d7dd4f55e28699bb783563b8bece5bf23f392995 chmalee Wed May 13 11:07:57 2026 -0700 Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808 diff --git src/hg/lib/myVariants.c src/hg/lib/myVariants.c index 3a037263ab5..cf1785a1593 100644 --- src/hg/lib/myVariants.c +++ src/hg/lib/myVariants.c @@ -1,803 +1,997 @@ #include "common.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "myVariants.h" #include "myVariantsShare.h" #include "customTrack.h" #include "hdb.h" #include "hgConfig.h" #include "cheapcgi.h" #include "trashDir.h" #include "obscure.h" #include "wikiLink.h" void myVariantsStaticLoad(char **row, struct myVariants *ret) /* Load a row from myVariants 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]; ret->score = sqlUnsigned(row[5]); safecpy(ret->strand, sizeof(ret->strand), row[6]); ret->thickStart = sqlUnsigned(row[7]); ret->thickEnd = sqlUnsigned(row[8]); ret->itemRgb = sqlUnsigned(row[9]); ret->description = row[10]; ret->db = row[11]; ret->ref = row[12]; ret->alt = row[13]; ret->project = row[14]; ret->mouseover = row[15]; ret->id = sqlUnsigned(row[16]); } struct myVariants *myVariantsLoadByQuery(struct sqlConnection *conn, char *query) /* Load all myVariants from table that satisfy the query given. Dispose of this with myVariantsFreeList(). */ { struct myVariants *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = myVariantsLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void myVariantsSaveToDb(struct sqlConnection *conn, struct myVariants *el, char *tableName, int updateSize) /* Save myVariants as a row to the table specified by tableName. * Uses explicit column names so custom fields in el->customFields are included. * If el->name is NULL or empty, fills it in post-INSERT as "Variant N" using * the row's auto-increment id; sqlLastAutoId wraps MariaDB's mysql_insert_id, * which is per-connection and unaffected by concurrent INSERTs on other * connections. */ { struct dyString *update = dyStringNew(updateSize); sqlDyStringPrintf(update, "insert into %s (bin,chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,description,db,ref,alt,project,mouseover", tableName); /* Append custom field column names */ struct slPair *cf; for (cf = el->customFields; cf != NULL; cf = cf->next) sqlDyStringPrintf(update, ",%s", cf->name); char *insertName = isEmpty(el->name) ? "" : el->name; sqlDyStringPrintf(update, ") values (%u,'%s',%u,%u,'%s',%u,'%s',%u,%u,%u,'%s','%s','%s','%s','%s','%s'", el->bin, el->chrom, el->chromStart, el->chromEnd, insertName, el->score, el->strand, el->thickStart, el->thickEnd, el->itemRgb, el->description, el->db, el->ref, el->alt, el->project, el->mouseover); /* Append custom field values */ for (cf = el->customFields; cf != NULL; cf = cf->next) sqlDyStringPrintf(update, ",'%s'", (char *)cf->val); sqlDyStringPrintf(update, ")"); sqlUpdate(conn, update->string); dyStringFree(&update); if (isEmpty(el->name)) { unsigned int newId = sqlLastAutoId(conn); struct dyString *nameUpdate = sqlDyStringCreate( "update %s set name = 'Variant %u' where id = %u", tableName, newId, newId); sqlUpdate(conn, dyStringCannibalize(&nameUpdate)); el->id = newId; freez(&el->name); struct dyString *dy = dyStringNew(0); dyStringPrintf(dy, "Variant %u", newId); el->name = dyStringCannibalize(&dy); } } struct myVariants *myVariantsLoad(char **row) /* Load a myVariants from row fetched with select * from myVariants from database. Dispose of this with myVariantsFree(). */ { struct myVariants *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]); ret->score = sqlUnsigned(row[5]); safecpy(ret->strand, sizeof(ret->strand), row[6]); ret->thickStart = sqlUnsigned(row[7]); ret->thickEnd = sqlUnsigned(row[8]); ret->itemRgb = sqlUnsigned(row[9]); ret->description = cloneString(row[10]); ret->db = cloneString(row[11]); ret->ref = cloneString(row[12]); ret->alt = cloneString(row[13]); ret->project = cloneString(row[14]); ret->mouseover = cloneString(row[15]); ret->id = sqlUnsigned(row[16]); return ret; } struct myVariants *myVariantsLoadAll(char *fileName) /* Load all myVariants from a whitespace-separated file. Dispose of this with myVariantsFreeList(). */ { struct myVariants *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[17]; while (lineFileRow(lf, row)) { el = myVariantsLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct myVariants *myVariantsLoadAllByChar(char *fileName, char chopper) /* Load all myVariants from a chopper separated file. Dispose of this with myVariantsFreeList(). */ { struct myVariants *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[17]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = myVariantsLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct myVariants *myVariantsCommaIn(char **pS, struct myVariants *ret) /* Create a myVariants out of a comma separated string. This will fill in ret if non-null, otherwise will return a new myVariants */ { 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); ret->score = sqlUnsignedComma(&s); sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); ret->thickStart = sqlUnsignedComma(&s); ret->thickEnd = sqlUnsignedComma(&s); ret->itemRgb = sqlUnsignedComma(&s); ret->description = sqlStringComma(&s); ret->db = sqlStringComma(&s); ret->ref = sqlStringComma(&s); ret->alt = sqlStringComma(&s); ret->project = sqlStringComma(&s); ret->mouseover = sqlStringComma(&s); ret->id = sqlUnsignedComma(&s); *pS = s; return ret; } void myVariantsFree(struct myVariants **pEl) /* Free a single dynamically allocated myVariants such as created with myVariantsLoad(). */ { struct myVariants *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->name); freeMem(el->description); freeMem(el->db); freeMem(el->ref); freeMem(el->alt); freeMem(el->project); freeMem(el->mouseover); slPairFreeValsAndList(&el->customFields); freez(pEl); } void myVariantsFreeList(struct myVariants **pList) /* Free a list of dynamically allocated myVariants's */ { struct myVariants *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; myVariantsFree(&el); } *pList = NULL; } void myVariantsOutput(struct myVariants *el, FILE *f, char sep, char lastSep) /* Print out myVariants. 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); fprintf(f, "%u", el->score); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->strand); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->thickStart); fputc(sep,f); fprintf(f, "%u", el->thickEnd); fputc(sep,f); fprintf(f, "%u", el->itemRgb); 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->ref); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->alt); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->project); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->mouseover); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->id); fputc(lastSep,f); } static char *myVariantsAutoSqlString = "table myVariants\n" "\"An item in a myVariants type track.\"\n" " (\n" " uint bin; \"Bin for range index\"\n" " string chrom; \"Reference sequence chromosome or scaffold\"\n" " uint chromStart;\"Start position in chromosome\"\n" " uint chromEnd; \"End position in chromosome\"\n" " string name; \"Name of item - up to 16 chars\"\n" " uint score; \"0-1000. Higher numbers are darker.\"\n" " char[1] strand; \"+ or - for strand\"\n" " uint thickStart;\"Start of thick part\"\n" " uint thickEnd; \"End position of thick part\"\n" " uint itemRgb; \"RGB 8 bits each as in bed\"\n" " lstring description; \"Longer item description\"\n" " string db; \"database name of this annotation\"\n" " string ref; \"reference allele\"\n" " string alt; \"alternate allele\"\n" " string project; \"project name for grouping variants\"\n" " string mouseover; \"short mouseover text for hover display\"\n" " uint id; \"Unique ID for item\"\n" " )\n" ; struct asObject *myVariantsAsObj() /* Return asObject describing fields of myVariants */ { return asParseText(myVariantsAutoSqlString); } char *myVariantsGetDatabaseForUser(char *userName) /* Hash the userName and map it to 1..31 inclusive for deciding what * database the table should be created in */ { if (!userName) return NULL; unsigned hashed = hashString(userName); unsigned clamped = (hashed % 31) + 1; struct dyString *dbName = dyStringCreate("customData%02u", clamped); return dyStringCannibalize(&dbName); } static char *encodeUserNameForIdentifier(char *userName) /* Return a SQL-identifier-safe encoding of userName. Alphanumeric and * underscore characters are kept verbatim; every other byte becomes _XX where * XX is its lowercase two-digit hex value. This keeps the encoding * deterministic, reversible, and free of collisions for distinct inputs that * differ only by special characters. Caller frees. */ { if (isEmpty(userName)) return cloneString(""); struct dyString *dy = dyStringNew(strlen(userName) + 8); char *p; for (p = userName; *p; p++) { unsigned char c = (unsigned char)*p; if (isalnum(c) || c == '_') dyStringAppendC(dy, c); else dyStringPrintf(dy, "_%02x", c); } return dyStringCannibalize(&dy); } char *myVariantsGetTableName(char *userName) /* Build the SQL table name for this user's myVariants. Encodes the user * name so non-identifier characters (e.g. '@' in email-style logins) don't * fail sqlCheckIdentifier. */ { if (!userName) return NULL; char *encoded = encodeUserNameForIdentifier(userName); struct dyString *tableName = dyStringCreate("myVariants_%s", encoded); freeMem(encoded); return dyStringCannibalize(&tableName); } char *myVariantsGetDbTable(char *userName) /* Return the string db.tableName based on the userName for use in sql statements * without specifying the database */ { char *db = myVariantsGetDatabaseForUser(userName); char *tbl = myVariantsGetTableName(userName); if (isNotEmpty(db) && isNotEmpty(tbl)) { struct dyString *ret = dyStringCreate("%s.%s", db, tbl); return dyStringCannibalize(&ret); } return NULL; } void myVariantsDeleteForDb(char *userName, char *targetDb) /* Delete the user's myVariants items for the given assembly. No-op if the * table doesn't exist. */ { if (isEmpty(userName) || isEmpty(targetDb)) return; char *dbTable = myVariantsTableExists(userName); if (isEmpty(dbTable)) return; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct dyString *del = sqlDyStringCreate("DELETE FROM %s WHERE db='%s'", dbTable, targetDb); sqlUpdate(conn, del->string); dyStringFree(&del); hFreeConn(&conn); } struct myVariantsShare *myVariantsResolveSharedTrack(char *trackName, struct cart *cart) /* For a "myVariants_shared_*" custom-track name, look up and revalidate the * share record from hgcentral. Returns NULL if the track is not a shared * track, the cart cookie is missing, the share has been revoked, or the * current user is not authorized (target user mismatch). The returned share * carries the validated owner/db/project/permission; callers should use these * (not the cart-supplied values) for authorization or scoping decisions. * Caller frees with myVariantsShareFree. */ { if (isEmpty(trackName) || !startsWith("myVariants_shared_", trackName)) return NULL; char *token = trackName + strlen("myVariants_shared_"); char cartVar[256]; safef(cartVar, sizeof(cartVar), MYVAR_SHARED_CART_PREFIX "%s", token); /* The cart-cookie presence gate is belt-and-suspenders: it ensures the share * was once accepted into this session before we hit hgcentral. The real * authorization is the targetUser check below against the live share row. */ if (cart == NULL || !cartVarExists(cart, cartVar)) return NULL; struct sqlConnection *conn = hConnectCentral(); if (!sqlTableExists(conn, "myVariantsShares")) { hDisconnectCentral(&conn); return NULL; } struct myVariantsShare *share = myVariantsGetShareByToken(conn, token); hDisconnectCentral(&conn); if (share == NULL) return NULL; if (isNotEmpty(share->targetUser)) { char *userName = getUserName(); if (isEmpty(userName) || !sameString(share->targetUser, userName)) { myVariantsShareFree(&share); return