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/protVar.c src/hg/cgilib/protVar.c
new file mode 100644
index 0000000..456e1a2
--- /dev/null
+++ src/hg/cgilib/protVar.c
@@ -0,0 +1,695 @@
+/* protVar.c was originally generated by the autoSql program, which also 
+ * generated protVar.h and protVar.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 "protVar.h"
+
+
+void protVarStaticLoad(char **row, struct protVar *ret)
+/* Load a row from protVar table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->id = row[0];
+ret->name = row[1];
+ret->srcId = row[2];
+ret->baseChangeType = row[3];
+ret->location = row[4];
+ret->coordinateAccuracy = sqlUnsigned(row[5]);
+}
+
+struct protVar *protVarLoad(char **row)
+/* Load a protVar from row fetched with select * from protVar
+ * from database.  Dispose of this with protVarFree(). */
+{
+struct protVar *ret;
+
+AllocVar(ret);
+ret->id = cloneString(row[0]);
+ret->name = cloneString(row[1]);
+ret->srcId = cloneString(row[2]);
+ret->baseChangeType = cloneString(row[3]);
+ret->location = cloneString(row[4]);
+ret->coordinateAccuracy = sqlUnsigned(row[5]);
+return ret;
+}
+
+struct protVar *protVarLoadAll(char *fileName) 
+/* Load all protVar from a whitespace-separated file.
+ * Dispose of this with protVarFreeList(). */
+{
+struct protVar *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[6];
+
+while (lineFileRow(lf, row))
+    {
+    el = protVarLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVar *protVarLoadAllByChar(char *fileName, char chopper) 
+/* Load all protVar from a chopper separated file.
+ * Dispose of this with protVarFreeList(). */
+{
+struct protVar *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[6];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = protVarLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVar *protVarLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all protVar 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 protVarFreeList(). */
+{
+struct protVar *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = protVarLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void protVarSaveToDb(struct sqlConnection *conn, struct protVar *el, char *tableName, int updateSize)
+/* Save protVar 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','%s',%u)", 
+	tableName,  el->id,  el->name,  el->srcId,  el->baseChangeType,  el->location,  el->coordinateAccuracy);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+}
+
+
+struct protVar *protVarCommaIn(char **pS, struct protVar *ret)
+/* Create a protVar out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new protVar */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlStringComma(&s);
+ret->name = sqlStringComma(&s);
+ret->srcId = sqlStringComma(&s);
+ret->baseChangeType = sqlStringComma(&s);
+ret->location = sqlStringComma(&s);
+ret->coordinateAccuracy = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void protVarFree(struct protVar **pEl)
+/* Free a single dynamically allocated protVar such as created
+ * with protVarLoad(). */
+{
+struct protVar *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->id);
+freeMem(el->name);
+freeMem(el->srcId);
+freeMem(el->baseChangeType);
+freeMem(el->location);
+freez(pEl);
+}
+
+void protVarFreeList(struct protVar **pList)
+/* Free a list of dynamically allocated protVar's */
+{
+struct protVar *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    protVarFree(&el);
+    }
+*pList = NULL;
+}
+
+void protVarOutput(struct protVar *el, FILE *f, char sep, char lastSep) 
+/* Print out protVar.  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->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->srcId);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->baseChangeType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->location);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->coordinateAccuracy);
+fputc(lastSep,f);
+}
+
+void protVarPosStaticLoad(char **row, struct protVarPos *ret)
+/* Load a row from protVarPos 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->name = row[4];
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->label = row[6];
+}
+
+struct protVarPos *protVarPosLoad(char **row)
+/* Load a protVarPos from row fetched with select * from protVarPos
+ * from database.  Dispose of this with protVarPosFree(). */
+{
+struct protVarPos *ret;
+
+AllocVar(ret);
+ret->bin = sqlUnsigned(row[0]);
+ret->chrom = cloneString(row[1]);
+ret->chromStart = sqlUnsigned(row[2]);
+ret->chromEnd = sqlUnsigned(row[3]);
+ret->name = cloneString(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->label = cloneString(row[6]);
+return ret;
+}
+
+struct protVarPos *protVarPosLoadAll(char *fileName) 
+/* Load all protVarPos from a whitespace-separated file.
+ * Dispose of this with protVarPosFreeList(). */
+{
+struct protVarPos *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileRow(lf, row))
+    {
+    el = protVarPosLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarPos *protVarPosLoadAllByChar(char *fileName, char chopper) 
+/* Load all protVarPos from a chopper separated file.
+ * Dispose of this with protVarPosFreeList(). */
+{
+struct protVarPos *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[7];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = protVarPosLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarPos *protVarPosLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all protVarPos 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 protVarPosFreeList(). */
+{
+struct protVarPos *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = protVarPosLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void protVarPosSaveToDb(struct sqlConnection *conn, struct protVarPos *el, char *tableName, int updateSize)
+/* Save protVarPos 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->name,  el->strand,  el->label);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+}
+
+
+struct protVarPos *protVarPosCommaIn(char **pS, struct protVarPos *ret)
+/* Create a protVarPos out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new protVarPos */
+{
+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->name = sqlStringComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->label = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void protVarPosFree(struct protVarPos **pEl)
+/* Free a single dynamically allocated protVarPos such as created
+ * with protVarPosLoad(). */
+{
+struct protVarPos *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->label);
+freez(pEl);
+}
+
+void protVarPosFreeList(struct protVarPos **pList)
+/* Free a list of dynamically allocated protVarPos's */
+{
+struct protVarPos *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    protVarPosFree(&el);
+    }
+*pList = NULL;
+}
+
+void protVarPosOutput(struct protVarPos *el, FILE *f, char sep, char lastSep) 
+/* Print out protVarPos.  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->name);
+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->label);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+void protVarAttrStaticLoad(char **row, struct protVarAttr *ret)
+/* Load a row from protVarAttr table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->id = row[0];
+ret->attrType = row[1];
+ret->attrVal = row[2];
+}
+
+struct protVarAttr *protVarAttrLoad(char **row)
+/* Load a protVarAttr from row fetched with select * from protVarAttr
+ * from database.  Dispose of this with protVarAttrFree(). */
+{
+struct protVarAttr *ret;
+
+AllocVar(ret);
+ret->id = cloneString(row[0]);
+ret->attrType = cloneString(row[1]);
+ret->attrVal = cloneString(row[2]);
+return ret;
+}
+
+struct protVarAttr *protVarAttrLoadAll(char *fileName) 
+/* Load all protVarAttr from a whitespace-separated file.
