3a3e7f9931622d8837bf08c3de5dfb328c384203 tdreszer Fri Jun 22 15:59:56 2012 -0700 Third batch of many checkins as dictated by Jim's OCD. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way. Only affect is to my sanity and Jim's. diff --git src/hg/hgCustom/hgCustom.c src/hg/hgCustom/hgCustom.c index 03f56d2..e67120c 100644 --- src/hg/hgCustom/hgCustom.c +++ src/hg/hgCustom/hgCustom.c @@ -1,1338 +1,1338 @@ /* 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 #include "jsHelper.h" #include <signal.h> static long loadTime = 0; void usage() /* Explain usage and exit. */ { errAbort( "hgCustom - Custom track management CGI\n" "usage:\n" " hgCustom <CGI settings>\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" #ifdef PROGRESS_METER #define hgCtDoProgress hgCtDo "progress" #endif /* 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" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1'>BED</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bigBed.html'>bigBed</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bedgraph.html'>bedGraph</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format3'>GFF</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format4'>GTF</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/wiggle.html'>WIG</A>\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bigWig.html'>bigWig</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1.7'>BED detail</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format10'>Personal Genome SNP</A>,\n" " or <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format2'>PSL</A>\n" " formats. To configure the display, set\n" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#TRACK'>track</A>\n" " and" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#BROWSER'>browser</A>\n" " line attributes as described in the \n" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html'>User's Guide</A>.\n" " URLs for data in the bigBed, bigWig, BAM and VCF formats must be embedded in a track\n" " line in the box below.\n" ); } else { puts(" Data must be formatted in\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1'>BED</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bigBed.html'>bigBed</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bedgraph.html'>bedGraph</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format3'>GFF</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format4'>GTF</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/wiggle.html'>WIG</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bigWig.html'>bigWig</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format5'>MAF</A>,\n" " <A TARGET=_BLANK HREF='../goldenPath/help/bam.html'>BAM</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format1.7'>BED detail</A>,\n" " <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format10'>Personal Genome SNP,</A>\n" " <A TARGET=_BLANK HREF='../goldenPath/help/vcf.html'>VCF</A>,\n" " or <A TARGET=_BLANK HREF='../FAQ/FAQformat.html#format2'>PSL</A>\n" " formats. To configure the display, set\n" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#TRACK'>track</A>\n" " and" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#BROWSER'>browser</A>\n" " line attributes as described in the \n" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html'>User's Guide</A>.\n" " URLs for data in the bigBed, bigWig, BAM and VCF formats must be embedded in a track\n" " line in the box below.\n" " Publicly available custom tracks are listed\n" " <A HREF='../goldenPath/customTracks/custTracks.html'>here</A>.\n" " Examples are\n" " <A TARGET=_BLANK HREF='../goldenPath/help/customTrack.html#EXAMPLE1'>here</A>.\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(); jsIncludeFile("jquery.js", NULL); jsIncludeFile("hgCustom.js", NULL); jsIncludeFile("utils.js", NULL); jsIncludeFile("ajax.js", NULL); /* main form */ printf("<FORM ACTION=\"%s\" METHOD=\"%s\" " " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\" onsubmit=\"$('input[name=Submit]').attr('disabled', 'disabled');\" >\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("<span style='color:red;'>The Custom Track function and its documentation is currently under development ...