f558f8888fc486e82384f05665be19c6f8e5f452
markd
  Wed Dec 15 21:00:16 2010 -0800
assign ids in seq and extFile tables locally rather than globally (RM #26)
diff --git src/hg/lib/hgRelate.c src/hg/lib/hgRelate.c
index 225cb4c..fc546c2 100644
--- src/hg/lib/hgRelate.c
+++ src/hg/lib/hgRelate.c
@@ -1,310 +1,271 @@
 /*****************************************************************************
  * Copyright (C) 2000 Jim Kent.  This source code may be freely used         *
  * for personal, academic, and non-profit purposes.  Commercial use          *
  * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) *
  *****************************************************************************/
 /* hgRelate - Especially relational parts of browser data base. */
 #include "common.h"
 #include "portable.h"
 #include "localmem.h"
 #include "dystring.h"
 #include "hash.h"
 #include "fa.h"
 #include "jksql.h"
 #include "hgRelate.h"
 #include "hdb.h"
 
 static char const rcsid[] = "$Id: hgRelate.c,v 1.28 2010/04/28 17:42:53 galt Exp $";
 
 static char extFileCreate[] =
 /* This keeps track of external files and directories. */
 "create table %s ("
   "id int unsigned not null primary key,"  /* Unique ID across all tables. */
   "name varchar(64) not null,"	  /* Symbolic name of file.  */
   "path varchar(255) not null,"   /* Full path. Ends in '/' if a dir. */
   "size bigint unsigned not null,"           /* Size of file (checked) */
                    /* Extra indices. */
   "index (name))";
 
 static char historyCreate[] =	
 /* This contains a row for each update made to database.
  * (The idea is that this is just updated in batch.)
  * It keeps track of which id global ids are used
  * as well as providing a record of updates. */
 "create table history ("
   "ix int not null auto_increment primary key,"  /* Update number. */
   "startId int unsigned not null,"              /* Start this session's ids. */
   "endId int unsigned not null,"                /* First id for next session. */
   "who varchar(255) not null,"         /* User who updated. */
   "what varchar(255) not null,"        /* What they did. */
   "modTime timestamp not null,"        /* Modification time. */
   "errata varchar(255) )";            /* Deleted data */
 
-HGID hgIdQuery(struct sqlConnection *conn, char *query)
-/* Return first field of first table as HGID. 0 return ok. */
-{
-struct sqlResult *sr;
-char **row;
-HGID ret = 0;
-
-sr = sqlGetResult(conn, query);
-row = sqlNextRow(sr);
-if (row == NULL)
-    errAbort("Couldn't find ID in response to %s\nDatabase needs updating", query);
-ret = sqlUnsigned(row[0]);
-sqlFreeResult(&sr);
-return ret;
-}
-
-HGID hgRealIdQuery(struct sqlConnection *conn, char *query)
-/* Return first field of first table as HGID- abort if 0. */
-{
-HGID ret = hgIdQuery(conn, query);
-if (ret == 0)
-    errAbort("Unexpected NULL response to %s", query);
-return ret;
-}
-
 HGID hgGetMaxId(struct sqlConnection *conn, char *tableName)
 /* get the maximum value of the id column in a table or zero if empry  */
 {
 /* we get a row with NULL if the table is empty */
 char query[128];
 char **row = NULL;
 HGID maxId;
 struct sqlResult *sr;
 
 safef(query, sizeof(query), "SELECT MAX(id) from %s", tableName);
 
 sr = sqlGetResult(conn, query);
 if (sr != NULL)
     row = sqlNextRow(sr);
 if ((row == NULL) || (row[0] == NULL))
     maxId = 0;  /* empty table */
 else
     maxId = sqlUnsigned(row[0]);
 sqlFreeResult(&sr);
 return maxId;
 }
 
-static HGID startUpdateId;	/* First ID in this update. */
-static HGID endUpdateId;	/* One past last ID in this update. */
+static void ensureHistoryTableExists(struct sqlConnection *conn)
+/* create history table if it doesn't exist */
+{
+static boolean first = TRUE;
+if (first)
+    {
+    sqlMaybeMakeTable(conn, "history", historyCreate);
+    first = FALSE;
+    }
+}
 
