396071902267c1654f7eafaf60962aad935a9558
galt
Thu Sep 15 17:08:36 2016 -0700
Changing htmlSafef to use %s|none| instead of %-s because %-s has some legitimate uses in html output which means left-justifying the text. Jim uses it in hgBlat. This will make it more general, although it is longer to read and write. For sqlSafef, there was no legitimate expected need to have left-justified output in the production of a SQL statement.
diff --git src/hg/hgTables/identifiers.c src/hg/hgTables/identifiers.c
index 8b83535..272350f 100644
--- src/hg/hgTables/identifiers.c
+++ src/hg/hgTables/identifiers.c
@@ -1,630 +1,630 @@
/* identifiers - handle identifier lists: uploading, pasting,
* and restricting to just things on the list. */
/* 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 "hash.h"
#include "cheapcgi.h"
#include "cart.h"
#include "jksql.h"
#include "trackDb.h"
#include "portable.h"
#include "hgTables.h"
#include "trashDir.h"
#include "web.h"
#include "wikiTrack.h"
#include "htmshell.h"
static boolean forCurTable()
/* Return TRUE if cart Identifier stuff is for curTable. */
{
char *identifierDb = cartOptionalString(cart, hgtaIdentifierDb);
char *identifierTable = cartOptionalString(cart, hgtaIdentifierTable);
return (identifierDb && identifierTable &&
sameString(identifierDb, database) &&
(sameString(identifierTable, curTable) ||
sameString(connectingTableForTrack(identifierTable), curTable)));
}
static void getXrefInfo(struct sqlConnection *conn,
char **retXrefTable, char **retIdField,
char **retAliasField)
/* See if curTrack specifies an xref/alias table for lookup of IDs. */
{
struct trackDb *tdb = hTrackDbForTrack(database, curTable);
if (tdb == NULL)
tdb = curTrack;
char *xrefSpec = tdb ? trackDbSettingClosestToHomeOrDefault(tdb, "idXref",NULL) : NULL;
char *xrefTable = NULL, *idField = NULL, *aliasField = NULL;
if (xrefSpec != NULL)
{
char *words[3];
chopLine(cloneString(xrefSpec), words);
if (isEmpty(words[2]))
errAbort("trackDb error: track %s, setting idXref must be followed "
"by three words (xrefTable, idField, aliasField).",
curTrack->track);
xrefTable = words[0];
idField = words[1];
aliasField = words[2];
if (!sqlTableExists(conn, xrefTable) ||
sqlFieldIndex(conn, xrefTable, idField) < 0 ||
sqlFieldIndex(conn, xrefTable, aliasField) < 0)
xrefTable = idField = aliasField = NULL;
}
if (retXrefTable != NULL)
*retXrefTable = xrefTable;
if (retIdField != NULL)
*retIdField = idField;
if (retAliasField != NULL)
*retAliasField = aliasField;
}
static struct slName *getExamples(char *db, struct sqlConnection *conn,
char *table, char *field, int count)
/* Return a list of several example values of table.field. */
{
boolean isTabix = FALSE;
if (isBamTable(table))
{
assert(sameString(field, "qName"));
return randomBamIds(table, conn, count);
}
else if (isBigBed(db, table, curTrack, ctLookupName))
{
assert(sameString(field, "name"));
return randomBigBedIds(table, conn, count);
}
else if (isVcfTable(table, &isTabix))
{
assert(sameString(field, "id"));
return randomVcfIds(table, conn, count, isTabix);
}
else
{
char fullTable[HDB_MAX_TABLE_STRING];
char *c = strchr(table, '.');
if (c || ! hFindSplitTable(database, NULL, table, fullTable, NULL))
safecpy(fullTable, sizeof(fullTable), table);
return sqlRandomSampleConn(conn, fullTable, field, count);
}
}
static void explainIdentifiers(char *db, struct sqlConnection *conn, char *idField)
/* Tell the user what field(s) they may paste/upload values for, and give
* some examples. */
{
char *xrefTable = NULL, *xrefIdField = NULL, *aliasField = NULL;
getXrefInfo(conn, &xrefTable, &xrefIdField, &aliasField);
