8a648c2ffc0e2c8a671a9074e00a0a3d56575589 Merge parents e6d1189bea4 67f660dc951 max Wed Sep 2 04:48:57 2026 -0700 Merge remote-tracking branch 'origin/master' # Conflicts: # src/hg/hgSession/hgSession.c diff --cc src/hg/hgSession/hgSession.c index bf8e16e50a8,8d9a2f6f8a8..11a3538c8d8 --- src/hg/hgSession/hgSession.c +++ src/hg/hgSession/hgSession.c @@@ -1,2826 -1,2758 +1,2837 @@@ /* hgSession - Interface with wiki login and do session saving/loading. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* WARNING: testing this CGI on hgwbeta can lead to missed bugs. This is * because on hgwbeta, the login links go just to hgwbeta. But on genome-euro * and genome-asia, the login links go to genome.ucsc.edu and session links to * genome-euro/asia. For proper testing of session loading on hgSession and * hgLogin, configure your sandbox to use genome.ucsc.edu as a "remote login" * (wiki.host=genome.ucsc.edu). Make sure that links to load sessions go to * your sandbox, but login links go to genome.ucsc.edu. For QA, tell them to * use genome-preview to test this CGI. */ #include "common.h" #include "hash.h" #include "htmshell.h" #include "cheapcgi.h" #include "linefile.h" #include "net.h" #include "textOut.h" #include "hCommon.h" #include "hui.h" #include "cart.h" #include "jsHelper.h" #include "web.h" #include "hdb.h" #include "ra.h" #include "wikiLink.h" #include "customTrack.h" #include "customFactory.h" #include "udc.h" #include "hgSession.h" #include "hgConfig.h" #include "sessionThumbnail.h" #include "filePath.h" #include "obscure.h" #include "trashDir.h" #include "hubConnect.h" #include "trackHub.h" #include "errCatch.h" #include "sessionData.h" +#include "snapshotSession.h" #include "jsonParse.h" #include "jsonWrite.h" #include "perfTimer.h" char *database = NULL; struct perfTimer *hgSessionTiming = NULL; /* Non-NULL when &measureTiming is set; times the page * and is emitted as hgSessionData.timing for the JS. */ void usage() /* Explain usage and exit. */ { errAbort( "hgSession - Interface with wiki login and do session saving/loading.\n" "usage:\n" " hgSession <various CGI settings>\n" ); } /* Global variables. */ struct cart *cart; char *excludeVars[] = {"Submit", "submit", hgsSessionDataDbSuffix, NULL}; /* Javascript to confirm that the user truly wants to delete a session. */ #define confirmDeleteFormat "return confirm('Are you sure you want to delete ' + decodeURIComponent('%s') + '?');" /* Forward declarations for the experimental client-rendered Sessions page (hgSession.js), which is * an opt-in alternative gated by the sessionNewPage / sessionNewPageBanner hg.conf flags, mirroring * hgBlat's blatNewForm / blatNewFormBanner facelift. Defined below. */ static boolean sessionNewPageActive(); static void printSessionNewPageBanner(boolean onNewPage); void doMainPageNew(char *userName, char *message); char *cgiDecodeClone(char *encStr) /* Allocate and return a CGI-decoded copy of encStr. */ { size_t len = strlen(encStr); char *decStr = needMem(len+1); cgiDecode(encStr, decStr, len); return decStr; } void welcomeUser(char *wikiUserName) /* Tell the user they are not logged in to the wiki or other login * system and tell them how to do so. */ { char *wikiHost = wikiLinkHost(); cartWebStart(cart, NULL, "Welcome %s", wikiUserName); jsInit(); jsIncludeDataTablesLibs(); if (loginSystemEnabled()) /* Using the new hgLogin CGI for login */ { printf("<h4 style=\"margin: 0pt 0pt 7px;\">Your Account Information</h4>" "<ul style=\"list-style: none outside none; margin: 0pt; padding: 0pt;\">" "<li>Username: %s</li>",wikiUserName); if (loginUseBasicAuth()) printf("<li>The Genome Browser is configured to use HTTP Basic Authentication, so the password cannot be changed here.