-HGID hgNextId(void)
-/* Get next free global ID. */
+static void hgHistoryEnterVa(struct sqlConnection *conn, int startId, int endId, char *comment, va_list args)
+/* add an entry to the history table */
 {
-return endUpdateId++;
+// create SQL encoded string for comment
+struct dyString *commentBuf = dyStringNew(256);
+dyStringVaPrintf(commentBuf, comment, args);
+char *commentStr = sqlEscapeString(commentBuf->string);
+dyStringFree(&commentBuf);
+struct dyString *query = dyStringNew(256);
+ensureHistoryTableExists(conn);
+dyStringPrintf(query, "INSERT into history (ix, startId, endId, who, what, modTime, errata) VALUES(NULL,%d,%d,'%s',\"%s\",NOW(), NULL)",
+               startId, endId, getUser(), commentStr);
+sqlUpdate(conn,query->string);
+dyStringFree(&query); 
+freeMem(commentStr);
 }
 
 void hgHistoryComment(struct sqlConnection *conn, char *comment, ...)
-/* Add comment to history table.  Does not lock the process. */
+/* Add comment to history table. */
 {
-struct dyString *query = newDyString(256);
 va_list args;
-static boolean initialized = FALSE;
-
 va_start(args, comment);
-/* create history table if it does not exist already */
-if (!initialized)
-    {
-    if (sqlMaybeMakeTable(conn, "history", historyCreate))
-	{
-        char query[256];
-	safef(query, sizeof(query),
-		"INSERT into history (ix, startId, endId, who, what, modTime, errata) VALUES(NULL,0,10,'%s','New',NOW(), NULL)",
-		getUser());
-        sqlUpdate(conn, query);
-	}
-    initialized = TRUE;
+hgHistoryEnterVa(conn, 0, 0, comment, args);
+va_end(args);
     }
-/* add comment with startId and endId as 0 */
-dyStringPrintf(query, "INSERT into history (ix, startId, endId, who, what, modTime, errata) VALUES(NULL,%d,%d,'%s',\"",
-         0, 0, getUser());
-dyStringVaPrintf(query, comment, args);
-dyStringAppend(query, "\",NOW(), NULL)");
-sqlUpdate(conn,query->string);
-dyStringFree(&query); 
+
+void hgHistoryCommentWithIds(struct sqlConnection *conn, int startId, int endId, char *comment, ...)
+/* Add comment to history table, with id range. */
+{
+va_list args;
+va_start(args, comment);
+hgHistoryEnterVa(conn, startId, endId, comment, args);
+va_end(args);
 }
 
 struct sqlConnection *hgStartUpdate(char *db)
-/* Open and connection and get next global id from the history table */
+/* Open and connection and lock the history table */
 {
-static boolean initialized = FALSE;
 struct sqlConnection *conn = sqlConnect(db);
-
-if (!initialized)
-    {
-    if (sqlMaybeMakeTable(conn, "history", historyCreate))
-	{
-        char query[256];
-	safef(query, sizeof(query),
-		"INSERT into history (ix, startId, endId, who, what, modTime, errata) VALUES(NULL,0,10,'%s','New',NOW(), NULL)",
-		getUser());
-        sqlUpdate(conn, query);
-	}
-    initialized = TRUE;
-    }
-/* put advisory lock on process while adding Ids to tables */
+ensureHistoryTableExists(conn);
 sqlGetLock(conn, "history");
-startUpdateId = endUpdateId = hgIdQuery(conn, "SELECT MAX(endId) from history");
-
 return conn;
-
 }
 
-void hgEndUpdate(struct sqlConnection **pConn, char *comment, ...)
-/* Finish up connection with a printf format comment. */
+void hgEndUpdate(struct sqlConnection **pConn, int startId, int endId, char *comment, ...)
+/* Finish up connection with a printf format comment and optional id range */
 {
 struct sqlConnection *conn = *pConn;
-struct dyString *query = newDyString(256);
 va_list args;
 va_start(args, comment);
-
-dyStringPrintf(query, "INSERT into history (ix, startId, endId, who, what, modTime, errata) VALUES(NULL,%d,%d,'%s',\"", 
-	startUpdateId, endUpdateId, getUser());
-dyStringVaPrintf(query, comment, args);
-dyStringAppend(query, "\",NOW(), NULL)");
-sqlUpdate(conn,query->string);
+hgHistoryEnterVa(conn, startId, endId, comment, args);
+va_end(args);
 sqlReleaseLock(conn, "history");
 sqlDisconnect(pConn);
 }
 
 static void getTabFile(char *tmpDir, char *tableName, char path[PATH_LEN])
 /* generate path to tab file.  If tmpDir is NULL, use TMPDIR environment, or
  * "/var/tmp".  tmpDir NULL also include pid in file name */
 {
 boolean inclPid = (tmpDir == NULL);
 if (tmpDir == NULL)
     tmpDir = getenv("TMPDIR");
 if (tmpDir == NULL)
     tmpDir = "/var/tmp";
 if (inclPid)
     safef(path, PATH_LEN, "%s/%s.%d.tab", tmpDir, tableName, (int) getpid()); /* int cast for Solaris */
 else
     safef(path, PATH_LEN, "%s/%s.tab", tmpDir, tableName);
 }
 