hPrintf("The items must be values of the %s field of the currently "
"selected table, %s",
idField, curTable);
if (aliasField != NULL)
{
if (sameString(curTable, xrefTable))
{
if (!sameString(idField, aliasField))
hPrintf(", or the %s field.\n", aliasField);
else
hPrintf(".\n");
}
else
hPrintf(", or the %s field of the alias table %s.\n",
aliasField, xrefTable);
}
else
hPrintf(".\n");
hPrintf("(The \"describe table schema\" button shows more information about "
"the table fields.)\n");
// on a browserbox, db is on the UCSC server, so cannot select into db, even if temporary
if (!isCustomTrack(curTable) && !hIsBrowserbox() && (conn == NULL || sqlCanCreateTemp(conn)))
{
struct slName *exampleList = NULL, *ex;
hPrintf("Some example values:
\n");
exampleList = getExamples(db, conn, curTable, idField,
aliasField != NULL ? 3 : 5);
for (ex = exampleList; ex != NULL; ex = ex->next)
{
char *tmp = htmlEncode(ex->name);
hPrintf("%s
\n", tmp);
freeMem(tmp);
}
if (aliasField != NULL)
{
char tmpTable[512];
char query[2048];
// do not use any db. prefix on curTable for name
char *plainXrefTable = strrchr(xrefTable, '.');
if (plainXrefTable)
plainXrefTable++;
else
plainXrefTable = xrefTable;
char *plainCurTable = strrchr(curTable, '.');
if (plainCurTable)
plainCurTable++;
else
plainCurTable = curTable;
safef(tmpTable, sizeof(tmpTable), "hgTemp.tmp%s%s", plainCurTable, plainXrefTable);
if (differentString(xrefTable, curTable))
sqlSafef(query, sizeof(query),
"create temporary table %s select %s.%s as %s from %s,%s "
"where %s.%s = %s.%s and %s.%s != %s.%s limit 100000",
tmpTable, xrefTable, aliasField, aliasField, xrefTable, curTable,
xrefTable, xrefIdField, curTable, idField,
xrefTable, xrefIdField, xrefTable, aliasField);
else
sqlSafef(query, sizeof(query),
"create temporary table %s select %s from %s "
"where %s != %s limit 100000",
tmpTable, aliasField, xrefTable, aliasField, xrefIdField);
sqlUpdate(conn, query);
exampleList = getExamples(db, conn, tmpTable, aliasField, 3);
for (ex = exampleList; ex != NULL; ex = ex->next)
hPrintf("%s
\n", ex->name);
}
hPrintf("\n");
}
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
void doUploadIdentifiers(struct sqlConnection *conn)
/* Respond to upload identifiers button. */
{
struct hTableInfo *hti = maybeGetHti(database, curTable, conn);
char *idField = getIdField(database, curTrack, curTable, hti);
htmlOpen("Upload Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("");
cgiDown(0.9);
htmlClose();
}
static void addPrimaryIdsToHash(struct sqlConnection *conn, struct hash *hash,
char *idField, struct slName *tableList,
struct lm *lm, char *extraWhere)
/* For each table in tableList, query all idField values and add to hash,
* id -> uppercased id for case-insensitive matching. */
{
struct slName *table;
struct sqlResult *sr;
char **row;
struct dyString *query = dyStringNew(0);
for (table = tableList; table != NULL; table = table->next)
{
dyStringClear(query);
sqlDyStringPrintf(query, "select %s from %s", idField, table->name);
if (extraWhere != NULL)
dyStringPrintf(query, " where %s", extraWhere);
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
if (isNotEmpty(row[0]))
{
char *origCase = lmCloneString(lm, row[0]);
touppers(row[0]);
hashAdd(hash, row[0], origCase);
}
}
sqlFreeResult(&sr);
}
}
static void addXrefIdsToHash(struct sqlConnection *conn, struct hash *hash,
char *idField, char *xrefTable, char *xrefIdField,
char *aliasField, struct lm *lm, char *extraWhere)
/* Query all id-alias pairs from xrefTable (where id actually appears
* in curTable) and hash alias -> id. Convert alias to upper case for
* case-insensitive matching.
