8fdc86ea29f656cf7efee9954fdae6b573190fb3 tdreszer Fri May 6 17:23:22 2011 -0700 Standardized replacement for

with cgiDown and worked out more spacing issues in hgFileUi and hgTrackUi. diff --git src/hg/hgCustom/hgCustom.c src/hg/hgCustom/hgCustom.c index cddd6d4..05b4181 100644 --- src/hg/hgCustom/hgCustom.c +++ src/hg/hgCustom/hgCustom.c @@ -1,1255 +1,1255 @@ /* hgCustom - Custom track management CGI. */ #include "common.h" #include "obscure.h" #include "linefile.h" #include "hash.h" #include "cart.h" #include "cheapcgi.h" #include "web.h" #include "htmshell.h" #include "hdb.h" #include "hui.h" #include "hCommon.h" #include "customTrack.h" #include "customFactory.h" #include "portable.h" #include "errCatch.h" #if (defined USE_BAM && defined KNETFILE_HOOKS) #include "knetUdc.h" #include "udc.h" #endif//def USE_BAM && KNETFILE_HOOKS static long loadTime = 0; static char const rcsid[] = "$Id: hgCustom.c,v 1.142 2010/05/28 23:04:56 kuhn Exp $"; void usage() /* Explain usage and exit. */ { errAbort( "hgCustom - Custom track management CGI\n" "usage:\n" " hgCustom \n" ); } /* DON'T EDIT THIS -- use CGI param "&measureTiming=." */ static boolean measureTiming = FALSE; #define TEXT_ENTRY_ROWS 7 #define TEXT_ENTRY_COLS 73 #define CONFIG_ENTRY_ROWS 3 #define SAVED_LINE_COUNT 50 /* CGI variables */ #define hgCt "hgct_" /* prefix for all control variables */ /* these are shared with other modules */ #define hgCtDataText CT_CUSTOM_TEXT_ALT_VAR #define hgCtDataFile CT_CUSTOM_FILE_VAR #define hgCtDataFileName CT_CUSTOM_FILE_NAME_VAR #define hgCtDocText CT_CUSTOM_DOC_TEXT_VAR #define hgCtDocFile CT_CUSTOM_DOC_FILE_VAR #define hgCtTable CT_SELECTED_TABLE_VAR #define hgCtUpdatedTable CT_UPDATED_TABLE_VAR /* misc */ #define hgCtUpdatedTrack "hgct_updatedTrack" #define hgCtDeletePrefix "hgct_del" #define hgCtRefreshPrefix "hgct_refresh" #define hgCtConfigLines "hgct_configLines" /* commands */ #define hgCtDo hgCt "do_" /* prefix for all commands */ #define hgCtDoAdd hgCtDo "add" #define hgCtDoDelete hgCtDo "delete" #define hgCtDoDeleteSet hgCtDo "delete_set" #define hgCtDoDeleteClr hgCtDo "delete_clr" #define hgCtDoRefresh hgCtDo "refresh" #define hgCtDoRefreshSet hgCtDo "refresh_set" #define hgCtDoRefreshClr hgCtDo "refresh_clr" #define hgCtDoGenomeBrowser hgCtDo "gb" #define hgCtDoTableBrowser hgCtDo "tb" /* Global variables */ struct cart *cart; struct hash *oldVars = NULL; char *excludeVars[] = {"Submit", "submit", "SubmitFile", NULL}; char *database = NULL; char *organism = NULL; struct customTrack *ctList = NULL; void makeClearButton(char *field) /* UI button that clears a text field */ { char javascript[1024]; safef(javascript, sizeof javascript, "document.mainForm.%s.value = '';", field); cgiMakeOnClickButton(javascript, " Clear "); } void addIntro() /* display overview and help message for "add" screen */ { if (hIsGsidServer()) { puts(" Data must be formatted in\n" " BED,\n" " bigBed,\n" " bedGraph,\n" " GFF,\n" " GTF,\n" " WIG\n" " bigWig,\n" " BED detail,\n" " Personal Genome SNP,\n" " or PSL\n" " formats. To configure the display, set\n" " track\n" " and" " browser\n" " line attributes as described in the \n" " User's Guide.\n" " URLs for data in the bigBed, bigWig and BAM formats must be embedded in a track\n" " line in the box below.\n" ); } else { puts(" Data must be formatted in\n" " BED,\n" " bigBed,\n" " bedGraph,\n" " GFF,\n" " GTF,\n" " WIG,\n" " bigWig,\n" " MAF,\n" " BAM,\n" " BED detail,\n" " Personal Genome SNP,\n" " or PSL\n" " formats. To configure the display, set\n" " track\n" " and" " browser\n" " line attributes as described in the \n" " User's Guide.\n" " URLs for data in the bigBed and bigWig formats must be embedded in a track\n" " line in the box below.\n" " Publicly available custom tracks are listed\n" " here.\n" " Examples are\n" " here.\n" ); } } void addCustomForm(struct customTrack *ct, char *err) /* display UI for adding custom tracks by URL or pasting data */ { char *dataUrl = NULL; char buf[1024]; boolean gotClade = FALSE; boolean isUpdateForm = FALSE; if (ct) { isUpdateForm = TRUE; dataUrl = ctDataUrl(ct); } else /* add form needs clade for assembly menu */ gotClade = hGotClade(); /* main form */ printf("