+ * Dispose of this with protVarAttrFreeList(). */
+{
+struct protVarAttr *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileRow(lf, row))
+    {
+    el = protVarAttrLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarAttr *protVarAttrLoadAllByChar(char *fileName, char chopper) 
+/* Load all protVarAttr from a chopper separated file.
+ * Dispose of this with protVarAttrFreeList(). */
+{
+struct protVarAttr *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[3];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = protVarAttrLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarAttr *protVarAttrLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all protVarAttr 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 protVarAttrFreeList(). */
+{
+struct protVarAttr *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = protVarAttrLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void protVarAttrSaveToDb(struct sqlConnection *conn, struct protVarAttr *el, char *tableName, int updateSize)
+/* Save protVarAttr 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->attrType,  el->attrVal);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+}
+
+
+struct protVarAttr *protVarAttrCommaIn(char **pS, struct protVarAttr *ret)
+/* Create a protVarAttr out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new protVarAttr */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlStringComma(&s);
+ret->attrType = sqlStringComma(&s);
+ret->attrVal = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void protVarAttrFree(struct protVarAttr **pEl)
+/* Free a single dynamically allocated protVarAttr such as created
+ * with protVarAttrLoad(). */
+{
+struct protVarAttr *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->id);
+freeMem(el->attrType);
+freeMem(el->attrVal);
+freez(pEl);
+}
+
+void protVarAttrFreeList(struct protVarAttr **pList)
+/* Free a list of dynamically allocated protVarAttr's */
+{
+struct protVarAttr *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    protVarAttrFree(&el);
+    }
+*pList = NULL;
+}
+
+void protVarAttrOutput(struct protVarAttr *el, FILE *f, char sep, char lastSep) 
+/* Print out protVarAttr.  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->attrType);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->attrVal);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+void protVarLinkStaticLoad(char **row, struct protVarLink *ret)
+/* Load a row from protVarLink table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->id = row[0];
+ret->attrType = row[1];
+ret->raKey = row[2];
+ret->acc = row[3];
+ret->displayVal = row[4];
+}
+
+struct protVarLink *protVarLinkLoad(char **row)
+/* Load a protVarLink from row fetched with select * from protVarLink
+ * from database.  Dispose of this with protVarLinkFree(). */
+{
+struct protVarLink *ret;
+
+AllocVar(ret);
+ret->id = cloneString(row[0]);
+ret->attrType = cloneString(row[1]);
+ret->raKey = cloneString(row[2]);
+ret->acc = cloneString(row[3]);
+ret->displayVal = cloneString(row[4]);
+return ret;
+}
+
+struct protVarLink *protVarLinkLoadAll(char *fileName) 
+/* Load all protVarLink from a whitespace-separated file.
+ * Dispose of this with protVarLinkFreeList(). */
+{
+struct protVarLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileRow(lf, row))
+    {
+    el = protVarLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarLink *protVarLinkLoadAllByChar(char *fileName, char chopper) 
+/* Load all protVarLink from a chopper separated file.
+ * Dispose of this with protVarLinkFreeList(). */
+{
+struct protVarLink *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[5];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = protVarLinkLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct protVarLink *protVarLinkLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all protVarLink 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 protVarLinkFreeList(). */
+{
+struct protVarLink *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = protVarLinkLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void protVarLinkSaveToDb(struct sqlConnection *conn, struct protVarLink *el, char *tableName, int updateSize)
+/* Save protVarLink 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','%s')", 
+	tableName,  el->id,  el->attrType,  el->raKey,  el->acc,  el->displayVal);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+}
+
+
+struct protVarLink *protVarLinkCommaIn(char **pS, struct protVarLink *ret)
+/* Create a protVarLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new protVarLink */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->id = sqlStringComma(&s);
+ret->attrType = sqlStringComma(&s);
+ret->raKey = sqlStringComma(&s);
+ret->acc = sqlStringComma(&s);
+ret->displayVal = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void protVarLinkFree(struct protVarLink **pEl)
+/* Free a single dynamically allocated protVarLink such as created
+ * with protVarLinkLoad(). */
+{
+struct protVarLink *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->id);
+freeMem(el->attrType);
+freeMem(el->raKey);
+freeMem(el->acc);
+freeMem(el->displayVal);
+freez(pEl);
+}
+
+void protVarLinkFreeList(struct protVarLink **pList)
+/* Free a list of dynamically allocated protVarLink's */
+{
+struct protVarLink *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    protVarLinkFree(&el);
+    }
+*pList = NULL;
+}
+
+void protVarLinkOutput(struct protVarLink *el, FILE *f, char sep, char lastSep) 
+/* Print out protVarLink.  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->attrType);
+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->acc);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->displayVal);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+