</li>"); else printf("<li><A HREF=\"%s\">Change password</A></li>", wikiLinkChangePasswordUrl(cartSessionId(cart))); char *changeEmailUrl = wikiLinkChangeEmailUrl(cartSessionId(cart)); if (changeEmailUrl != NULL) printf("<li><A HREF=\"%s\">Change email</A></li>", changeEmailUrl); printf("</ul>"); printf("<p><A id='logoutLink' HREF=\"%s\">Sign out</A></p>", wikiLinkUserLogoutUrl(cartSessionId(cart))); if (loginUseBasicAuth()) wikiFixLogoutLinkWithJs(); } else /* this part is not used anymore at UCSC since 2014 */ { printf("If you are not %s (on the wiki at " "<A HREF=\"http://%s/\" TARGET=_BLANK>%s</A>) " "and would like to sign out or change identity, \n", wikiUserName, wikiHost, wikiHost); printf("<A HREF=\"%s\"><B>click here to sign out.</B></A>\n", wikiLinkUserLogoutUrl(cartSessionId(cart))); } } void offerLogin() /* Tell the user they are not logged in to the system and tell them how to * do so. */ { char *wikiHost = wikiLinkHost(); cartWebStart(cart, NULL, "Sign in to UCSC Genome Bioinformatics"); jsInit(); if (loginSystemEnabled()) { printf("<ul style=\"list-style: none outside none; margin: 0pt; padding: 0pt;\">" "<li><A HREF=\"%s\">Login</A></li>", wikiLinkUserLoginUrl(cartSessionId(cart))); printf("<li><A HREF=\"%s\">" "Create an account</A></li></ul>", wikiLinkUserSignupUrl(cartSessionId(cart))); printf("<P>Signing in enables you to save current settings into a " "named session, and then restore settings from the session later. <BR>" "If you wish, you can share named sessions with other users.</P>"); } else // the following block is not used at UCSC anymore since 2014 { printf("Signing in enables you to save current settings into a " "named session, and then restore settings from the session later.\n" "If you wish, you can share named sessions with other users.\n"); printf("<P>The sign-in page is handled by our " "<A HREF=\"http://%s/\" TARGET=_BLANK>wiki system</A>:\n", wikiHost); printf("<A HREF=\"%s\"><B>click here to sign in.</B></A>\n", wikiLinkUserLoginUrl(cartSessionId(cart))); printf("The wiki also serves as a forum for users " "to share knowledge and ideas.\n"); } } void showCartLinks() /* Print out links to cartDump and cartReset. */ { char *session = cartSidUrlString(cart); char returnAddress[512]; safef(returnAddress, sizeof(returnAddress), "%s?%s", hgSessionName(), session); printf("<A HREF=\"../cgi-bin/cartReset?%s&destination=%s\">Click here to " "reset</A> the browser user interface settings to their defaults.\n", session, cgiEncodeFull(returnAddress)); } void addSessionLink(struct dyString *dy, char *userName, char *sessionName, boolean encode, boolean tryShortLink) /* Add to dy an URL that tells hgSession to load a saved session. * If encode, cgiEncodeFull the URL. * If tryShortLink, print a shortened link that apache can redirect. * The link is an absolute link that includes the server name so people can * copy-paste it into emails. * * NOTE: Do not append CGI variables here, as it will break short links if they are enabled. */ { struct dyString *dyTmp = dyStringNew(1024); if (tryShortLink && cfgOptionBooleanDefault("hgSession.shortLink", FALSE) && !stringIn("%2F", userName) && !stringIn("%2F", sessionName)) dyStringPrintf(dyTmp, "http%s://%s/s/%s/%s", cgiAppendSForHttps(), cgiServerNamePort(), userName, sessionName); else dyStringPrintf(dyTmp, "%shgTracks?hgS_doOtherUser=submit&" "hgS_otherUserName=%s&hgS_otherUserSessionName=%s", hLocalHostCgiBinUrl(), userName, sessionName); if (encode) { dyStringPrintf(dy, "%s", cgiEncodeFull(dyTmp->string)); } else { dyStringPrintf(dy, "%s", dyTmp->string); } dyStringFree(&dyTmp); } void printCopyToClipboardButton(struct dyString *dy, char *iconId, char *targetId, char *buttonLabel) /* print a copy-to-clipboard button with DOM id iconId that copies the node text of targetId */ { dyStringPrintf(dy, " <button title='Copy URL to clipboard' id='%s' data-target='%s'><svg style='width:0.9em' xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'><!--! Font Awesome Pro 6.1.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license (Commercial License) Copyright 2022 Fonticons, Inc. --><path d='M502.6 70.63l-61.25-61.25C435.4 3.371 427.2 0 418.7 0H255.1c-35.35 0-64 28.66-64 64l.0195 256C192 355.4 220.7 384 256 384h192c35.2 0 64-28.8 64-64V93.25C512 84.77 508.6 76.63 502.6 70.63zM464 320c0 8.836-7.164 16-16 16H255.1c-8.838 0-16-7.164-16-16L239.1 64.13c0-8.836 7.164-16 16-16h128L384 96c0 17.67 14.33 32 32 32h47.1V320zM272 448c0 8.836-7.164 16-16 16H63.1c-8.838 0-16-7.164-16-16L47.98 192.1c0-8.836 7.164-16 16-16H160V128H63.99c-35.35 0-64 28.65-64 64l.0098 256C.002 483.3 28.66 512 64 512h192c35.2 0 64-28.8 64-64v-32h-47.1L272 448z'/></svg>%s</button>\n", iconId, targetId, buttonLabel); jsOnEventById("click", iconId, "copyToClipboard(event);"); } void printShareMessage(struct dyString *dy, char *userName, char *sessionName, boolean encode) { struct dyString *dyTmp = dyStringNew(0); addSessionLink(dyTmp, userName, sessionName, encode, TRUE); dyStringPrintf(dy, "<p>You can share this session with the following URL:<br><span id='urlText'>%s</span> ", dyTmp->string); printCopyToClipboardButton(dy, "copyIcon", "urlText", " Copy to clipboard"); dyStringAppend(dy, "</p>"); } char *getSessionLink(char *encUserName, char *encSessionName) /* Form a link that will take the user to a bookmarkable page that * will load the given session. */ { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "<A HREF=\""); addSessionLink(dy, encUserName, encSessionName, FALSE, TRUE); dyStringPrintf(dy, "\">Browser</A>\n"); return dyStringCannibalize(&dy); } char *getSessionEmailLink(char *encUserName, char *encSessionName) /* Invoke mailto: with a cgi-encoded link that will take the user to a * bookmarkable page that will load the given session. */ { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "<A HREF=\"mailto:?subject=UCSC browser session %s&" "body=Here is a UCSC browser session I%%27d like to share with " "you:%%20", cgiDecodeClone(encSessionName)); addSessionLink(dy, encUserName, encSessionName, TRUE, TRUE); dyStringPrintf(dy, "\">Email</A>\n"); return dyStringCannibalize(&dy); } void addUrlLink(struct dyString *dy, char *url, boolean encode) /* Add to dy an URL that tells hgSession to load settings from the given url. * If encode, cgiEncodeFull the whole thing. */ { struct dyString *dyTmp = dyStringNew(1024); char *encodedUrl = cgiEncodeFull(url); dyStringPrintf(dyTmp, "%shgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=%s", hLocalHostCgiBinUrl(), encodedUrl); if (encode) { dyStringPrintf(dy, "%s", cgiEncodeFull(dyTmp->string)); } else { dyStringPrintf(dy, "%s", dyTmp->string); } freeMem(encodedUrl); dyStringFree(&dyTmp); } char *getUrlLink(char *url) /* Form a link that will take the user to a bookmarkable page that * will load the given url. */ { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "<A HREF=\""); addUrlLink(dy, url, FALSE); dyStringPrintf(dy, "\">Browser</A>\n"); return dyStringCannibalize(&dy); } char *getUrlEmailLink(char *url) /* Invoke mailto: with a cgi-encoded link that will take the user to a * bookmarkable page that will load the given url. */ { struct dyString *dy = dyStringNew(1024); dyStringPrintf(dy, "<A HREF=\"mailto:?subject=UCSC browser session&" "body=Here is a UCSC browser session I%%27d like to share with " "you:%%20"); addUrlLink(dy, url, TRUE); dyStringPrintf(dy, "\">Email</A>\n"); return dyStringCannibalize(&dy); } static char *getSetting(char *settings, char *name) /* Dig out one setting from a settings string that we're only going to * look at once (so we don't keep the hash around). */ { if (isEmpty(settings)) return NULL; struct hash *settingsHash = raFromString(settings); char *val = cloneString(hashFindVal(settingsHash, name)); hashFree(&settingsHash); return val; } static struct slName *showExistingSessions(char *userName) /* Print out a table with buttons for sharing/unsharing/loading/deleting * previously saved sessions. Return a list of session names. */ { struct slName *existingSessionNames = NULL; struct sqlConnection *conn = hConnectCentral(); struct sqlResult *sr = NULL; char **row = NULL; char query[512]; boolean foundAny = FALSE; char *encUserName = cgiEncodeFull(userName); boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); /* DataTables configuration: only allow ordering on session name, creation date, and database. * https://datatables.net/reference/option/columnDefs */ jsInlineF( "if (theClient.isIePre11() === false)\n{\n" "$(document).ready(function () {\n" " $('#sessionTable').DataTable({\"columnDefs\": [{\"orderable\":false, \"targets\":[0,4,5,6,7,8]}],\n" " \"order\":[2,'desc'],\n" " \"stateSave\":true,\n" " \"stateSaveCallback\": %s,\n" " \"stateLoadCallback\": %s\n" " });\n" "} );\n" "}\n" , jsDataTableStateSave(hgSessionPrefix), jsDataTableStateLoad(hgSessionPrefix, cart)); printf("<style>#sessionTable_filter { float:left !important; margin-left:20px; }</style>\n"); printf("<H3>My Sessions</H3>\n"); printf("<table id=\"sessionTable\" class=\"sessionTable stripe hover row-border compact\" borderwidth=0>\n"); printf("<thead><tr>"); printf("<th></th>" "<th style=\"white-space:nowrap;text-align:left\">Session name (click to load)</th>" "<th style=\"text-align:left\">Created on</th><th style=\"text-align:left\">View count</th>" "<th style=\"text-align:left\">Assembly</th>" "<th style=\"text-align:left\">View/edit <BR>details </th>" "<th style=\"text-align:left\">Delete this <BR>session </th>" "<th style=\"text-align:left\">Share with <BR>others? </th>" "<th style=\"text-align:left\">Post in <br><a href=\"../cgi-bin/hgPublicSessions?%s\">public listing</a>?