\n", hgCustomName(), cartUsualString(cart, "formMethod", "POST")); cartSaveSession(cart); if (!isUpdateForm) { /* Print clade, genome and assembly */ /* NOTE: this uses an additional, hidden form (orgForm), below */ char *onChangeDb = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\""; char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\""; char *onChangeClade = "onchange=\"document.orgForm.clade.value = document.mainForm.clade.options[document.mainForm.clade.selectedIndex].value; document.orgForm.org.value = 0; document.orgForm.db.value = 0; document.orgForm.submit();\""; if (hIsGsidServer()) { printf("The Custom Track function and its documentation is currently under development ...

\n"); } puts("\n"); if (gotClade) { puts("
clade\n"); printCladeListHtml(hOrganism(database), onChangeClade); puts("   "); puts("genome\n"); printGenomeListForCladeHtml(database, onChangeOrg); } else { puts("
genome\n"); printGenomeListHtml(database, onChangeOrg); } puts("   "); puts("assembly\n"); printAssemblyListHtml(database, onChangeDb); if (! stringIn(database, hFreezeFromDb(database))) { puts("   "); printf("[%s]", database); } puts("
\n"); } /* intro text */ puts("

"); if (isUpdateForm) puts("Update your custom track configuration, data, and/or documentation."); else puts("Display your own data as custom annotation tracks in the browser."); addIntro(); puts("

"); /* row for error message */ if (err) printf("

    Error %s

", err); cgiSimpleTableStart(); /* first rows for update form are for track and browser line entry */ if (isUpdateForm) { /* row for instructions */ cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); if (dataUrl) puts("Configuration:"); else { puts("Edit configuration:"); } cgiTableFieldEnd(); cgiTableField(" "); puts(""); cgiMakeSubmitButton(); cgiTableFieldEnd(); cgiTableField(" "); cgiTableRowEnd(); /* row for text entry box */ cgiSimpleTableRowStart(); puts(""); if (dataUrl) { /* can't update via pasting if loaded from URL */ cgiMakeTextAreaDisableable(hgCtConfigLines, cartUsualString(cart, hgCtConfigLines, customTrackUserConfig(ct)), CONFIG_ENTRY_ROWS, TEXT_ENTRY_COLS, TRUE); } else { cgiMakeTextArea(hgCtConfigLines, cartUsualString(cart, hgCtConfigLines, customTrackUserConfig(ct)), CONFIG_ENTRY_ROWS, TEXT_ENTRY_COLS); } cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); cgiTableFieldEnd(); cgiTableRowEnd(); } /* next row - label entry for file upload */ cgiSimpleTableRowStart(); if (isUpdateForm) { /* update existing */ /* extra space */ cgiSimpleTableRowStart(); puts(""); cgiTableRowEnd(); if (dataUrl) cgiTableField("Data:"); else cgiTableField("Paste in replacement data:"); } else cgiTableField("Paste URLs or data:"); if (isUpdateForm && dataUrl) cgiTableField(" "); else { puts(""); puts("Or upload: "); cgiMakeFileEntry(hgCtDataFile); cgiTableFieldEnd(); } if (!isUpdateForm) { cgiSimpleTableFieldStart(); cgiMakeSubmitButton(); cgiTableFieldEnd(); } cgiTableRowEnd(); /* next row - text entry box for data, and clear button */ cgiSimpleTableRowStart(); puts(""); if (dataUrl) { /* can't update via pasting if loaded from URL */ safef(buf, sizeof buf, "Replace data at URL: %s", ctDataUrl(ct)); cgiMakeTextAreaDisableable(hgCtDataText, buf, TEXT_ENTRY_ROWS, TEXT_ENTRY_COLS, TRUE); } else { int rows = (isUpdateForm ? TEXT_ENTRY_ROWS - CONFIG_ENTRY_ROWS : TEXT_ENTRY_ROWS); cgiMakeTextArea(hgCtDataText, cartUsualString(cart, hgCtDataText, ""), rows, TEXT_ENTRY_COLS); } cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); if (!