/* wikiTrack.h was originally generated by the autoSql program, which also * generated wikiTrack.c and wikiTrack.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef WIKITRACK_H #define WIKITRACK_H #ifndef JKSQL_H #include "jksql.h" #endif #ifndef HTMLPAGE_H #include "htmlPage.h" #endif #ifndef CART_H #include "cart.h" #endif #define WIKITRACK_NUM_COLS 16 struct wikiTrack /* wikiTrack bed 6+ structure */ { struct wikiTrack *next; /* Next in singly linked list. */ unsigned short bin; /* used for efficient position indexing */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name of item */ unsigned score; /* Score from 0-1000 */ char strand[2]; /* + or - */ char *db; /* database for item */ char *owner; /* creator of item */ char *color; /* rgb color of item (currently unused) */ char *class; /* classification of item (browser group) */ char *creationDate; /* date item created */ char *lastModifiedDate; /* date item last updated */ char *descriptionKey; /* name of wiki description page */ unsigned id; /* auto-increment item ID */ char *geneSymbol; /* knownGene kgXref geneSymbol name */ }; void wikiTrackStaticLoad(char **row, struct wikiTrack *ret); /* Load a row from wikiTrack table into ret. The contents of ret will * be replaced at the next call to this function. */ struct wikiTrack *wikiTrackLoad(char **row); /* Load a wikiTrack from row fetched with select * from wikiTrack * from database. Dispose of this with wikiTrackFree(). */ struct wikiTrack *wikiTrackLoadAll(char *fileName); /* Load all wikiTrack from whitespace-separated file. * Dispose of this with wikiTrackFreeList(). */ struct wikiTrack *wikiTrackLoadAllByChar(char *fileName, char chopper); /* Load all wikiTrack from chopper separated file. * Dispose of this with wikiTrackFreeList(). */ #define wikiTrackLoadAllByTab(a) wikiTrackLoadAllByChar(a, '\t'); /* Load all wikiTrack from tab separated file. * Dispose of this with wikiTrackFreeList(). */ struct wikiTrack *wikiTrackLoadByQuery(struct sqlConnection *conn, char *query); /* Load all wikiTrack from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with wikiTrackFreeList(). */ void wikiTrackSaveToDb(struct sqlConnection *conn, struct wikiTrack *el, char *tableName, int updateSize); /* Save wikiTrack as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */ struct wikiTrack *wikiTrackCommaIn(char **pS, struct wikiTrack *ret); /* Create a wikiTrack out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new wikiTrack */ void wikiTrackFree(struct wikiTrack **pEl); /* Free a single dynamically allocated wikiTrack such as created * with wikiTrackLoad(). */ void wikiTrackFreeList(struct wikiTrack **pList); /* Free a list of dynamically allocated wikiTrack's */ void wikiTrackOutput(struct wikiTrack *el, FILE *f, char sep, char lastSep); /* Print out wikiTrack. Separate fields with sep. Follow last field with lastSep. */ #define wikiTrackTabOut(el,f) wikiTrackOutput(el,f,'\t','\n'); /* Print out wikiTrack as a line in a tab-separated file. */ #define wikiTrackCommaOut(el,f) wikiTrackOutput(el,f,',',','); /* Print out wikiTrack as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ /* configuration variables */ #define CFG_WIKI_URL "wikiTrack.URL" #define CFG_WIKI_BROWSER "wikiTrack.browser" #define CFG_WIKI_EDITORS "wikiTrack.editors" #define CFG_WIKI_DB_LIST "wikiTrack.dbList" #define CFG_WIKI_TRACK_READ_ONLY "wikiTrack.readOnly" /* name of database table in hgcentral */ #define WIKI_TRACK_TABLE "wikiTrack" /* trackDb settings */ #define WIKI_TRACK_LABEL "Wiki Track" #define WIKI_TRACK_LONGLABEL "Wiki Track user annotations" #define WIKI_TRACK_PRIORITY 100 /* hgc variables */ #define G_CREATE_WIKI_ITEM "htcCreateWikiItem" #define G_ADD_WIKI_COMMENTS "htcAddWikiComments" #define G_DELETE_WIKI_ITEM "htcDeleteWikiItem" /* hgc and hgGene variables */ #define WIKI_NO_TEXT_RESPONSE "There is currently no text in this page" #define ADD_ITEM_COMMENT_DEFAULT "add comments" #define NEW_ITEM_COMMENT "wikiCommentText" #define NEW_ITEM_SCORE "wikiItemScore" #define NEW_ITEM_COMMENT_DEFAULT "enter description and comments" #define NEW_ITEM_NAME "wikiDefaultName" #define NEW_ITEM_COLOR "wikiItemColor" #define NEW_ITEM_STRAND "wikiItemStrand" #define NEW_ITEM_CLASS "wikiItemClass" #define NEW_ITEM_CATEGORY "[[Category:Genome Annotation]]" #define ITEM_NOT_CLASSIFIED "Not classified" #define NO_ITEM_COMMENT_SUPPLIED "(no initial description supplied)" #define DEFAULT_BROWSER "genome.ucsc.edu" #define TEST_EMAIL_VERIFIED "GenomeAnnotation:TestEmailVerified" #define EMAIL_NEEDS_TO_BE_VERIFIED \ "You must confirm your e-mail address before editing" #define USER_PREFERENCES_MESSAGE \ "Please set and validate your e-mail address through your" #define GENE_CLASS "Genes and Gene Prediction Tracks" #define LOGIN_EXPIRED \ "You do not have permission to edit pages, for the following reasons:" boolean wikiTrackReadOnly(); /* return TRUE if wiki track is in Read-Only mode, default answer is FALSE */ boolean wikiTrackEnabled(char *database, char **wikiUserName); /*determine if wikiTrack can be used, and is this user logged into the wiki ?*/ char *wikiTrackGetCreateSql(char *tableName); /* return sql create statement for wiki track with tableName */ char *wikiDbName(); /* return name of database where wiki track is located currently this is central.db but the future may be configurable */ struct sqlConnection *wikiConnect(); /* connect to db where wikiTrack table is located * currently this is hConnectCentral() but the future may be * configurable */ void wikiDisconnect(struct sqlConnection **pConn); /* disconnect from wikiTrack table database */ struct wikiTrack *findWikiItemId(char *wikiItemId); /* given a wikiItemId return the row from the table */ struct wikiTrack *findWikiItemByGeneSymbol(char *db, char *geneSymbol); /* given a db and UCSC known gene geneSymbol, find the wiki item */ struct wikiTrack *findWikiItemByName(char *db, char *name); /* given a db,name pair return the row from the table, can return NULL */ void htmlCloneFormVarSet(struct htmlForm *parent, struct htmlForm *clone, char *name, char *val); /* clone form variable from parent, with new value, * if *val is NULL, clone val from parent */ char *fetchWikiRawText(char *descriptionKey); /* fetch page from wiki in raw form as it is in the edit form */ char *fetchWikiRenderedText(char *descriptionKey); /* fetch page from wiki in rendered form, strip it of edit URLs, * html comments, and test for actual proper return. * returned string can be freed after use */ void displayComments(struct wikiTrack *item); /* display the rendered comments for this item */ void createPageHelp(char *pageFileName); /* find the specified html help page and display it, or issue a missing * page message so the site administrator can fix it. */ struct htmlPage *fetchEditPage(char *descriptionKey); /* fetch edit page for descriptionKey page name in wiki */ void prefixComments(struct wikiTrack *item, char *comments, char *userName, char *seqName, int winStart, int winEnd, char *database, char *extraHeader, char *extraTag, char *category); /* add comments at the beginning of an existing wiki item */ void addDescription(struct wikiTrack *item, char *userName, char *seqName, int winStart, int winEnd, struct cart *cart, char *database, char *extraHeader, char *extraTag, char *category); /* add description to the end of an existing wiki item */ char *encodedReturnUrl(char *(*hgUrl)()); /* Return a CGI-encoded URL with hgsid. Free when done. * The given function hgUrl() will construct the actual cgi binary URL */ boolean emailVerified(boolean showMessage); /* TRUE indicates email has been verified for this wiki user */ boolean isWikiEditor(char *userName); /* check if user name is on list of editors */ char *wikiUrl(struct wikiTrack *item); /* construct a URL to the wiki page for the specified item free the returned string when done with it. */ struct trackDb *wikiTrackDb(); /* Create & return a trackDb for the wiki track. */ #endif /* WIKITRACK_H */