oregannoAttr *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attribute = cloneString(row[1]);
 ret->attrVal = cloneString(row[2]);
 return ret;
 }
 
 struct oregannoAttr *oregannoAttrLoadAll(char *fileName) 
 /* Load all oregannoAttr from a whitespace-separated file.
  * Dispose of this with oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoAttr *oregannoAttrLoadAllByChar(char *fileName, char chopper) 
 /* Load all oregannoAttr from a chopper separated file.
  * Dispose of this with oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoAttr *oregannoAttrLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oregannoAttr 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 oregannoAttrFreeList(). */
 {
 struct oregannoAttr *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoAttrLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoAttrSaveToDb(struct sqlConnection *conn, struct oregannoAttr *el, char *tableName, int updateSize)
 /* Save oregannoAttr 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','%s','%s')", 
 	tableName,  el->id,  el->attribute,  el->attrVal);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct oregannoAttr *oregannoAttrCommaIn(char **pS, struct oregannoAttr *ret)
 /* Create a oregannoAttr out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oregannoAttr */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->attrVal = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoAttrFree(struct oregannoAttr **pEl)
 /* Free a single dynamically allocated oregannoAttr such as created
  * with oregannoAttrLoad(). */
 {
 struct oregannoAttr *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attribute);
 freeMem(el->attrVal);
 freez(pEl);
 }
 
 void oregannoAttrFreeList(struct oregannoAttr **pList)
 /* Free a list of dynamically allocated oregannoAttr's */
 {
 struct oregannoAttr *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoAttrFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoAttrOutput(struct oregannoAttr *el, FILE *f, char sep, char lastSep) 
 /* Print out oregannoAttr.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attribute);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrVal);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void oregannoLinkStaticLoad(char **row, struct oregannoLink *ret)
 /* Load a row from oregannoLink table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = row[0];
 ret->attribute = row[1];
 ret->raKey = row[2];
 ret->attrAcc = row[3];
 }
 
 struct oregannoLink *oregannoLinkLoad(char **row)
 /* Load a oregannoLink from row fetched with select * from oregannoLink
  * from database.  Dispose of this with oregannoLinkFree(). */
 {
 struct oregannoLink *ret;
 
 AllocVar(ret);
 ret->id = cloneString(row[0]);
 ret->attribute = cloneString(row[1]);
 ret->raKey = cloneString(row[2]);
 ret->attrAcc = cloneString(row[3]);
 return ret;
 }
 
 struct oregannoLink *oregannoLinkLoadAll(char *fileName) 
 /* Load all oregannoLink from a whitespace-separated file.
  * Dispose of this with oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoLink *oregannoLinkLoadAllByChar(char *fileName, char chopper) 
 /* Load all oregannoLink from a chopper separated file.
  * Dispose of this with oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct oregannoLink *oregannoLinkLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all oregannoLink 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 oregannoLinkFreeList(). */
 {
 struct oregannoLink *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = oregannoLinkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void oregannoLinkSaveToDb(struct sqlConnection *conn, struct oregannoLink *el, char *tableName, int updateSize)
 /* Save oregannoLink 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','%s','%s','%s')", 
 	tableName,  el->id,  el->attribute,  el->raKey,  el->attrAcc);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct oregannoLink *oregannoLinkCommaIn(char **pS, struct oregannoLink *ret)
 /* Create a oregannoLink out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new oregannoLink */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlStringComma(&s);
 ret->attribute = sqlStringComma(&s);
 ret->raKey = sqlStringComma(&s);
 ret->attrAcc = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void oregannoLinkFree(struct oregannoLink **pEl)
 /* Free a single dynamically allocated oregannoLink such as created
  * with oregannoLinkLoad(). */
 {
 struct oregannoLink *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->id);
 freeMem(el->attribute);
 freeMem(el->raKey);
 freeMem(el->attrAcc);
 freez(pEl);
 }
 
 void oregannoLinkFreeList(struct oregannoLink **pList)
 /* Free a list of dynamically allocated oregannoLink's */
 {
 struct oregannoLink *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     oregannoLinkFree(&el);
     }
 *pList = NULL;
 }
 
 void oregannoLinkOutput(struct oregannoLink *el, FILE *f, char sep, char lastSep) 
 /* Print out oregannoLink.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->id);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attribute);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->raKey);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->attrAcc);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct hash *oregannoLoadAttrHash(struct sqlConnection *conn)
 /* Construct a hash table of the entries in the oregannoAttr table, indexed by ID.
  * Free with hashFreeWithVals(&attrHash, oregannoAttrFree).
  */
 {
 struct hash *attrHash = hashNew(0);
 struct sqlResult *result = NULL;
 struct oregannoAttr *attr = NULL;
 char query[2048], **row = NULL;
 
 sqlSafef(query, sizeof(query), "select * from oregannoAttr where attribute = 'type'");
 result = sqlGetResult (conn, query);
 while ((row = sqlNextRow(result)) != NULL)
     {
     attr = oregannoAttrLoad(row);
     hashAdd (attrHash, attr->id, attr);
     }
 sqlFreeResult(&result);
 return attrHash;
 }