 FILE *hgCreateTabFile(char *tmpDir, char *tableName)
 /* Open a tab file with name corresponding to tableName in tmpDir.  If tmpDir is NULL,
  * use TMPDIR environment, or "/var/tmp" */
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, tableName, path);
 return mustOpen(path, "w");
 }
 
 int hgUnlinkTabFile(char *tmpDir, char *tableName)
 /* Unlink tab file.   If tmpDir is NULL, use TMPDIR environment, or "/var/tmp" */
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, tableName, path);
 return unlink(path);
 }
 
 void hgLoadTabFile(struct sqlConnection *conn, char *tmpDir, char *tableName,
                    FILE **tabFh)
 /* Load tab delimited file corresponding to tableName. close fh if not NULL.
  * If tmpDir is NULL, use TMPDIR environment, or "/var/tmp"*/
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, tableName, path);
 carefulClose(tabFh);
 sqlLoadTabFile(conn, path, tableName, SQL_TAB_FILE_WARN_ON_ERROR);
 }
 
 void hgLoadNamedTabFile(struct sqlConnection *conn, char *tmpDir, char *tableName,
                         char *fileName, FILE **tabFh)
 /* Load named tab delimited file corresponding to tableName. close fh if not
  * NULL If tmpDir is NULL, use TMPDIR environment, or "/var/tmp"*/
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, fileName, path);
 carefulClose(tabFh);
 sqlLoadTabFile(conn, path, tableName, SQL_TAB_FILE_WARN_ON_ERROR);
 }
 
 void hgLoadTabFileOpts(struct sqlConnection *conn, char *tmpDir, char *tableName,
                        unsigned options, FILE **tabFh)
 /* Load tab delimited file corresponding to tableName. close tabFh if not NULL
  * If tmpDir is NULL, use TMPDIR environment, or "/var/tmp". Options are those
  * supported by sqlLoadTabFile */
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, tableName, path);
 carefulClose(tabFh);
 sqlLoadTabFile(conn, path, tableName, options);
 }
 
 void hgRemoveTabFile(char *tmpDir, char *tableName)
 /* Remove file.* If tmpDir is NULL, use TMPDIR environment, or "/var/tmp" */
 {
 char path[PATH_LEN];
 getTabFile(tmpDir, tableName, path);
 if (remove(path) == -1)
     errnoAbort("Couldn't remove %s", path);
 }
 
 
 int hgAddToExtFileTbl(char *path, struct sqlConnection *conn, char *extFileTbl)
 /* Add entry to the specified extFile table.  Delete it if it already exists.
  * Returns extFile id. */
 {
 char root[128], ext[64], name[256];
 struct dyString *dy = newDyString(1024);
 long long size = fileSize(path);
-HGID id = hgNextId();
 
 /* create table if it doesn't exist */
 if (!sqlTableExists(conn, extFileTbl))
     {
     char query[1024];
     safef(query, sizeof(query), extFileCreate, extFileTbl);
     sqlMaybeMakeTable(conn, extFileTbl, query);
     }
 
+HGID id = hgGetMaxId(conn, extFileTbl) + 1;
+
 /* Construct file name without the directory. */
 splitPath(path, NULL, root, ext);
 safef(name, sizeof(name), "%s%s", root, ext);
 
 /* Delete it from database. */
 dyStringPrintf(dy, "delete from %s where path = '%s'", extFileTbl, path);
 sqlUpdate(conn, dy->string);
 
 /* Add it to table. */
 dyStringClear(dy);
 dyStringPrintf(dy, "INSERT into %s (id, name, path, size) VALUES(%u,'%s','%s',%lld)",
                extFileTbl, id, name, path, size);
 sqlUpdate(conn, dy->string);
-
+hgHistoryCommentWithIds(conn, id, id, "extFile table %s: added %s (%lld)", extFileTbl, path, size);
 dyStringFree(&dy);
 return id;
 }
 
 int hgAddToExtFile(char *path, struct sqlConnection *conn)
 /* Add entry to ext file table.  Delete it if it already exists. 
  * Returns extFile id. */
 {
 return hgAddToExtFileTbl(path, conn, "extFile");
 }
 
 void hgPurgeExtFileTbl(int id, struct sqlConnection *conn, char *extFileTbl)
 /* remove an entry from the extFile table.  Called
  * when there is an error loading the referenced file
  */
 {
 struct dyString *dy = newDyString(1024);
 
 /* Delete it from database. */
 dyStringPrintf(dy, "delete from %s where id = '%d'", extFileTbl, id);
 sqlUpdate(conn, dy->string);
 
 dyStringFree(&dy);
 }
 
 void hgPurgeExtFile(int id,  struct sqlConnection *conn)
 /* remove an entry from the extFile table.  Called
  * when there is an error loading the referenced file
  */
 {
 hgPurgeExtFileTbl(id, conn, "extFile");
 }