(isUpdateForm && dataUrl)) makeClearButton(hgCtDataText); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); cgiTableFieldEnd(); cgiTableRowEnd(); /* extra space */ cgiSimpleTableRowStart(); -puts(""); +cgiDown(0.7); cgiTableRowEnd(); /* next row - label for description text entry */ cgiSimpleTableRowStart(); cgiTableField("Optional track documentation: "); if (isUpdateForm && ctHtmlUrl(ct)) cgiTableField(" "); else { puts(""); puts("Or upload: "); cgiMakeFileEntry(hgCtDocFile); cgiTableFieldEnd(); } cgiTableRowEnd(); /* next row - text entry for description, and clear button(s) */ cgiSimpleTableRowStart(); puts(""); if (ct && ctHtmlUrl(ct)) { safef(buf, sizeof buf, "Replace doc at URL: %s", dataUrl); cgiMakeTextAreaDisableable(hgCtDocText, buf, TEXT_ENTRY_ROWS, TEXT_ENTRY_COLS, TRUE); } else { cgiMakeTextArea(hgCtDocText, cartUsualString(cart, hgCtDocText, ""), TEXT_ENTRY_ROWS, TEXT_ENTRY_COLS); cgiSimpleTableFieldStart(); cgiSimpleTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); makeClearButton(hgCtDocText); cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); cgiTableFieldEnd(); } cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); /* help text at bottom of screen - link for HTML description template */ puts("Click here for an HTML document template that may be used for Genome Browser track descriptions."); if (isUpdateForm) { /* hidden variables to identify track */ cgiMakeHiddenVar(hgCtUpdatedTable, ct->tdb->track); char buf[512]; char *shortLabel = htmlEncode(ct->tdb->shortLabel); char *longLabel = htmlEncode(ct->tdb->longLabel); safef(buf, sizeof buf, "track name='%s' description='%s'", shortLabel, longLabel); char *trackLine = htmlEncode(ctOrigTrackLine(ct)); cgiMakeHiddenVar(hgCtUpdatedTrack, trackLine ? trackLine : buf); freeMem(trackLine); freeMem(shortLabel); freeMem(longLabel); } else { /* hidden form to handle clade/genome/assembly dropdown. * This is at end of page for layout reasons (preserve vertical space) */ puts("

"); printf("
", hgCustomName()); cartSaveSession(cart); if (gotClade) printf("\n"); printf("\n", organism); printf("\n", database); printf("\n"); } puts("
"); -puts("
"); +cgiDown(0.9); } void tableHeaderFieldStart(int columns) { /* print table column header with white text on black background */ printf("", columns); } void tableHeaderField(char *label, char *description) { /* print table column header with white text on black background */ puts("%s ", wrapWhiteFont(label)); } void showCustomTrackList(struct customTrack *ctList, int numCts) /* print table of custom tracks with controls */ { struct customTrack *ct; char buf[256]; char *pos = NULL; char *dataUrl; /* handle 'set all' and 'clr all' */ boolean setAllDelete = FALSE; boolean setAllUpdate = FALSE; if (cartVarExists(cart, hgCtDoDeleteSet)) setAllDelete = TRUE; if (cartVarExists(cart, hgCtDoRefreshSet)) setAllUpdate = TRUE; /* determine which columns to display (avoid empty columns) */ int updateCt = 0, itemCt = 0, posCt = 0, errCt = 0; for (ct = ctList; ct != NULL; ct = ct->next) { if (ctDataUrl(ct)) updateCt++; if (ctItemCount(ct) > 0) itemCt++; if (ctInitialPosition(ct) || ctFirstItemPos(ct)) posCt++; if (ct->networkErrMsg) errCt++; } hTableStart(); cgiSimpleTableRowStart(); tableHeaderField("Name", "Short track identifier"); tableHeaderField("Description", "Long track identifier"); tableHeaderField("Type", "Data format of track"); tableHeaderField("Doc", "HTML track description"); if (itemCt) tableHeaderField("Items", "Count of discrete items in track"); if (posCt) tableHeaderField("Pos"," Go to genome browser at default track position or first item"); if (errCt) tableHeaderField("Error"," Error in custom track"); boolean showAllButtons = FALSE; if (numCts > 3) showAllButtons = TRUE; tableHeaderFieldStart(showAllButtons ? 