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/oreganno.c src/hg/lib/oreganno.c
deleted file mode 100644
index 7644e15..0000000
--- src/hg/lib/oreganno.c
+++ /dev/null
@@ -1,531 +0,0 @@
-/* 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. */
-
-#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;
-}