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/targetDb.c src/hg/lib/targetDb.c
deleted file mode 100644
index 00d3aab..0000000
--- src/hg/lib/targetDb.c
+++ /dev/null
@@ -1,301 +0,0 @@
-/* targetDb.c was originally generated by the autoSql program, which also 
- * generated targetDb.h and targetDb.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 "targetDb.h"
-#include "udc.h"
-#include "hdb.h"
-
-
-void targetDbStaticLoad(char **row, struct targetDb *ret)
-/* Load a row from targetDb table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->name = row[0];
-ret->description = row[1];
-ret->db = row[2];
-ret->pslTable = row[3];
-ret->seqTable = row[4];
-ret->extFileTable = row[5];
-ret->seqFile = row[6];
-ret->priority = sqlFloat(row[7]);
-ret->time = row[8];
-ret->settings = row[9];
-}
-
-struct targetDb *targetDbLoad(char **row)
-/* Load a targetDb from row fetched with select * from targetDb
- * from database.  Dispose of this with targetDbFree(). */
-{
-struct targetDb *ret;
-
-AllocVar(ret);
-ret->name = cloneString(row[0]);
-ret->description = cloneString(row[1]);
-ret->db = cloneString(row[2]);
-ret->pslTable = cloneString(row[3]);
-ret->seqTable = cloneString(row[4]);
-ret->extFileTable = cloneString(row[5]);
-ret->seqFile = hReplaceGbdb(row[6]);
-ret->priority = sqlFloat(row[7]);
-ret->time = cloneString(row[8]);
-ret->settings = cloneString(row[9]);
-return ret;
-}
-
-struct targetDb *targetDbLoadAll(char *fileName) 
-/* Load all targetDb from a whitespace-separated file.
- * Dispose of this with targetDbFreeList(). */
-{
-struct targetDb *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
-
-while (lineFileRow(lf, row))
-    {
-    el = targetDbLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct targetDb *targetDbLoadAllByChar(char *fileName, char chopper) 
-/* Load all targetDb from a chopper separated file.
- * Dispose of this with targetDbFreeList(). */
-{
-struct targetDb *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[10];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = targetDbLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct targetDb *targetDbCommaIn(char **pS, struct targetDb *ret)
-/* Create a targetDb out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new targetDb */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->name = sqlStringComma(&s);
-ret->description = sqlStringComma(&s);
-ret->db = sqlStringComma(&s);
-ret->pslTable = sqlStringComma(&s);
-ret->seqTable = sqlStringComma(&s);
-ret->extFileTable = sqlStringComma(&s);
-ret->seqFile = sqlStringComma(&s);
-ret->priority = sqlFloatComma(&s);
-ret->time = sqlStringComma(&s);
-ret->settings = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void targetDbFree(struct targetDb **pEl)
-/* Free a single dynamically allocated targetDb such as created
- * with targetDbLoad(). */
-{
-struct targetDb *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->name);
-freeMem(el->description);
-freeMem(el->db);
-freeMem(el->pslTable);
-freeMem(el->seqTable);
-freeMem(el->extFileTable);
-freeMem(el->seqFile);
-freeMem(el->time);
-freeMem(el->settings);
-freez(pEl);
-}
-
-void targetDbFreeList(struct targetDb **pList)
-/* Free a list of dynamically allocated targetDb's */
-{
-struct targetDb *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    targetDbFree(&el);
-    }
-*pList = NULL;
-}
-
-void targetDbOutput(struct targetDb *el, FILE *f, char sep, char lastSep) 
-/* Print out targetDb.  Separate fields with sep. Follow last field with lastSep. */
-{
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->name);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->description);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->db);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->pslTable);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->seqTable);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->extFileTable);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->seqFile);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%g", el->priority);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->time);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->settings);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-