2 : 1); cgiMakeButtonWithMsg(hgCtDoDelete, "delete", "Remove custom track"); cgiTableFieldEnd(); /* add column with Update button if any custom tracks are updateable */ if (updateCt) { tableHeaderFieldStart(showAllButtons ? 2 : 1); cgiMakeButtonWithMsg(hgCtDoRefresh, "update", "Refresh from data URL"); cgiTableFieldEnd(); } cgiTableRowEnd(); for (ct = ctList; ct != NULL; ct = ct->next) { /* Name field */ char *shortLabel = htmlEncode(ct->tdb->shortLabel); if ((ctDataUrl(ct) && ctHtmlUrl(ct)) || sameString(ct->tdb->type, "chromGraph")) printf("%s", shortLabel); else { char *cgiName = cgiEncode(ct->tdb->track); printf("%s", shortLabel, hgCustomName(),cartSidUrlString(cart), hgCtTable, cgiName, shortLabel); freeMem(cgiName); } freeMem(shortLabel); /* Description field */ char *longLabel = htmlEncode(ct->tdb->longLabel); printf("%s", longLabel); freeMem(longLabel); /* Type field */ printf("%s", ctInputType(ct)); /* Doc field */ printf("%s", isNotEmpty(ct->tdb->html) ? "Y" : " "); /* Items field */ if (itemCt) { int count = ctItemCount(ct); if (count > 0) printf("%d", count); else puts(" "); } /* Pos field; indicates initial position for the track, * or first element */ if (posCt) { pos = ctInitialPosition(ct); if (!pos) pos = ctFirstItemPos(ct); if (pos) { char *chrom = cloneString(pos); chopSuffixAt(chrom, ':'); if (hgOfficialChromName(database, chrom)) printf("%s:", hgTracksName(), cartSidUrlString(cart),pos, pos, chrom); else puts(" "); } else puts(" "); } if (errCt) { if (ct->networkErrMsg) { printf("\nShow\n", javaScriptLiteralEncode(ct->networkErrMsg)); } else puts(" "); } /* Delete checkboxes */ printf("", showAllButtons ? 2 : 1); safef(buf, sizeof(buf), "%s_%s", hgCtDeletePrefix, ct->tdb->track); cgiMakeCheckBox(buf, setAllDelete); puts(""); /* Update checkboxes */ if (updateCt) { printf("", showAllButtons ? 2 : 1); safef(buf, sizeof(buf), "%s_%s", hgCtRefreshPrefix, ct->tdb->track); if ((dataUrl = ctDataUrl(ct)) != NULL) cgiMakeCheckBoxWithMsg(buf, setAllUpdate, dataUrl); else puts(" "); puts(""); } puts("\n"); } if (showAllButtons) { cgiSimpleTableRowStart(); puts("check all / clear all "); cgiSimpleTableFieldStart(); cgiMakeButtonWithMsg(hgCtDoDeleteSet, "+", "Select all for deletion"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeButtonWithMsg(hgCtDoDeleteClr, "-", "Clear all for deletion"); cgiTableFieldEnd(); if (updateCt) { cgiSimpleTableFieldStart(); cgiMakeButtonWithMsg(hgCtDoRefreshSet, "+", "Select all for update"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeButtonWithMsg(hgCtDoRefreshClr, "-", "Clear all for update"); cgiTableFieldEnd(); } cgiTableRowEnd(); } hTableEnd(); } struct dbDb *getCustomTrackDatabases() /* Get list of databases having custom tracks for this user. * Dispose of this with dbDbFreeList. */ { struct dbDb *dbList = NULL, *dbDb; char *db; /* Get list of assemblies with custom tracks */ struct hashEl *hels = cartFindPrefix(cart, CT_FILE_VAR_PREFIX); struct hashEl *hel = NULL; for (hel = hels; hel != NULL; hel = hel->next) { /* TODO: chop actual prefix */ db = chopPrefixAt(cloneString(hel->name), '_'); /* TODO: check if file exists, if not remove ctfile_ var */ dbDb = hDbDb(db); if (dbDb) slAddTail(&dbList, dbDb); } return dbList; } static void manageCustomForm(char *warn) /* list