* Ignore self (alias = id) mappings -- we already got those above. */
{
struct sqlResult *sr;
char **row;
struct dyString *query = dyStringNew(0);
if (sameString(xrefTable, curTable))
sqlDyStringPrintf(query, "select %s,%s from %s", aliasField, xrefIdField, xrefTable);
else
/* Get only the aliases for items actually in curTable.idField: */
sqlDyStringPrintf(query,
"select %s.%s,%s.%s from %s,%s where %s.%s = %s.%s",
xrefTable, aliasField, xrefTable, xrefIdField,
xrefTable, curTable,
xrefTable, xrefIdField, curTable, idField);
if (extraWhere != NULL)
// extraWhere begins w/ID field of curTable=xrefTable. Skip that field name and
// use "xrefTable.aliasField" with the IN (...) condition that follows:
sqlDyStringPrintf(query, " %s %s.%s %-s",
(sameString(xrefTable, curTable) ? "where" : "and"),
xrefTable, aliasField, skipToSpaces(extraWhere));
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
if (sameString(row[0], row[1]))
continue;
touppers(row[0]);
hashAdd(hash, row[0], lmCloneString(lm, row[1]));
}
sqlFreeResult(&sr);
}
static struct hash *getAllPossibleIds(struct sqlConnection *conn,
struct lm *lm, char *idField, char *extraWhere)
/* If curTable is a custom track or bigFile, return NULL. Otherwise,
* make a hash of all identifiers in curTable (and alias tables if specified)
* so that we can check the validity of pasted/uploaded identifiers. */
{
if (isCustomTrack(curTable) || isLongTabixTable(curTable) || isBamTable(curTable) || isVcfTable(curTable, NULL) ||
isBigBed(database, curTable, curTrack, ctLookupName))
return NULL;
struct hash *matchHash = hashNew(20);
struct slName *tableList;
char *xrefTable = NULL, *xrefIdField = NULL, *aliasField = NULL;
struct sqlConnection *alternateConn = conn;
if (sameWord(curTable, WIKI_TRACK_TABLE))
alternateConn = wikiConnect();
if (sameWord(curTable, WIKI_TRACK_TABLE))
tableList = slNameNew(WIKI_TRACK_TABLE);
else if (strchr(curTable, '.'))
tableList = slNameNew(curTable);
else
tableList = hSplitTableNames(database, curTable);
if (idField != NULL)
addPrimaryIdsToHash(alternateConn, matchHash, idField, tableList, lm, extraWhere);
getXrefInfo(alternateConn, &xrefTable, &xrefIdField, &aliasField);
if (xrefTable != NULL)
{
addXrefIdsToHash(alternateConn, matchHash, idField,
xrefTable, xrefIdField, aliasField, lm, extraWhere);
}
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
return matchHash;
}
static char *slNameToInExpression(char *field, struct slName *allTerms)
/* Given an slName list, return a SQL "field IN ('term1', 'term2', ...)" expression
* to be used in a WHERE clause. */
{
struct dyString *dy = dyStringNew(0);
sqlDyStringPrintfFrag(dy, "%s in (", field);
boolean first = TRUE;
struct slName *term;
for (term = allTerms; term != NULL; term = term->next)
{
if (first)
first = FALSE;
else
dyStringAppend(dy, ", ");
sqlDyStringPrintf(dy, "'%s'", term->name);
}
dyStringAppend(dy, ")");
return dyStringCannibalize(&dy);
}
#define MAX_IDTEXT (64 * 1024)
#define DEFAULT_MAX_IDS_IN_WHERE 10000
void doPastedIdentifiers(struct sqlConnection *conn)
/* Process submit in paste identifiers page. */
{
char *idText = trimSpaces(cartString(cart, hgtaPastedIdentifiers));
htmlOpen("Table Browser (Input Identifiers)");