-#include "portable.h"
-#include "hdb.h"
-#include "ra.h"
-
-static boolean timeMoreRecentThanTable(int time, struct sqlConnection *conn,
-				char *table)
-/* Return TRUE if the given UNIX time is more recent than the time that 
- * table was last updated. */
-{
-if (! sqlTableExists(conn, table))
-    return FALSE;
-long tableUpdateTime = sqlTableUpdateTime(conn, table);
-return (time > tableUpdateTime);
-}
-
-static boolean timeMoreRecentThanFile(long time, char *fileName)
-/* Return TRUE if the given UNIX time is more recent than the time that
- * fileName was last modified. */
-{
-bool ret = FALSE;
-char *fileName2 = hReplaceGbdb(fileName);
-if (fileExists(fileName2))
-    {
-    long fileUpdateTime = fileModTime(fileName2);
-    ret = (time > fileUpdateTime);
-    }
-else 
-    // file is a http url
-    {
-    struct udcFile *uf = udcFileMayOpen(fileName2, NULL);
-    if (uf != NULL)
-        {
-        long urlUpdateTime = udcUpdateTime(uf);
-        ret = (time > urlUpdateTime);
-        }
-    }
-freeMem(fileName2);
-return ret;
-}
-
-struct targetDb *targetDbMaybeLoad(struct sqlConnection *conn, char **row)
-/* If row specifies a target whose tables and file exist, and are not newer
- * than target, allocate and return a targetDb; otherwise, return NULL
- * and log a warning to stderr for QA monitoring. */
-{
-struct targetDb target;
-targetDbStaticLoad(row, &target);
-long time = sqlDateToUnixTime(target.time);
-if (timeMoreRecentThanTable(time, conn, target.pslTable) &&
-    (isEmpty(target.seqTable) ||
-     timeMoreRecentThanTable(time, conn, target.seqTable)) &&
-    (isEmpty(target.extFileTable) ||
-     timeMoreRecentThanTable(time, conn, target.extFileTable)) &&
-/* Here is where we could add a configurable slush factor: */
-    timeMoreRecentThanFile(time, target.seqFile))
-    {
-    return targetDbLoad(row);
-    }
-else
-    fprintf(stderr, "targetDb entry %s is dated %s -- older than at "
-	    "least one of its db tables (%s, %s, %s) "
-	    "or its sequence file in %s.\n",
-	    target.name, target.time, target.pslTable, target.seqTable,
-	    target.extFileTable, target.seqFile);
-return NULL;
-}
-
-struct targetDb *targetDbLookup(char *db, char *name)
-/* Given the name of a genomic database and the name of a PCR target
- * (or NULL to get all available PCR targets for db), query the
- * central database targetDb table and load the results.  Remove 
- * entries that are out of sync or have missing tables. */
-{
-struct sqlConnection *conn = hConnectCentral();
-if (! sqlTableExists(conn, "targetDb"))
-    {
-    hDisconnectCentral(&conn);
-    return NULL;
-    }
-
-struct targetDb *targetList = NULL;
-struct sqlConnection *conn2 = hAllocConn(db);
-struct sqlResult *sr;
-char **row;
-struct dyString *dy = dyStringNew(0);
-sqlDyStringPrintf(dy, "select * from targetDb where db = '%s' ", db);
-if (isNotEmpty(name))
-    sqlDyStringPrintf(dy, "and name = '%s' ", name);
-dyStringAppend(dy, "order by priority");
-sr = sqlGetResult(conn, dy->string);
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    struct targetDb *newTarg = targetDbMaybeLoad(conn2, row);
-    if (newTarg)
-	slAddHead(&targetList, newTarg);
-    }
-dyStringFree(&dy);
-hFreeConn(&conn2);
-hDisconnectCentral(&conn);
-return targetList;
-}
-
-char *targetDbSetting(struct targetDb *tdb, char *name)
-/* Return setting string or NULL if none exists. */
-{
-if (tdb == NULL)
-    errAbort("Program error: null tdb passed to targetDbSetting.");
-if (tdb->settingsHash == NULL)
-    tdb->settingsHash = raFromString(tdb->settings);
-return hashFindVal(tdb->settingsHash, name);
-}
-