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