if (isNotEmpty(idText))
{
/* Write terms to temp file, checking whether they have matches, and
* save temp file name. */
boolean saveIdText = (strlen(idText) < MAX_IDTEXT);
char *idTextForLf = saveIdText ? cloneString(idText) : idText;
struct lineFile *lf = lineFileOnString("idText", TRUE, idTextForLf);
char *line, *word;
struct tempName tn;
FILE *f;
int totalTerms = 0, foundTerms = 0;
struct slName* missingTerms = NULL;
struct dyString *exampleMissingIds = dyStringNew(256);
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
actualDb = wikiDbName();
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
if (idField == NULL)
{
warn("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
webNewSection("Table Browser");
cartRemove(cart, hgtaIdentifierDb);
cartRemove(cart, hgtaIdentifierTable);
cartRemove(cart, hgtaIdentifierFile);
mainPageAfterOpen(conn);
htmlClose();
return;
}
struct slName *allTerms = NULL, *term;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
{
term = slNameNew(word);
slAddHead(&allTerms, term);
totalTerms++;
}
}
slReverse(&allTerms);
lineFileClose(&lf);
char *extraWhere = NULL;
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (totalTerms > 0 && totalTerms <= maxIdsInWhere)
extraWhere = slNameToInExpression(idField, allTerms);
struct lm *lm = lmInit(0);
struct hash *matchHash = getAllPossibleIds(conn, lm, idField, extraWhere);
trashDirFile(&tn, "hgtData", "identifiers", ".key");
f = mustOpen(tn.forCgi, "w");
for (term = allTerms; term != NULL; term = term->next)
{
struct slName *matchList = NULL, *match;
if (matchHash == NULL)
{
matchList = slNameNew(term->name);
}
else
{
/* Support multiple alias->id mappings: */
char upcased[1024];
safecpy(upcased, sizeof(upcased), term->name);
touppers(upcased);
struct hashEl *hel = hashLookup(matchHash, upcased);
if (hel != NULL)
{
matchList = slNameNew((char *)hel->val);
while ((hel = hashLookupNext(hel)) != NULL)
{
match = slNameNew((char *)hel->val);
slAddHead(&matchList, match);
}
}
}
if (matchList != NULL)
{
foundTerms++;
for (match = matchList; match != NULL; match = match->next)
{
mustWrite(f, match->name, strlen(match->name));
mustWrite(f, "\n", 1);
}
}
else
{
slAddHead(&missingTerms, slNameNew(term->name));
}
}
slReverse(&missingTerms);
carefulClose(&f);
cartSetString(cart, hgtaIdentifierDb, database);
cartSetString(cart, hgtaIdentifierTable, curTable);
cartSetString(cart, hgtaIdentifierFile, tn.forCgi);
if (saveIdText)
freez(&idTextForLf);
else
cartRemove(cart, hgtaPastedIdentifiers);
int missingCount = totalTerms - foundTerms;
if (missingCount > 0)
{
char *xrefTable, *aliasField;
getXrefInfo(conn, &xrefTable, NULL, &aliasField);
boolean xrefIsSame = xrefTable && sameString(curTable, xrefTable);
struct tempName tn;
trashDirFile(&tn, "hgt/missingIds", cartSessionId(cart), ".tmp");
FILE *f = mustOpen(tn.forCgi, "w");
int exampleCount = 0;
for (term = missingTerms; term != NULL; term = term->next)
{
if (exampleCount < 10)
{
++exampleCount;
dyStringPrintf(exampleMissingIds, "%s\n", term->name);
}
fprintf(f, "%s\n", term->name);
}
carefulClose(&f);
warn("Note: %d of the %d given identifiers have no match in "
"table %s, field %s%s%s%s%s. "