custom tracks and display checkboxes so user can select for delete */ { struct dbDb *dbList = getCustomTrackDatabases(); struct dbDb *dbDb = NULL; /* add this database to the list, as it may have no custom * tracks, but we still want to see it in the menu */ slAddTail(&dbList, hDbDb(database)); slReverse(&dbList); /* remove duplicate entry for this database, if any */ for (dbDb = dbList->next; dbDb != NULL; dbDb = dbDb->next) if (sameString(dbDb->name, database)) slRemoveEl(&dbList, dbDb); boolean assemblyMenu = FALSE; if (slCount(dbList) > 1) assemblyMenu = TRUE; if (assemblyMenu) { /* hidden form to handle genome/assembly dropdown */ printf("
", hgCustomName()); cartSaveSession(cart); printf("\n", organism); printf("\n", database); puts("
"); } /* the main form contains a table of all tracks, with checkboxes to delete */ printf("
\n", hgCustomName(), cartUsualString(cart, "formMethod", "POST")); cartSaveSession(cart); if (assemblyMenu) { /* Print clade, genome and assembly */ char *onChangeDb = "onchange=\"document.orgForm.db.value = document.mainForm.db.options[document.mainForm.db.selectedIndex].value; document.orgForm.submit();\""; char *onChangeOrg = "onchange=\"document.orgForm.org.value = document.mainForm.org.options[document.mainForm.org.selectedIndex].value; document.orgForm.db.value = 0; document.orgForm.submit();\""; puts("\n"); puts("
genome\n"); printSomeGenomeListHtml(database, dbList, onChangeOrg); puts("   "); puts("assembly\n"); printSomeAssemblyListHtml(database, dbList, onChangeDb); puts("   "); printf("[%s]", database); puts("

\n"); } else printf("genome: %s    assembly: %s    [%s]\n", organism, hFreezeDate(database), database); if (measureTiming && (loadTime > 0)) printf("\n
load time: %ld ms
\n", loadTime); /* place for warning messages to appear */ if (isNotEmpty(warn)) { char *encoded = htmlEncode(warn); printf("

    %s", encoded); freeMem(encoded); } /* count up number of custom tracks for this genome */ int numCts = slCount(ctList); cgiSimpleTableStart(); cgiSimpleTableRowStart(); if (numCts) { puts(""); showCustomTrackList(ctList, numCts); } else puts("No custom tracks for this genome:  "); puts(""); /* navigation buttons */ puts(""); puts(""); /* button to add custom tracks */ int buttonWidth = 13; puts(""); puts(""); /* determine if there's a navigation position for this screen */ char *pos = NULL; if (ctList) { pos = ctInitialPosition(ctList); if (!pos) pos = ctFirstItemPos(ctList); } /* button for GB navigation */ puts(""); /* button for TB navigation */ puts(""); puts("
"); printf("", hgCtDoAdd, "add custom tracks", buttonWidth); puts("
"); printf("
\n", hgTracksName()); cartSaveSession(cart); printf("", "go to genome browser", buttonWidth); if (pos) cgiMakeHiddenVar("position", pos); puts("
"); puts("
"); printf("
\n", hgTablesName()); cartSaveSession(cart); printf("", "go to table browser", buttonWidth); puts("
"); puts("
"); puts(""); cgiTableRowEnd(); cgiTableEnd(); cartSetString(cart, "hgta_group", "user"); } void helpCustom() /* display documentation */ { webNewSection("Loading Custom Tracks"); char *browserVersion; if (btIE == cgiClientBrowser(&browserVersion, NULL, NULL) && *browserVersion < '8') puts(""); else puts(""); webIncludeHelpFile("customTrackLoad", FALSE); puts(""); } void doBrowserLines(struct slName *browserLines, char **retErr) /* parse variables from browser lines into the cart */ { char *err = NULL; struct slName *bl; for (bl = browserLines; bl != NULL; bl = bl->next) { char *words[96]; int wordCount; wordCount = chopLine(bl->name, words); if (wordCount > 1) { char *command = words[1]; if (sameString(command, "hide") || sameString(command, "dense") || sameString(command, "pack") || sameString(command, "squish") || sameString(command, "full")) { if (wordCount > 2) { int i; for (i=2; i hChromSize(database, chrom)) { err ="Invalid browser position (use chrN:123-456 format)"; break; } cartSetString(cart, "position", words[2]); } } } if (retErr) *retErr = err; } void doAddCustom(char *err) /* display form for adding custom tracks. * Include error message, if any */ { cartWebStart(cart, database, "Add Custom Tracks"); addCustomForm(NULL, err); helpCustom(); cartWebEnd(cart); } void doUpdateCustom(struct customTrack *ct, char *err) /* display form for adding custom tracks. * Include error message, if any */ { char *longLabel = htmlEncode(ct->tdb->longLabel); cartWebStart(cart, database, "Update Custom Track: %s [%s]", longLabel, database); freeMem(longLabel); cartSetString(cart, hgCtDocText, ct->tdb->html); addCustomForm(ct, err); helpCustom(); cartWebEnd(cart); } static void doManageCustom(char *warn) /* display form for deleting & updating custom tracks. * Include warning message, if any */ { cartWebStart(cart, database, "Manage Custom Tracks"); manageCustomForm(warn); webNewSection("Managing Custom Tracks"); webIncludeHelpFile("customTrackManage", FALSE); cartWebEnd(cart); } char *fixNewData(struct cart *cart) /* append a newline to incoming data, to keep custom preprocessor happy */ { char *customText = cartUsualString(cart, hgCtDataText, ""); if (isNotEmpty(customText)) { struct dyString *ds = dyStringNew(0); dyStringPrintf(ds, "%s\n", customText); customText = dyStringCannibalize(&ds); cartSetString(cart, hgCtDataText, customText); } return customText; } char *replacedTracksMsg(struct customTrack *replacedCts) /* make warning message listing replaced tracks */ { struct customTrack *ct; if (!slCount(replacedCts)) return NULL; struct dyString *dsWarn = dyStringNew(0); dyStringAppend(dsWarn, "Replaced: "); for (ct = replacedCts; ct != NULL; ct = ct->next) { if (ct != replacedCts) /* not the first */ dyStringAppend(dsWarn, ", "); dyStringAppend(dsWarn, ct->tdb->shortLabel); } return dyStringCannibalize(&dsWarn); } void doDeleteCustom() /* remove custom tracks from list based on cart variables */ { struct customTrack *ct; for (ct = ctList; ct != NULL; ct = ct->next) { char var[256]; safef(var, sizeof var, "%s_%s", hgCtDeletePrefix, ct->tdb->track); if (cartBoolean(cart, var)) slRemoveEl(&ctList, ct); } } void doRefreshCustom(char **warn) /* reparse custom tracks from URLs based on cart variables */ { struct customTrack *ct; struct customTrack *replacedCts = NULL; struct customTrack *refreshCts = NULL; for (ct = ctList; ct != NULL; ct = ct->next) { char var[256]; safef(var, sizeof var, "%s_%s", hgCtRefreshPrefix, ct->tdb->track); if (cartUsualBoolean(cart, var, FALSE)) { struct customTrack *nextCt = NULL, *urlCt = NULL; struct customTrack *urlCts = customFactoryParse(database, ctDataUrl(ct), FALSE, NULL); for (urlCt = urlCts; urlCt != NULL; urlCt = nextCt) { nextCt = urlCt->next; if (sameString(ct->tdb->track, urlCt->tdb->track)) slAddHead(&refreshCts, urlCt); } } } ctList = customTrackAddToList(ctList, refreshCts, &replacedCts, FALSE); if (warn) *warn = replacedTracksMsg(replacedCts); customTrackHandleLift(database, ctList); } void addWarning(struct dyString *ds, char *msg) /* build up a warning message from parts */ { if (!msg) return; if (isNotEmpty(ds->string)) dyStringAppend(ds, ". "); dyStringAppend(ds, msg); } char *saveLines(char *text, int max) /* save lines from input, up to 'max'. * Prepend with comment, if truncated */ { if (!text) return NULL; char buf[128]; int count = 0; char *line; boolean truncated = FALSE; struct dyString *ds = dyStringNew(0); safef(buf, sizeof buf, "# Displaying first %d lines of