NULL; } } return share; } char *myVariantsResolveDbTableForCustomTrack(char *trackName, struct cart *cart) /* For a custom-track name of the form "myVariants_*", return the fully * qualified SQL table (db.tableName) holding the items. Handles both own * tracks and shared tracks. For shared tracks, revalidates the share against * hgcentral; returns NULL if the share has been revoked, downgraded out of * scope, or is not for the current user. */ { if (isEmpty(trackName)) return NULL; if (startsWith("myVariants_shared_", trackName)) { struct myVariantsShare *share = myVariantsResolveSharedTrack(trackName, cart); if (share == NULL) return NULL; char *dbTable = myVariantsGetDbTable(share->ownerUser); myVariantsShareFree(&share); return dbTable; } if (startsWith("myVariants_", trackName)) { /* trackName is the SQL-identifier-encoded form "myVariants_<encoded>". * Resolve via the current logged-in user (an own track is only viewable * by its owner) and verify the trackName matches the encoded form for * that user before returning their db.tableName. */ char *userName = getUserName(); if (isEmpty(userName)) return NULL; char *expected = myVariantsGetTableName(userName); boolean match = sameOk(expected, trackName); freeMem(expected); if (!match) return NULL; return myVariantsGetDbTable(userName); } return NULL; } char *myVariantsSharedScopeWhere(char *trackName, struct cart *cart) /* For a "myVariants_shared_*" custom-track, return a SQL WHERE-clause * fragment that limits a query to the share's authorized project and db * (e.g. "db='hg38' and project='Variants'", or "db='hg38'" alone when the * share's project is "*"). Returns NULL for non-shared tracks or revoked * shares. Memoized per-process: callers receive a fresh cloneString that * they own. */ { static struct hash *cache = NULL; if (cache == NULL) cache = hashNew(0); if (isEmpty(trackName) || !startsWith("myVariants_shared_", trackName)) return NULL; char *cached = hashFindVal(cache, trackName); if (cached != NULL) return cached[0] ? cloneString(cached) : NULL; char *result = NULL; struct myVariantsShare *share = myVariantsResolveSharedTrack(trackName, cart); if (share != NULL && isNotEmpty(share->db)) { struct dyString *dy = sqlDyStringCreate("db='%s'", share->db); if (isNotEmpty(share->project) && !sameString(share->project, "*")) sqlDyStringPrintf(dy, " and project='%s'", share->project); result = dyStringCannibalize(&dy); } myVariantsShareFree(&share); hashAdd(cache, trackName, cloneString(result ? result : "")); return result; } void myVariantsStripHiddenFields(struct slName **pFieldList) /* Remove any field whose name starts with "_hidden_" from the list in place. * Handles bare names ("_hidden_foo") and dotted/qualified names * ("db.table._hidden_foo") by checking the segment after the last '.'. * Used by hgTables for myVariants_shared_* tables so a recipient does not * see columns the owner has hidden. (Custom non-hidden columns are kept, * since they are part of the data the owner intentionally shared.) */ { struct slName *kept = NULL, *fld, *next; for (fld = *pFieldList; fld != NULL; fld = next) { next = fld->next; char *bare = strrchr(fld->name, '.'); bare = bare ? bare + 1 : fld->name; if (startsWith("_hidden_", bare)) freeMem(fld); else slAddHead(&kept, fld); } slReverse(&kept); *pFieldList = kept; } char *myVariantsTableExists(char *userName) /* See if we already have a table for this user. If so, return the name * of the table (in db.tableName format), else NULL */ { if (!userName) return NULL; char *dbTable = myVariantsGetDbTable(userName); if (!dbTable) return NULL; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); boolean exists = sqlTableExists(conn, dbTable); hFreeConn(&conn); if (exists) return dbTable; return NULL; } char *myVariantsCreateTable(char *userName) /* Return name of myVariants table (in db.tableName format) for user if it exists or * we can create, NULL otherwise */ { if (!userName) return NULL; char *db = myVariantsGetDatabaseForUser(userName); char *tableName = myVariantsGetTableName(userName); if (!tableName) return NULL; char *dbTable = myVariantsGetDbTable(userName); struct sqlConnection *existConn = hAllocConn(CUSTOM_TRASH); boolean exists = sqlTableExists(existConn, dbTable); hFreeConn(&existConn); if (exists) return dbTable; else { struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct dyString *createTable = sqlDyStringCreate( "CREATE TABLE %s.