</span><BR><BR>\n"); + printf("<span style='color:red;'>The Custom Track function and its documentation is " + "currently under development ...</span><BR><BR>\n"); } puts("<TABLE BORDER=0>\n"); if (gotClade) { puts("<TR><TD>clade\n"); printCladeListHtml(hOrganism(database), onChangeClade); puts(" "); puts("genome\n"); printGenomeListForCladeHtml(database, onChangeOrg); } else { puts("<TR><TD>genome\n"); printGenomeListHtml(database, onChangeOrg); } puts(" "); puts("assembly\n"); printAssemblyListHtml(database, onChangeDb); if (! stringIn(database, hFreezeFromDb(database))) { puts(" "); printf("[%s]", database); } puts("</TD></TR></TABLE>\n"); } /* intro text */ puts("<P>"); 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("<P>"); /* row for error message */ if (err) - printf("<P><B> <span style='color:RED; font-style:italic;'>Error</span> %s</B><P>", err); + printf("<P><B> <span style='color:RED; font-style:italic;'>" + "Error</span> %s</B><P>", 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("<TD ALIGN='RIGHT'>"); cgiMakeButtonWithOnClick("Submit", "Submit", NULL, "return submitClick(this);"); printf("<img id='loadingImg' src='../images/loading.gif' />\n"); cgiTableFieldEnd(); cgiTableField(" "); cgiTableRowEnd(); /* row for text entry box */ cgiSimpleTableRowStart(); puts("<TD COLSPAN=2>"); 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("<TD STYLE='padding-top:9';\"></TD>"); cgiTableRowEnd(); if (dataUrl) cgiTableField("Data:"); else cgiTableField("Paste in replacement data:"); } else cgiTableField("Paste URLs or data:"); if (isUpdateForm && dataUrl) cgiTableField(" "); else { puts("<TD ALIGN='RIGHT'>"); puts("Or upload: "); cgiMakeFileEntry(hgCtDataFile); cgiTableFieldEnd(); } if (!isUpdateForm) { cgiSimpleTableFieldStart(); cgiMakeButtonWithOnClick("Submit", "Submit", NULL, "return submitClick(this);"); printf("<img id='loadingImg' src='../images/loading.gif' />\n"); cgiTableFieldEnd(); } cgiTableRowEnd(); /* next row - text entry box for data, and clear button */ cgiSimpleTableRowStart(); puts("<TD COLSPAN=2>"); 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)) { printf("<span id='loadingMsg'></span>\n"); makeClearButton(hgCtDataText); } cgiTableFieldEnd(); cgiTableRowEnd(); cgiTableEnd(); cgiTableFieldEnd(); cgiTableRowEnd(); /* extra space */ cgiSimpleTableRowStart(); cgiDown(0.7); cgiTableRowEnd(); /* next row - label for description text entry */ cgiSimpleTableRowStart(); cgiTableField("Optional track documentation: "); if (isUpdateForm && ctHtmlUrl(ct)) cgiTableField(" "); else { puts("<TD ALIGN='RIGHT'>"); puts("Or upload: "); cgiMakeFileEntry(hgCtDocFile); cgiTableFieldEnd(); } cgiTableRowEnd(); /* next row - text entry for description, and clear button(s) */ cgiSimpleTableRowStart(); puts("<TD COLSPAN=2>"); 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 <A HREF=\"../goldenPath/help/ct_description.txt\" TARGET=_blank>here</A> 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("</FORM>"); printf("<FORM STYLE=\"margin-bottom:0;\" ACTION=\"%s\" METHOD=\"GET\" NAME=\"orgForm\">", hgCustomName()); cartSaveSession(cart); if (gotClade) printf("<INPUT TYPE=\"HIDDEN\" NAME=\"clade\" VALUE=\"\">\n"); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"org\" VALUE=\"%s\">\n", organism); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"db\" VALUE=\"%s\">\n", database); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"hgct_do_add\" VALUE=\"1\">\n"); } puts("</FORM>"); cgiDown(0.9); } void tableHeaderFieldStart(int columns) { /* print table column header with white text on black background */ printf("<TD COLSPAN=%d ALIGN='CENTER' BGCOLOR='#536ED3'>", columns); } void tableHeaderField(char *label, char *description) { /* print table column header with white text on black background */ puts("<TD ALIGN='CENTER' BGCOLOR='#536ED3' "); if (description) printf("TITLE='%s'", description); printf("><B>%s</B></TD> ", 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; int colSpan = 4; /* handle 'set all' and 'clr all' (won't be used if user has javascript enabled). */ 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"); colSpan++; } if (posCt) { tableHeaderField("Pos"," Go to genome browser at default track position or first item"); colSpan++; } if (errCt) { tableHeaderField("Error"," Error in custom track"); colSpan++; } 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("<TR><TD>%s</A></TD>", shortLabel); else { char *cgiName = cgiEncode(ct->tdb->track); printf("<TR><TD><A TITLE='Update custom track: %s' HREF='%s?