data", max); struct lineFile *lf = lineFileOnString("saved custom text", TRUE, text); while (lineFileNext(lf, &line, NULL)) { if (startsWith(buf, line)) continue; if (++count > max) { truncated = TRUE; break; } dyStringAppend(ds, line); dyStringAppend(ds, "\n"); } if (truncated) { struct dyString *dsNew = dyStringNew(0); dyStringPrintf(dsNew, "%s\n%s", buf, dyStringCannibalize(&ds)); return dyStringCannibalize(&dsNew); } return (dyStringCannibalize(&ds)); } struct customTrack *ctFromList(struct customTrack *ctList, char *track) /* return custom track from list */ { struct customTrack *ct = NULL; for (ct = ctList; ct != NULL; ct = ct->next) if (sameString(track, ct->tdb->track)) return ct; return NULL; } boolean customTrackHasConfig(char *text) /* determine if there are track or browser lines in text */ { text = skipLeadingSpaces(text); return startsWith("track ", text) || startsWith("browser ", text); } void doMiddle(struct cart *theCart) /* create web page */ { char *ctFileName = NULL; struct slName *browserLines = NULL; struct customTrack *replacedCts = NULL; char *err = NULL, *warn = NULL; char *selectedTable = NULL; struct customTrack *ct = NULL; boolean ctUpdated = FALSE; char *initialDb = NULL; long thisTime = clock1000(); cart = theCart; measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming")); initialDb = cloneString(cartString(cart, "db")); getDbAndGenome(cart, &database, &organism, oldVars); setUdcCacheDir(); customFactoryEnableExtraChecking(TRUE); #if (defined USE_BAM && defined KNETFILE_HOOKS) knetUdcInstall(); if (udcCacheTimeout() < 300) udcSetCacheTimeout(300); #endif//def USE_BAM && KNETFILE_HOOKS if (sameString(initialDb, "0")) { /* when an organism is selected from the custom track management page, * set the database to be the default only if it has custom tracks. * Otherwise, pick an assembly for that organism that does have custom tracks. */ struct dbDb *dbDb, *dbDbs = getCustomTrackDatabases(); char *dbWithCts = NULL; for (dbDb = dbDbs; dbDb != NULL; dbDb = dbDb->next) { if (sameString(database, dbDb->name)) break; if (sameString(organism, dbDb->organism)) { if (!dbWithCts) dbWithCts = cloneString(dbDb->name); } } if (dbWithCts) /* set the database for the selected organism to an assembly that * has custom tracks */ { database = dbWithCts; cartSetString(cart, "db", database); } } if (cartVarExists(cart, hgCtDoAdd)) doAddCustom(NULL); else if (cartVarExists(cart, hgCtTable)) { /* update track */ /* need to clone the hgCtTable value, as the ParseCart will remove the variable */ selectedTable = cloneString(cartString(cart, hgCtTable)); if (isNotEmpty(selectedTable)) { ctList = customTracksParseCart(database, cart, NULL, NULL); ct = ctFromList(ctList, selectedTable); } if (ct) doUpdateCustom(ct, NULL); else doAddCustom(NULL); } else { /* get new and existing custom tracks from cart and decide what to do */ char *customText = fixNewData(cart); /* save input so we can display if there's an error */ char *savedCustomText = saveLines(cloneString(customText), SAVED_LINE_COUNT); char *trackConfig = cartOptionalString(cart, hgCtConfigLines); char *savedConfig = cloneString(trackConfig); struct dyString *dsWarn = dyStringNew(0); char *fileName = cartOptionalString(cart, hgCtDataFileName); boolean hasData = (isNotEmpty(customText) || isNotEmpty(fileName)); if (cartVarExists(cart, hgCtUpdatedTrack) && hasData) { /* from 'update' screen */ /* prepend config to data for parser */ struct dyString *dsTrack = dyStringNew(0); if (!trackConfig) trackConfig = cartOptionalString(cart, hgCtUpdatedTrack); char *fileContents = NULL; if (isNotEmpty(fileName)) { if (customTrackIsCompressed(fileName)) fileContents = "Compressed files not supported