%s (\n" " bin int unsigned not null,\n" " chrom varchar(255) not null,\n" " chromStart int unsigned not null,\n" " chromEnd int unsigned not null,\n" " name varchar(255) not null,\n" " score int unsigned not null,\n" " strand char(1) not null,\n" " thickStart int unsigned not null,\n" " thickEnd int unsigned not null,\n" " itemRgb int unsigned not null,\n" " description longblob not null,\n" " db varchar(255) not null,\n" " ref varchar(255) not null,\n" " alt varchar(255) not null,\n" " project varchar(255) not null,\n" " mouseover varchar(255) not null,\n" " id int auto_increment,\n" " PRIMARY KEY(id),\n" " INDEX(chrom(16),bin),\n" " INDEX(db),\n" " INDEX(project)\n" ") ENGINE=InnoDB;", db, tableName); sqlUpdate(conn, dyStringCannibalize(&createTable)); return myVariantsGetDbTable(userName); } } +static void readLabelsFromCtFile(char *path, char *trackName, + char **retShort, char **retLong) +/* Parse the matching track line in an existing ctfile and pull shortLabel + * and longLabel via hashVarLine. Leaves *ret as NULL when not found or + * path is missing. */ +{ +*retShort = NULL; +*retLong = NULL; +if (isEmpty(path) || isEmpty(trackName) || !fileExists(path)) + return; +struct lineFile *lf = lineFileOpen(path, TRUE); +char *line = NULL; +while (lineFileNext(lf, &line, NULL)) + { + if (!startsWith("track ", line)) + continue; + struct hash *settings = hashVarLine(line + strlen("track "), lf->lineIx); + char *name = hashFindVal(settings, "name"); + if (name != NULL && sameString(name, trackName)) + { + char *s = hashFindVal(settings, "shortLabel"); + char *l = hashFindVal(settings, "longLabel"); + if (s != NULL) + *retShort = cloneString(s); + if (l != NULL) + *retLong = cloneString(l); + hashFree(&settings); + break; + } + hashFree(&settings); + } +lineFileClose(&lf); +} + +static char *sanitizeLabel(char *raw, int maxLen) +/* Strip both quote characters, newlines and carriage returns, then cap to + * maxLen characters. Returns NULL for NULL/empty input or when sanitizing + * leaves nothing behind. Matches the precedent in hgCustom.c for + * user-supplied CT labels written into the trackline. */ +{ +if (isEmpty(raw)) + return NULL; +char *s = cloneString(raw); +stripChar(s, '"'); +stripChar(s, '\''); +stripChar(s, '\\'); +stripChar(s, '\n'); +stripChar(s, '\r'); +if ((int)strlen(s) > maxLen) + s[maxLen] = '\0'; +if (isEmpty(s)) + { + freeMem(s); + return NULL; + } +return s; +} + +static void myVariantsCtFilePath(struct tempName *tn, + char *encodedTableName, char *targetDb) +/* Build the per-user-per-db ctfile path. Prefers + * cfgOption("myVariantsDataDir") so the file lives outside trash and the + * trashCleaner doesn't expire it; falls back to trashDirReusableFile when + * the dir isn't configured. */ +{ +char *persistentDir = cfgOption("myVariantsDataDir"); +if (isNotEmpty(persistentDir)) + { + /* Group files per user so one user's tracks live together: + * ${persistentDir}/<encodedTableName>/<db>.bed. */ + char *subdir = isNotEmpty(encodedTableName) ? encodedTableName : "shared"; + char *sep = endsWith(persistentDir, "/") ? "" : "/"; + char path[PATH_LEN]; + safef(path, sizeof path, "%s%s%s/%s.bed", persistentDir, sep, subdir, targetDb); + char dirPart[PATH_LEN]; + splitPath(path, dirPart, NULL, NULL); + makeDirsOnPath(dirPart); + safef(tn->forCgi, sizeof tn->forCgi, "%s", path); + safef(tn->forHtml, sizeof tn->forHtml, "%s", path); + } +else + { + char base[PATH_LEN]; + char *hostPort = cgiServerNamePort(); + safef(base, sizeof base, "myVariants_%s_%s_%s", + hostPort ? hostPort : "localhost", targetDb, + isNotEmpty(encodedTableName) ? encodedTableName : "shared"); + for (char *p = base; *p; p++) if (*p == '/') *p = '_'; + trashDirReusableFile(tn, "ct", base, ".bed"); + } +} + +void myVariantsUnlinkCtFile(char *userName, char *targetDb) +/* Delete the on-disk ctfile for this user+assembly if it exists. Uses the + * same path resolution as myVariantsWriteCtFile so it targets either the + * persistent dir (myVariantsDataDir) or the trash fallback. */ +{ +if (isEmpty(userName) || isEmpty(targetDb)) + return; +char *encodedTableName = myVariantsGetTableName(userName); +if (isEmpty(encodedTableName)) + return; +struct tempName tn; +myVariantsCtFilePath(&tn, encodedTableName, targetDb); +if (fileExists(tn.forCgi)) + unlink(tn.forCgi); +freeMem(encodedTableName); +} + char *myVariantsWriteCtFile(char *userName, char *targetDb, struct cart *cart) -/* Write a Custom Track file to trash for user's myVariants in targetDb and any shared - * tracks found in cart. Return filename or NULL if nothing to write. */ +/* Write a Custom Track file for user's myVariants in targetDb and any shared + * tracks found in cart. Return filename or NULL if nothing to write. + * If cfgOption("myVariantsDataDir") is set the file is placed there so the + * trashCleaner doesn't expire it; otherwise it goes in trash/ct as before. */ { if (isEmpty(targetDb)) return NULL; /* Identifier-safe form of userName for the CT track name and trash filename. * The raw userName may contain non-ASCII or characters unsafe in trackDb * syntax, filesystem paths, or SQL (e.g. '@', ';', spaces, quotes). */ char *encodedTableName = NULL; if (isNotEmpty(userName)) encodedTableName = myVariantsGetTableName(userName); /* Check if user has their own items */ boolean hasOwnItems = FALSE; if (isNotEmpty(userName)) { char *dbTable = myVariantsGetDbTable(userName); struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); if (isNotEmpty(dbTable) && sqlTableExists(conn, dbTable)) { char countQuery[512]; sqlSafef(countQuery, sizeof countQuery, "select count(*) from %s where db='%s'", dbTable, targetDb); hasOwnItems = (sqlQuickNum(conn, countQuery) > 0); } hFreeConn(&conn); } /* Collect shared track lines from cart. All authoritative metadata * (owner/db/project/label) comes from the live share row, never from * cart-parsed values. */ struct dyString *sharedLines = dyStringNew(0); if (cart != NULL) { struct hashEl *shareVars = cartFindPrefix(cart, MYVAR_SHARED_CART_PREFIX); struct hashEl *el; for (el = shareVars; el != NULL; el = el->next) { char *token = el->name + strlen(MYVAR_SHARED_CART_PREFIX); char trackName[512]; safef(trackName, sizeof(trackName), "myVariants_shared_%s", token); struct myVariantsShare *share = myVariantsResolveSharedTrack(trackName, cart); if (share == NULL) continue; if (!sameString(share->db, targetDb)) { myVariantsShareFree(&share); continue; } /* Skip if the sharer is the current user - they already see their own track */ if (isNotEmpty(userName) && sameString(share->ownerUser, userName)) { myVariantsShareFree(&share); continue; } /* Verify the owner's table exists */ char *ownerDbTable = myVariantsGetDbTable(share->ownerUser); struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); boolean tableOk = (isNotEmpty(ownerDbTable) && sqlTableExists(conn, ownerDbTable)); hFreeConn(&conn); if (!tableOk) { myVariantsShareFree(&share); continue; } /* Strip double quotes from owner-controlled values to prevent injection * of additional trackDb settings via the CT file track line. */ char *owner = cloneString(share->ownerUser); char *project = cloneString(share->project); char *label = isNotEmpty(share->label) ? cloneString(share->label) : NULL; stripChar(owner, '"'); stripChar(project, '"'); if (label != NULL) stripChar(label, '"'); char *projectLabel = sameString(project, "*") ? "All" : project; char shortLabel[64]; if (isNotEmpty(label)) safef(shortLabel, sizeof(shortLabel), "%s", label); else safef(shortLabel, sizeof(shortLabel), "%s's %s", owner, projectLabel); dyStringPrintf(sharedLines, "track name=\"myVariants_shared_%s\" type=\"myVariants\" itemRgb=\"on\"" " visibility=\"pack\"" " shortLabel=\"%s\"" - " longLabel=\"Shared variants: %s (from %s)\"\n", + " longLabel=\"Shared annotations: %s (from %s)\"\n", token, shortLabel, projectLabel, owner); freeMem(owner); freeMem(project); freeMem(label); myVariantsShareFree(&share); } hashElFreeList(&shareVars); } if (!hasOwnItems && dyStringLen(sharedLines) == 0) { + /* Nothing to write: remove any stale on-disk file so it doesn't leak + * when the user empties their table. Under the old trash-only path + * the trashCleaner would have done this for us. */ + if (isNotEmpty(encodedTableName)) + { + struct tempName stale; + myVariantsCtFilePath(&stale, encodedTableName, targetDb); + if (fileExists(stale.forCgi)) + unlink(stale.forCgi); + } dyStringFree(&sharedLines); freeMem(encodedTableName); return NULL; } /* Reusable, stable filename per user+db - always rewrite since shares are dynamic */ struct tempName tn; -char base[PATH_LEN]; -char *hostPort = cgiServerNamePort(); -safef(base, sizeof base, "myVariants_%s_%s_%s", - hostPort ? hostPort : "localhost", targetDb, - isNotEmpty(encodedTableName) ? encodedTableName : "shared"); -for (char *p = base; *p; p++) if (*p == '/') *p = '_'; -trashDirReusableFile(&tn, "ct", base, ".bed"); +myVariantsCtFilePath(&tn, encodedTableName, targetDb); + +/* Resolve display labels for the user's own track: cart vars set by the + * rename UI win, then the existing on-disk file (so a rename survives a + * cart reset), then the default. */ +char *shortLabel = NULL, *longLabel = NULL; +if (hasOwnItems) + { + if (cart != NULL) + { + char cartVar[256]; + safef(cartVar, sizeof cartVar, "%s.%s.shortLabel", + encodedTableName, targetDb); + shortLabel = sanitizeLabel(cartOptionalString(cart, cartVar), 80); + safef(cartVar, sizeof cartVar, "%s.%s.longLabel", + encodedTableName, targetDb); + longLabel = sanitizeLabel(cartOptionalString(cart, cartVar), 200); + } + if (shortLabel == NULL || longLabel == NULL) + { + char *diskShort = NULL, *diskLong = NULL; + readLabelsFromCtFile(tn.forCgi, encodedTableName, &diskShort, &diskLong); + if (shortLabel == NULL) + shortLabel = sanitizeLabel(diskShort, 80); + if (longLabel == NULL) + longLabel = sanitizeLabel(diskLong, 200); + freeMem(diskShort); + freeMem(diskLong); + } + if (shortLabel == NULL) + shortLabel = cloneString("My Annotations"); + if (longLabel == NULL) + longLabel = cloneString("My Annotations"); + } + FILE *f = mustOpen(tn.forCgi, "w"); if (hasOwnItems) fprintf(f, "track name=\"%s\" type=\"myVariants\" itemRgb=\"on\"" - " visibility=\"pack\" shortLabel=\"My Annotations\"" - " longLabel=\"My Annotations (%s)\"\n", encodedTableName, encodedTableName); + " visibility=\"pack\" shortLabel=\"%s\"" + " longLabel=\"%s\"\n", encodedTableName, shortLabel, longLabel); if (dyStringLen(sharedLines) > 0) fprintf(f, "%s", dyStringContents(sharedLines)); carefulClose(&f); dyStringFree(&sharedLines); freeMem(encodedTableName); +freeMem(shortLabel); +freeMem(longLabel); return cloneString(tn.forCgi); } +boolean myVariantsHandleCtRemoval(struct customTrack *ct, struct cart *cart, + char *database) +/* If ct is a myVariants own track: delete the user's rows for the current + * assembly, unlink the persistent ctfile, drop the per-db renamed labels + * and the visibility var. If ct is a myVariants shared track: drop the + * share-acceptance cart var and the visibility var. Returns TRUE when ct + * was a myVariants track and this function fully handled the cart cleanup + * (caller must skip its own per-track cart cleanup so other-assembly + * labels are preserved); FALSE otherwise. */ +{ +if (ct == NULL || ct->tdb == NULL || isEmpty(ct->tdb->track)) + return FALSE; +char *trackName = ct->tdb->track; +if (startsWith("myVariants_shared_", trackName)) + { + char *token = trackName + strlen("myVariants_shared_"); + char shareCartVar[256]; + safef(shareCartVar, sizeof shareCartVar, + MYVAR_SHARED_CART_PREFIX "%s", token); + cartRemove(cart, shareCartVar); + cartRemove(cart, trackName); + return TRUE; + } +if (startsWith("myVariants_", trackName)) + { + char *userName = wikiLinkUserName(); + if (isNotEmpty(userName)) + { + myVariantsDeleteForDb(userName, database); + myVariantsUnlinkCtFile(userName, database); + } + /* Drop the per-db renamed labels so a freshly created track on this + * assembly starts at "My Annotations" again. Labels for other + * assemblies stay because they belong to different displayed tracks. */ + char labelPrefix[256]; + safef(labelPrefix, sizeof labelPrefix, "%s.%s.", trackName, database); + cartRemovePrefix(cart, labelPrefix); + cartRemove(cart, trackName); + return TRUE; + } +return FALSE; +} + struct slName *myVariantsGetProjects(char *userName) /* Return list of distinct non-empty project values for this user's myVariants table. * Caller must slFreeList the result. Returns NULL if no projects or table doesn't exist. */ { if (isEmpty(userName)) return NULL; char *dbTable = myVariantsTableExists(userName); if (isEmpty(dbTable)) return NULL; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct slName *projects = NULL; char query[512]; sqlSafef(query, sizeof(query), "SELECT DISTINCT project FROM %s WHERE project IS NOT NULL AND project != '' ORDER BY project", dbTable); projects = sqlQuickList(conn, query); hFreeConn(&conn); return projects; } /* Built-in column names from myVariants.as - any column NOT in this list is a * user-added custom column. Filtering by name (rather than index) is robust * against column reordering or future schema changes. */ static const char *builtInColumns[] = { "bin", "chrom", "chromStart", "chromEnd", "name", "score", "strand", "thickStart", "thickEnd", "itemRgb", "description", "db", "ref", "alt", "project", "mouseover", "id", }; static boolean isBuiltInColumn(char *name) { int i; for (i = 0; i < ArraySize(builtInColumns); i++) if (sameString(name, builtInColumns[i])) return TRUE; return FALSE; } struct slName *myVariantsGetCustomFields(char *userName) /* Return list of user-added custom column names for this user's myVariants table. * Excludes built-in columns and _hidden_ prefixed columns. * Caller must slFreeList the result. Returns NULL if no custom fields or table doesn't exist. */ { if (isEmpty(userName)) return NULL; char *dbTable = myVariantsTableExists(userName); if (isEmpty(dbTable)) return NULL; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct slName *allFields = sqlListFields(conn, dbTable); hFreeConn(&conn); if (allFields == NULL) return NULL; struct slName *customFields = NULL; struct slName *field; for (field = allFields; field != NULL; field = field->next) { if (isBuiltInColumn(field->name)) continue; if (startsWith("_hidden_", field->name)) continue; slNameAddHead(&customFields, field->name); } slFreeList(&allFields); slReverse(&customFields); return customFields; } struct slName *myVariantsGetHiddenFields(char *userName) /* Return list of hidden custom column names (with _hidden_ prefix stripped) for this user's * myVariants table. Caller must slFreeList the result. Returns NULL if none. */ { if (isEmpty(userName)) return NULL; char *dbTable = myVariantsTableExists(userName); if (isEmpty(dbTable)) return NULL; struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); struct slName *allFields = sqlListFields(conn, dbTable); hFreeConn(&conn); if (allFields == NULL) return NULL; struct slName *hiddenFields = NULL; struct slName *field; for (field = allFields; field != NULL; field = field->next) { if (isBuiltInColumn(field->name)) continue; if (startsWith("_hidden_", field->name)) slNameAddHead(&hiddenFields, field->name + strlen("_hidden_")); } slFreeList(&allFields); slReverse(&hiddenFields); return hiddenFields; }