"Try the \"describe table schema\" button for more "
"information about the table and field.\n"
"%d %smissing identifier(s):\n"
"%s\n"
- "Complete list of missing identifiers\n",
+ "Complete list of missing identifiers\n",
(totalTerms - foundTerms), totalTerms,
curTable, idField,
(xrefTable ? (xrefIsSame ? "" : " or in alias table ") : ""),
(xrefTable ? (xrefIsSame ? "" : xrefTable) : ""),
(xrefTable ? (xrefIsSame ? " or in field " : ", field ") : ""),
(xrefTable ? aliasField : ""),
exampleCount,
exampleCount < missingCount ? "example " : "",
exampleMissingIds->string,
tn.forHtml
);
webNewSection("Table Browser");
}
lmCleanup(&lm);
hashFree(&matchHash);
}
else
{
cartRemove(cart, hgtaIdentifierFile);
}
mainPageAfterOpen(conn);
htmlClose();
}
char *identifierFileName()
/* File name identifiers are in, or NULL if not for curTable or no such file. */
{
char *fileName = cartOptionalString(cart, hgtaIdentifierFile);
if (fileName == NULL)
return NULL;
if (! forCurTable())
return NULL;
if (fileExists(fileName))
return fileName;
else
{
cartRemove(cart, hgtaIdentifierFile);
return NULL;
}
}
struct hash *identifierHash(char *db, char *table)
/* Return hash full of identifiers from the given table (or NULL). */
{
char dbDotTable[2048];
if (sameString(table, WIKI_TRACK_TABLE))
safecpy(dbDotTable, sizeof(dbDotTable), table);
else if (!sameString(db, database))
safef(dbDotTable, sizeof(dbDotTable), "%s.%s", db, table);
else
safecpy(dbDotTable, sizeof(dbDotTable), table);
if (! (sameString(dbDotTable, curTable) ||
sameString(connectingTableForTrack(dbDotTable), curTable)) )
return NULL;
char *fileName = identifierFileName();
if (fileName == NULL)
return NULL;
else
{
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct hash *hash = hashNew(18);
char *line, *word;
while (lineFileNext(lf, &line, NULL))
{
while ((word = nextWord(&line)) != NULL)
hashAdd(hash, word, NULL);
}
lineFileClose(&lf);
return hash;
}
}
char *identifierWhereClause(char *idField, struct hash *idHash)
/* If the number of pasted IDs is reasonably low, return a where-clause component for the IDs. */
{
if (idHash == NULL || idField == NULL)
return NULL;
int numIds = hashNumEntries(idHash);
int maxIdsInWhere = cartUsualInt(cart, "hgt_maxIdsInWhere", DEFAULT_MAX_IDS_IN_WHERE);
if (numIds > 0 && numIds <= maxIdsInWhere)
{
struct dyString *dy = dyStringNew(16 * numIds);
dyStringPrintf(dy, "%s in (", idField);
struct hashCookie hc = hashFirst(idHash);
boolean first = TRUE;
char *id;
while ((id = hashNextName(&hc)) != NULL)
{
if (first)
first = FALSE;
else
dyStringAppend(dy, ", ");
dyStringPrintf(dy, "'%s'", id);
}
dyStringAppend(dy, ")");
return dyStringCannibalize(&dy);
}
return NULL;
}
void doClearPasteIdentifierText(struct sqlConnection *conn)
/* Respond to clear within paste identifier page. */
{
cartRemove(cart, hgtaPastedIdentifiers);
doPasteIdentifiers(conn);
}
void doClearIdentifiers(struct sqlConnection *conn)
/* Respond to clear identifiers button. */
{
char *fileName;
htmlOpen("Table Browser (Cleared Identifiers)");
fileName = identifierFileName();
if (fileName != NULL)
remove(fileName);
cartRemove(cart, hgtaIdentifierFile);
cartRemove(cart, hgtaPastedIdentifiers);
mainPageAfterOpen(conn);
htmlClose();
}