%s&%s=%s'>%s</A></TD>", shortLabel, hgCustomName(),cartSidUrlString(cart), hgCtTable, cgiName, shortLabel); freeMem(cgiName); } freeMem(shortLabel); /* Description field */ char *longLabel = htmlEncode(ct->tdb->longLabel); printf("<TD>%s</TD>", longLabel); freeMem(longLabel); /* Type field */ printf("<TD>%s</TD>", ctInputType(ct)); /* Doc field */ printf("<TD ALIGN='CENTER'>%s</TD>", isNotEmpty(ct->tdb->html) ? "Y" : " "); /* Items field */ if (itemCt) { int count = ctItemCount(ct); if (count > 0) printf("<TD ALIGN='CENTER'>%d</TD>", count); else puts("<TD> </TD>"); } /* 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("<TD><A HREF='%s?%s&position=%s&hgTracksConfigPage=notSet' TITLE=%s>%s:</A></TD>", hgTracksName(), cartSidUrlString(cart),pos, pos, chrom); else puts("<TD> </TD>"); } else puts("<TD> </TD>"); } if (errCt) { if (ct->networkErrMsg) { printf("\n<TD><A href=\"javascript:void(0)\" onClick=\"alert('%s')\">Show</A></TD>\n", javaScriptLiteralEncode(ct->networkErrMsg)); } else puts("<TD> </TD>"); } /* Delete checkboxes */ printf("<TD COLSPAN=%d ALIGN=CENTER>", showAllButtons ? 2 : 1); safef(buf, sizeof(buf), "%s_%s", hgCtDeletePrefix, ct->tdb->track); cgiMakeCheckBoxJS(buf, setAllDelete, "class='deleteCheckbox'"); puts("</TD>"); /* Update checkboxes */ if (updateCt) { printf("<TD COLSPAN=%d ALIGN=CENTER>", showAllButtons ? 2 : 1); safef(buf, sizeof(buf), "%s_%s", hgCtRefreshPrefix, ct->tdb->track); if ((dataUrl = ctDataUrl(ct)) != NULL) { char js[1024]; safef(js, sizeof(js), "class='updateCheckbox' title='refresh data from: %s'", dataUrl); cgiMakeCheckBoxJS(buf, setAllUpdate, js); } else puts(" "); puts("</TD>"); } puts("</TR>\n"); } if (showAllButtons) { cgiSimpleTableRowStart(); printf("<TD COLSPAN=%d ALIGN='RIGHT'>check all / clear all </TD>", colSpan); cgiSimpleTableFieldStart(); cgiMakeButtonWithOnClick(hgCtDoDeleteSet, "+", "Select all for deletion", "$('.deleteCheckbox').attr('checked', true); return false;"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeButtonWithOnClick(hgCtDoDeleteClr, "-", "Clear all for deletion", "$('.deleteCheckbox').attr('checked', false); return false;"); cgiTableFieldEnd(); if (updateCt) { cgiSimpleTableFieldStart(); cgiMakeButtonWithOnClick(hgCtDoRefreshSet, "+", "Select all for update", "$('.updateCheckbox').attr('checked', true); return false;"); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); cgiMakeButtonWithOnClick(hgCtDoRefreshClr, "-", "Clear all for update", "$('.updateCheckbox').attr('checked', false); return false;"); 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("<FORM STYLE=\"margin-bottom:0;\" ACTION=\"%s\" METHOD=\"GET\" NAME=\"orgForm\">", hgCustomName()); cartSaveSession(cart); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"org\" VALUE=\"%s\">\n", organism); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"db\" VALUE=\"%s\">\n", database); puts("</FORM>"); } /* the main form contains a table of all tracks, with checkboxes to delete */ printf("<FORM ACTION=\"%s\" METHOD=\"%s\" NAME=\"mainForm\">\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("<TABLE BORDER=0>\n"); puts("<TR><TD>genome\n"); printSomeGenomeListHtml(database, dbList, onChangeOrg); puts(" "); puts("assembly\n"); printSomeAssemblyListHtml(database, dbList, onChangeDb); puts(" "); printf("[%s]", database); puts("</TD></TR></TABLE><P>\n"); } else printf("<B>genome:</B> %s <B>assembly:</B> %s [%s]\n", organism, hFreezeDate(database), database); if (measureTiming && (loadTime > 0)) printf("\n<BR>load time: %ld ms<BR>\n", loadTime); /* place for warning messages to appear */ if (isNotEmpty(warn)) { char *encoded = htmlEncode(warn); printf("<P><B> %s", encoded); freeMem(encoded); } /* count up number of custom tracks for this genome */ int numCts = slCount(ctList); cgiSimpleTableStart(); cgiSimpleTableRowStart(); if (numCts) { puts("<TD VALIGN=\"TOP\">"); showCustomTrackList(ctList, numCts); } else puts("<TD VALIGN=\"TOP\"><B><EM>No custom tracks for this genome:<B></EM> "); puts("</TD>"); /* navigation buttons */ puts("<TD VALIGN=\"TOP\">"); puts("<TABLE BORDER=0>"); /* button to add custom tracks */ int buttonWidth = 13; puts("<TR><TD>"); printf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" STYLE=\"width:%dem\">", hgCtDoAdd, "add custom tracks", buttonWidth); puts("</TD></TR>"); puts("</FORM>"); /* 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("<TR><TD>"); printf("<FORM STYLE=\"margin-bottom:0;\" ACTION=\"%s\" METHOD=\"GET\" NAME=\"tracksForm\">\n", hgTracksName()); cartSaveSession(cart); printf("<INPUT TYPE=SUBMIT NAME=\"Submit\" VALUE=\"%s\" STYLE=\"width:%dem\">", "go to genome browser", buttonWidth); if (pos) cgiMakeHiddenVar("position", pos); puts("</FORM>"); puts("</TD></TR>"); /* button for TB navigation */ puts("<TR><TD>"); printf("<FORM STYLE=\"margin-bottom:0;\" ACTION=\"%s\" METHOD=\"GET\" NAME=\"tablesForm\">\n", hgTablesName()); cartSaveSession(cart); printf("<INPUT TYPE=SUBMIT NAME=\"Submit\" VALUE=\"%s\" STYLE=\"width:%dem\">", "go to table browser", buttonWidth); puts("</FORM>"); puts("</TD></TR>"); puts("</TABLE>"); puts("</TD>"); 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("<span>"); else puts("<span style='position:relative; top:-1em;'>"); webIncludeHelpFile("customTrackLoad", FALSE); puts("</span>"); } 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<wordCount; ++i) { char *s = words[i]; if (sameWord(s, "all")) { cartSetString(cart, "hgt.visAllFromCt", command); } else { char buf[256]; safef(buf, sizeof buf, "hgtct.%s", s); cartSetString(cart, buf, command); } } } } else if (sameString(command, "position")) { char *chrom = NULL; int start = 0, end = 0; if (wordCount < 3) { err = "Expecting 3 words in browser position line"; break; } if (!hgParseChromRange(database, words[2], &chrom, &start, &end) || start < 0 || end > hChromSize(database, chrom)) { err ="Invalid browser position (use chrN:123-456 format)"; break; } cartSetString(cart, "position", words[2]); } } } if (retErr) *retErr = err; } #ifdef PROGRESS_METER static void progressMeter() { printf("<FORM STYLE=\"margin-bottom:0;\" ACTION=\"%s\" METHOD=\"GET\" NAME=\"orgForm\">", hgCustomName()); cartSaveSession(cart); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"org\" VALUE=\"%s\">\n", organism); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"db\" VALUE=\"%s\">\n", database); printf("<INPUT TYPE=\"HIDDEN\" NAME=\"hgct_do_add\" VALUE=\"1\">\n"); puts("</FORM>"); } static void doProgress(char *err) /* display progress meter to show loading process */ { cartWebStart(cart, database, "Custom Track loading progress meter"); progressMeter(); // addCustomForm(NULL, err); helpCustom(); cartWebEnd(cart); } #endif 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"); jsIncludeFile("jquery.js", NULL); 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); } int timerCounter; #define TIMER_INTERVAL 10 static void timer(int sig) { // Per HTML 4.01 spec (http://www.w3.org/TR/html401/struct/global.html#h-7.1): // // White space (spaces, newlines, tabs, and comments) may appear before or after each section [including the DOCTYPE]. // // So we print out comments periodically to keep this process from being killed by apache or the user's web browser. printf("<!-- processing (%d seconds) -->\n", timerCounter++ * TIMER_INTERVAL); fflush(stdout); alarm(TIMER_INTERVAL); } 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 USE_TABIX) && defined KNETFILE_HOOKS) knetUdcInstall(); if (udcCacheTimeout() < 300) udcSetCacheTimeout(300); #endif//def (USE_BAM || USE_TABIX) && 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 */ - { + 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); #ifdef PROGRESS_METER else if (cartVarExists(cart, hgCtDoProgress)) { doProgress(NULL); } #endif 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 */ // setup a timer to periodically print out something to stdout to make sure apache or the web browser doesn't time us out (see redmine #3002). // e.g. see http://stackoverflow.com/questions/5547166/how-to-avoid-cgi-timeout struct sigaction *act; AllocVar(act); act->sa_handler = timer; act->sa_flags = SA_RESTART; sigaction(SIGALRM, act, NULL); alarm(TIMER_INTERVAL); 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; }