/* Data structure for dealing with custom tracks in the browser. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef CUSTOMTRACK_H #define CUSTOMTRACK_H #ifndef BED_H #include "bed.h" #endif #ifndef TRACKDB_H #include "trackDb.h" #endif #include "cart.h" #include "portable.h" #define CT_PREFIX "ct_" #define CT_FILE_VAR_PREFIX "ctfile_" #define CT_DEFAULT_TRACK_NAME "User Track" #define CT_DEFAULT_TRACK_DESCR "User Supplied Track" #define CT_MANAGE_BUTTON_LABEL "manage custom tracks" #define CT_ADD_BUTTON_LABEL "add custom tracks" /* setting used when creating custom tracks in table browser -- indicates * custom track file in trash has not been through the factory parser */ #define CT_UNPARSED "unparsed" /* TODO: Remove this when hgCustom is ready for release. This cart variable is * only used to preserve old behavior during testing */ struct customTrack /* A custom track. */ /* NOTE: if you add any trash-stored *File members to struct customTrack, please make sure they * appear in the ctfile track line, or add it to stealthFiles in hgSession/sessionData.c. */ { struct customTrack *next; /* Next in list. */ struct trackDb *tdb; /* TrackDb description of track. */ char *genomeDb; /* Genome database the track is associated */ struct bed *bedList; /* List of beds. */ int fieldCount; /* Number of fields in bed. */ int maxChromName; /* max chromName length */ boolean needsLift; /* True if coordinates need lifting. */ boolean fromPsl; /* Track was derived from psl file. */ boolean wiggle; /* This is a wiggle track */ boolean dbTrack; /* This track is in the trash database */ char *dbTableName; /* name of table in trash database */ char *dbTrackType; /* type of data in this db table */ boolean dbDataLoad; /* FALSE == failed loading */ char *dbStderrFile; /* trash file to receive stderr of loaders */ char *wigFile; /* name of .wig file in trash */ char *wibFile; /* name of .wib file in trash */ char *wigAscii; /* wiggle ascii data file name in trash .wia */ char *htmlFile; /* name of .html file in trash */ struct gffFile *gffHelper; /* Used while processing GFF files. */ int offset; /* Base offset. */ char *groupName; /* Group name if any. */ struct bbiFile *bbiFile; /* Handle for bigWig/bigBed file. */ char *networkErrMsg; /* Network error message */ #ifdef PROGRESS_METER char *progressFile; /* name of download progress file in trash */ #endif }; /* cart/cgi variables */ #define CT_CUSTOM_TEXT_VAR "hgt.customText" /* alternate variable, compatible with javascript */ #define CT_CUSTOM_TEXT_ALT_VAR "hgct_customText" #define CT_CUSTOM_FILE_VAR "hgt.customFile" #define CT_CUSTOM_FILE_NAME_VAR "hgt.customFile__filename" #define CT_CUSTOM_DOC_TEXT_VAR "hgct_docText" #define CT_CUSTOM_DOC_FILE_VAR "hgct_docFile" #define CT_CUSTOM_DOC_FILE_NAME_VAR "hgct_docFile__filename" #define CT_DO_REMOVE_VAR "hgct_doRemoveCustomTrack" #define CT_SELECTED_TABLE_VAR "hgct_table" #define CT_UPDATED_TABLE_VAR "hgct_updatedTable" struct customTrack *customTracksParseCart(char *genomeDb, struct cart *cart, struct slName **retBrowserLines, char **retCtFileName); /* Parse custom tracks from cart */ /* Another method of creating customTracks is customFactoryParse. */ struct customTrack *customTracksParseCartDetailed(char *genomeDb, struct cart *cart, struct slName **retBrowserLines, char **retCtFileName, struct customTrack **retReplacedCts, int *retNumAdded, char **retErr, boolean *retWarnOnly); /* Figure out from cart variables where to get custom track text/file. * Parse text/file into a custom set of tracks. Lift if necessary. * If retBrowserLines is non-null then it will return a list of lines * starting with the word "browser". If retCtFileName is non-null then * it will return the custom track filename. If any existing custom tracks * are replaced with new versions, they are included in replacedCts. * * If there is a syntax error in the custom track this will report the * error, clear the custom track from the cart, and return NULL. It * will also leak memory. */ void customTracksSaveCart(char *genomeDb, struct cart *cart, struct customTrack *ctList); /* Save custom tracks to trash file for database in cart */ void customTracksSaveFile(char *genomeDb, struct customTrack *trackList, char *fileName); /* Save out custom tracks. This is just used by internally */ char *customTrackFileVar(char *database); /* return CGI var name containing custom track filename for a database */ void customTrackLift(struct customTrack *trackList, struct hash *ctgPosHash); /* Lift tracks based on hash of ctgPos. */ boolean customTrackNeedsLift(struct customTrack *trackList); /* Return TRUE if any track in list needs a lift. */ char *customTrackTableFromLabel(char *label); /* Convert custom track short label to table name. */ #define CUSTOM_TRASH "customTrash" /* custom tracks database name */ #define CUSTOM_TRACKS_PROFILE "customTracks" /* custom tracks database profile */ #define CT_META_INFO "metaInfo" /* table name in customTrash for last accessed memory and other data */ #define CT_EXTFILE "extFile" /* table with references to external files */ void ctTouchLastUse(struct sqlConnection *conn, char *table, boolean status); /* for status==TRUE - update metaInfo information for table * for status==FALSE - delete entry for table from metaInfo table */ boolean verifyWibExists(struct sqlConnection *conn, char *table); /* given a ct database wiggle table, see if the wib file is there */ boolean ctDbTableExists(struct sqlConnection *conn, char *table); /* verify if custom trash db table exists, touch access stats */ boolean ctDbUseAll(); /* check if hg.conf says to try DB loaders for all incoming data tracks */ void ctAddToSettings(struct customTrack *ct, char *name, char *val); /* add a variable to tdb settings */ void ctRemoveFromSettings(struct customTrack *ct, char *name); /* remove a variable from tdb settings */ struct trackDb *customTrackTdbDefault(); /* Return default custom table: black, dense, etc. */ boolean isCustomTrack(char *track); /* determine if track name refers to a custom track */ char* customTrackTypeFromBigFile(char *fileName); /* return most likely type for a file name or NULL, has * to be freed */ boolean customTrackIsBigData(char *fileName); /* return TRUE if fileName has a suffix that we * recognize as a bigDataUrl track type. */ boolean customTrackIsCompressed(char *fileName); /* test for file suffix indicating compression */ void customTrackDump(struct customTrack *track); /* Write out info on custom track to stdout */ struct customTrack *customTrackAddToList(struct customTrack *ctList, struct customTrack *addCts, struct customTrack **retReplacedCts, boolean makeDefaultUnique); /* add new tracks to the custom track list, removing older versions, * and saving the replaced tracks in a list for the caller */ void customTrackHandleLift(char *db, struct customTrack *ctList); /* lift any tracks with contig coords */ boolean customTracksExistDb(struct cart *cart, char *db, char **retCtFileName); /* determine if there are any custom tracks for db. Cleanup from expired tracks */ boolean customTracksExist(struct cart *cart, char **retCtFileName); /* determine if there are any custom tracks. Cleanup from expired tracks */ boolean ctConfigUpdate(char *filename); /* CT update is needed if database has been enabled since * the custom tracks in this file were created. The only way to check is * by file mod time, unless we add the enable time to * browser metadata somewhere */ struct customTrack *ctFind(struct customTrack *ctList,char *name); /* Find named custom track. */ #endif