for data update"; else fileContents = cartOptionalString(cart, hgCtDataFile); customText = fileContents; } /* check for duplicate track config in config and data entry */ if (customTrackHasConfig(trackConfig) && customTrackHasConfig(customText)) { if (startsWith(trackConfig, customText)) trackConfig = ""; else customText = "Duplicate track configuration found - remove track and browser lines from Configuration box or from Data"; } dyStringPrintf(dsTrack, "%s\n%s\n", trackConfig, customText); customText = dyStringCannibalize(&dsTrack); cartSetString(cart, hgCtDataText, customText); if (isNotEmpty(fileContents)) { /* already handled file */ cartRemove(cart, hgCtDataFile); cartRemove(cart, hgCtDataFileName); } } boolean ctParseError = FALSE; struct errCatch *catch = errCatchNew(); if (errCatchStart(catch)) ctList = customTracksParseCartDetailed(database, cart, &browserLines, &ctFileName, &replacedCts, NULL, &err); errCatchEnd(catch); if (catch->gotError) { addWarning(dsWarn, err); addWarning(dsWarn, catch->message->string); ctParseError = TRUE; } errCatchFree(&catch); /* exclude special setting used by table browser to indicate * db assembly for error-handling purposes only */ char *db = NULL; if (trackConfig && (db = stringIn("db=", trackConfig)) != NULL) { db += 3; char *nextTok = skipToSpaces(db); if (!nextTok) nextTok = strchr(db, 0); db = cloneStringZ(db,nextTok-db); if (!sameString(db,database)) err = "Invalid configuration found - remove db= or return it to it's original value"; } if (cartVarExists(cart, hgCtUpdatedTrack) && !hasData) { /* update custom track config and doc, but not data*/ selectedTable = cartOptionalString(cart, hgCtUpdatedTable); if (selectedTable) { ct = ctFromList(ctList, selectedTable); if (ct) { struct errCatch *catch = errCatchNew(); if (errCatchStart(catch)) { customTrackUpdateFromConfig(ct, database, trackConfig, &browserLines); ctUpdated = TRUE; } errCatchEnd(catch); if (catch->gotError) addWarning(dsWarn, catch->message->string); errCatchFree(&catch); } } } addWarning(dsWarn, replacedTracksMsg(replacedCts)); doBrowserLines(browserLines, &warn); addWarning(dsWarn, warn); if (err) { char *selectedTable = NULL; cartSetString(cart, hgCtDataText, savedCustomText); cartSetString(cart, hgCtConfigLines, savedConfig); if ((selectedTable= cartOptionalString(cart, hgCtUpdatedTable)) != NULL) { ct = ctFromList(ctList, selectedTable); doUpdateCustom(ct, err); } else doAddCustom(err); cartRemovePrefix(cart, hgCt); return; } if (cartVarExists(cart, hgCtDoDelete)) { doDeleteCustom(); ctUpdated = TRUE; } if (cartVarExists(cart, hgCtDoRefresh)) { doRefreshCustom(&warn); addWarning(dsWarn, warn); ctUpdated = TRUE; } if (ctUpdated || ctConfigUpdate(ctFileName)) { customTracksSaveCart(database, cart, ctList); /* refresh ctList again to pickup remote resource error state */ struct errCatch *catch = errCatchNew(); if (errCatchStart(catch)) ctList = customTracksParseCartDetailed(database, cart, &browserLines, &ctFileName, &replacedCts, NULL, &err); errCatchEnd(catch); if (catch->gotError) { addWarning(dsWarn, err); addWarning(dsWarn, catch->message->string); ctParseError = TRUE; } errCatchFree(&catch); } warn = dyStringCannibalize(&dsWarn); if (measureTiming) { long lastTime = clock1000(); loadTime = lastTime - thisTime; } if (!initialDb || ctList || cartVarExists(cart, hgCtDoDelete)) doManageCustom(warn); else if (ctParseError) doAddCustom(warn); else doAddCustom(NULL); } cartRemovePrefix(cart, hgCt); cartRemove(cart, CT_CUSTOM_TEXT_VAR); } int main(int argc, char *argv[]) /* Process command line. */ { htmlPushEarlyHandlers(); oldVars = hashNew(10); cgiSpoof(&argc, argv); cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }