a6770479059c1d3ed0a77f69ceac2ae19981e89f galt Thu Sep 26 18:29:31 2024 -0700 Since hubs like Tair10 call these functions with a NULL conn, just needed to add a check for that in hgTables identifiers getXrefInfo function. fixes #34495 diff --git src/hg/hgTables/identifiers.c src/hg/hgTables/identifiers.c index 7525818..21b58c9 100644 --- src/hg/hgTables/identifiers.c +++ src/hg/hgTables/identifiers.c @@ -1,636 +1,637 @@ /* 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 kent/LICENSE or http://genome.ucsc.edu/license/ 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) || + + if (!conn || !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, sizeof 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 \"data format description\" button shows more information about " "the fields in the data.)\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("
\n", getScriptName(), cartUsualString(cart, "formMethod", "POST")); cartSaveSession(cart); hPrintf("Please paste in the identifiers you want to include.\n"); if (sqlDatabaseExists("hgTemp")) explainIdentifiers(actualDb, alternateConn, idField); else warn("No hgTemp database found for temporary tables.
Please see https://genome.ucsc.edu/goldenPath/help/mirrorManual.html#mysql-setup for more information."); hPrintf("
\n"); cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70); hPrintf("
\n"); cgiMakeButton(hgtaDoPastedIdentifiers, "Submit"); hPrintf(" "); cgiMakeButton(hgtaDoClearPasteIdentifierText, "Clear"); hPrintf(" "); cgiMakeButton(hgtaDoMainPage, "Cancel"); 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("
\n", getScriptName()); cartSaveSession(cart); hPrintf("Please enter the name of a file from your computer that contains a "); hPrintf("space, tab, or "); hPrintf("line separated list of the items you want to include.\n"); explainIdentifiers(database, conn, idField); hPrintf("
\n"); hPrintf(" ", hgtaPastedIdentifiers); hPrintf("
\n"); cgiMakeButton(hgtaDoPastedIdentifiers, "Submit"); hPrintf(" "); cgiMakeButton(hgtaDoMainPage, "Cancel"); 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) sqlDyStringPrintf(query, " where %s %-s", idField, 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: if (sameString(xrefTable, curTable)) sqlDyStringPrintf(query, " where "); else sqlDyStringPrintf(query, " and "); sqlDyStringPrintf(query, "%s.%s %-s", xrefTable, aliasField, 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. */ { // this assumes that there is a knownGene table even if the track is a bigGenePred if (isCustomTrack(curTable) || isLongTabixTable(curTable) || isBamTable(curTable) || isVcfTable(curTable, NULL) || (differentString("knownGene", curTable) && 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(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); sqlDyStringPrintf(dy, " in ("); boolean first = TRUE; struct slName *term; for (term = allTerms; term != NULL; term = term->next) { if (first) first = FALSE; else sqlDyStringPrintf(dy, ", "); sqlDyStringPrintf(dy, "'%s'", term->name); } sqlDyStringPrintf(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(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 \"data format description\" button for more " "information about the data fields and their contents.\n" "%d %smissing identifier(s):\n" "%s\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); sqlDyStringPrintf(dy, "%s in (", idField); struct hashCookie hc = hashFirst(idHash); boolean first = TRUE; char *id; while ((id = hashNextName(&hc)) != NULL) { if (first) first = FALSE; else sqlDyStringPrintf(dy, ", "); sqlDyStringPrintf(dy, "'%s'", id); } sqlDyStringPrintf(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(); }