</th>" "<th style=\"text-align:left\">Send to<BR>mail</th>", cartSidUrlString(cart)); printf("</tr></thead>"); printf("<tbody>\n"); if (gotSettings) sqlSafef(query, sizeof(query), "SELECT sessionName, shared, firstUse, useCount, contents, settings from %s " "WHERE userName = '%s' ORDER BY sessionName;", namedSessionTable, encUserName); else sqlSafef(query, sizeof(query), "SELECT sessionName, shared, firstUse, useCount, contents from %s " "WHERE userName = '%s' ORDER BY sessionName;", namedSessionTable, encUserName); sr = sqlGetResult(conn, query); int rowIdx = 0; while ((row = sqlNextRow(sr)) != NULL) { char *encSessionName = row[0]; char *sessionName = cgiDecodeClone(encSessionName); char *link = NULL; int shared = atoi(row[1]); char *firstUse = row[2]; char buf[512]; boolean inGallery = FALSE; boolean hasDescription = FALSE; if (shared >=2) inGallery = TRUE; printf("<TR><TD> </TD><TD>"); char iconId[256]; char linkId[256]; safef(linkId, sizeof(linkId), "linkEl-%d", rowIdx); safef(iconId, sizeof(iconId), "iconEl-%d", rowIdx); struct dyString *buttonText = dyStringNew(4096); printCopyToClipboardButton(buttonText, iconId, linkId, ""); puts(dyStringCannibalize(&buttonText)); puts(" "); struct dyString *dy = dyStringNew(1024); addSessionLink(dy, encUserName, encSessionName, FALSE, TRUE); char *sessionUrl = dyStringContents(dy); printf("<a id='linkEl-%d' data-copy='%s' href=\"%s\">%s</a>", rowIdx, sessionUrl, sessionUrl, htmlEncode(sessionName)); dyStringFree(&dy); rowIdx++; struct tm firstUseTm; ZeroVar(&firstUseTm); strptime(firstUse, "%Y-%m-%d %T", &firstUseTm); char *spacePt = strchr(firstUse, ' '); if (spacePt != NULL) *spacePt = '\0'; char *useCount = row[3]; printf(" </TD>" "<TD data-order=\"%ld\"><nobr>%s</nobr> </TD>" "<TD>%s</TD>" "<TD align='left'>", mktime(&firstUseTm), firstUse, useCount); char *dbIdx = NULL; if (startsWith("db=", row[4])) dbIdx = row[4]+3; else dbIdx = strstr(row[4], "&db=") + 4; if (dbIdx != NULL) { char *dbEnd = strchr(dbIdx, '&'); char *db = NULL; if (dbEnd != NULL) db = cloneStringZ(dbIdx, dbEnd-dbIdx); else db = cloneString(dbIdx); printf("%s</td><td align='center'>", db); } else printf("n/a</td><td align=center>"); if (gotSettings) { safef(buf, sizeof(buf), "%s%s", hgsEditPrefix, encSessionName); cgiMakeButton(buf, "View/edit"); char *description = getSetting(row[5], "description"); if (!isEmpty(description)) hasDescription = TRUE; } else printf("unavailable"); printf("</TD><TD align=center>"); safef(buf, sizeof(buf), "%s%s", hgsDeletePrefix, encSessionName); char command[512]; safef(command, sizeof(command), confirmDeleteFormat, encSessionName); cgiMakeOnClickSubmitButton(command, buf, "Delete"); printf("</TD><TD align=center>"); safef(buf, sizeof(buf), "%s%s", hgsSharePrefix, encSessionName); cgiMakeCheckBoxWithId(buf, shared>0, buf); jsOnEventById("change",buf,"document.mainForm.submit();"); printf("</TD><TD align=center>"); safef(buf, sizeof(buf), "%s%s", hgsGalleryPrefix, encSessionName); cgiMakeCheckBoxFourWay(buf, inGallery, shared>0, buf, NULL, NULL); if (hasDescription || inGallery) jsOnEventById("change", buf, "document.mainForm.submit();"); else jsOnEventById("change", buf, "warn('Please first use the view/edit option to " "add a description for this session.'); this.checked = false;"); link = getSessionEmailLink(encUserName, encSessionName); printf("</td><td align=center>%s</td></tr>", link); freez(&link); foundAny = TRUE; struct slName *sn = slNameNew(sessionName); slAddHead(&existingSessionNames, sn); } if (!foundAny) printf("<TR><TD> </TD><TD>(none)</TD>" "<TD colspan=5></TD></TR>\n"); printf("</tbody>\n"); printf("</TABLE>\n"); printf("<P></P>\n"); sqlFreeResult(&sr); hDisconnectCentral(&conn); return existingSessionNames; } void showOtherUserOptions() /* Print out inputs for loading another user's saved session. */ { printf("<TABLE BORDERWIDTH=0>\n"); printf("<TR><TD colspan=2>" "Use settings from another user's saved session:</TD></TR>\n" "<TR><TD> </TD><TD>User: \n"); cgiMakeOnKeypressTextVar(hgsOtherUserName, cartUsualString(cart, hgsOtherUserName, ""), 20, "return noSubmitOnEnter(event);"); printf(" Session name: \n"); cgiMakeOnKeypressTextVar(hgsOtherUserSessionName, cartUsualString(cart, hgsOtherUserSessionName, ""), 20, jsPressOnEnter(hgsDoOtherUser)); printf(" "); cgiMakeButton(hgsDoOtherUser, "Submit"); printf("</TD></TR>\n"); printf("<TR><TD colspan=2></TD></TR>\n"); printf("</TABLE>\n"); } void showLoadingOptions(char *userName, boolean savedSessionsSupported) /* Show options for loading settings from another user's session, a file * or URL. */ { printf("<H3>Restore Settings</H3>\n"); if (savedSessionsSupported) showOtherUserOptions(); printf("<TABLE BORDERWIDTH=0>\n"); printf("<TR><TD colspan=2>Use settings from a local file:</TD>\n"); printf("<TD><INPUT TYPE=FILE NAME=\"%s\" id='%s'>\n", hgsLoadLocalFileName, hgsLoadLocalFileName); jsOnEventById("keypress", hgsLoadLocalFileName,"return noSubmitOnEnter(event);"); printf(" "); cgiMakeButton(hgsDoLoadLocal, "Submit"); printf("</TD></TR>\n"); printf("<TR><TD colspan=2></TD></TR>\n"); printf("<TR><TD colspan=2>Use settings from a URL (http://..., ftp://...):" "</TD>\n"); printf("<TD>\n"); cgiMakeOnKeypressTextVar(hgsLoadUrlName, cartUsualString(cart, hgsLoadUrlName, ""), 20, jsPressOnEnter(hgsDoLoadUrl)); printf(" "); cgiMakeButton(hgsDoLoadUrl, "Submit"); printf("</TD></TR>\n"); printf("</TABLE>\n"); printf("<P></P>\n"); printf("Please note: the above URL option is <em>not</em> for loading track hubs or assembly hubs.\n"); printf("To load those data resources into the browser, please visit the <a href=\"../cgi-bin/hgHubConnect\"\n"); printf("target=\"_blank\">Track Hubs</a> listing page, click the \"Connected Hubs\" tab, and enter the hub URL there.\n"); printf("<P></P>\n"); } static struct dyString *dyPrintCheckExistingSessionJs(struct slName *existingSessionNames, char *exceptName) /* Write JS that will pop up a confirm dialog if the user's new session name is the same * (case-insensitive) as any existing session name, i.e. they would be overwriting it. * If exceptName is given, then it's OK for the new session name to match that. */ { struct dyString *js = dyStringNew(1024); struct slName *sn; // MySQL does case-insensitive comparison because our DEFAULT CHARSET=latin1; // use case-insensitive comparison here to avoid clobbering (#15051). dyStringAppend(js, "var su, si = document.getElementsByName('" hgsNewSessionName "'); "); dyStringAppend(js, "if (si[0]) { su = si[0].value.trim().toUpperCase(); "); if (isNotEmpty(exceptName)) dyStringPrintf(js, "if (su !== '%s'.toUpperCase()) { ", exceptName); dyStringAppend(js, "if ( "); for (sn = existingSessionNames; sn != NULL; sn = sn->next) { char nameUpper[PATH_LEN]; safecpy(nameUpper, sizeof(nameUpper), sn->name); touppers(nameUpper); dyStringPrintf(js, "su === "); dyStringQuoteString(js, '\'', nameUpper); dyStringPrintf(js, "%s", (sn->next ? " || " : " )")); } dyStringAppend(js, " { return confirm('This will overwrite the contents of the existing " "session ' + si[0].value.trim() + '. Proceed?'); } }"); if (isNotEmpty(exceptName)) dyStringAppend(js, " }"); return js; } void showSavingOptions(char *userName, struct slName *existingSessionNames) /* Show options for saving a new named session in our db or to a file. */ { printf("<H3>Save Settings</H3>\n"); printf("<TABLE BORDERWIDTH=0>\n"); if (isNotEmpty(userName)) { printf("<TR><TD colspan=4>Save current settings as named session:" "</TD></TR>\n" "<TR><TD> </TD><TD>Name:</TD><TD>\n"); cgiMakeOnKeypressTextVar(hgsNewSessionName, hubConnectSkipHubPrefix(cartUsualString(cart, "db", "mySession")), 20, jsPressOnEnter(hgsDoNewSession)); printf(" "); cgiMakeCheckBox(hgsNewSessionShare, cartUsualBoolean(cart, hgsNewSessionShare, TRUE)); printf("Allow this session to be loaded by others\n"); printf("</TD><TD>"); printf(" "); if (existingSessionNames) { struct dyString *js = dyPrintCheckExistingSessionJs(existingSessionNames, NULL); cgiMakeOnClickSubmitButton(js->string, hgsDoNewSession, "Submit"); dyStringFree(&js); } else cgiMakeButton(hgsDoNewSession, "submit"); printf("</TD></TR>\n"); printf("<TR><TD colspan=4></TD></TR>\n"); } printf("<TR><TD colspan=4>Save current settings to a local file:</TD></TR>\n"); printf("<TR><TD> </TD><TD>File:</TD><TD>\n"); cgiMakeOnKeypressTextVar(hgsSaveLocalFileName, cartUsualString(cart, hgsSaveLocalFileName, ""), 20, jsPressOnEnter(hgsDoSaveLocal)); printf(" "); printf("File type returned: "); char *compressType = cartUsualString(cart, hgsSaveLocalFileCompress, textOutCompressNone); cgiMakeRadioButton(hgsSaveLocalFileCompress, textOutCompressNone, differentWord(textOutCompressGzip, compressType)); printf(" plain text "); cgiMakeRadioButton(hgsSaveLocalFileCompress, textOutCompressGzip, sameWord(textOutCompressGzip, compressType)); printf(" gzip compressed (ignored if output file is blank)"); printf("</TD><TD>"); printf(" "); cgiMakeButton(hgsDoSaveLocal, "Submit"); printf("</TD></TR>\n"); printf("<TR><TD></TD><TD colspan=3>(leave file blank to get output in " "browser window)</TD></TR>\n"); printf("<TR><TD colspan=4></TD></TR>\n"); printf("<TR><TD colspan=4>Save Custom Tracks:</TD></TR>\n"); printf("<TR><TD> </TD><TD colspan=2>"); printf("Back up custom tracks to archive .tar.gz</TD>"); printf("<TD>"); printf(" "); cgiMakeButton(hgsShowDownloadPrefix, "Submit"); printf("</TD></TR>\n"); printf("<TR><TD colspan=4></TD></TR>\n"); printf("</TABLE>\n"); } void showSessionControls(char *userName, boolean savedSessionsSupported, boolean webStarted) /* If userName is non-null, show sessions that belong to user and allow * saving of named sessions. * If savedSessionsSupported, allow import of named sessions. * Allow export/import of settings from file/URL. */ { char *formMethod = cartUsualString(cart, "formMethod", "POST"); if (webStarted) webNewSection("Session Management"); else { cartWebStart(cart, NULL, "Session Management"); jsInit(); } printSessionNewPageBanner(FALSE); printf("<P>See the <A HREF=\"../goldenPath/help/hgSessionHelp.html\" " "TARGET=_BLANK>Sessions User's Guide</A> " "for more information about this tool. " "See the <A HREF=\"../goldenPath/help/sessions.html\" " "TARGET=_BLANK>Session Gallery</A> " "for example sessions.</P>\n"); showCartLinks(); printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s " "ENCTYPE=\"multipart/form-data\">\n", hgSessionName(), formMethod); cartSaveSession(cart); struct slName *existingSessionNames = NULL; if (isNotEmpty(userName)) existingSessionNames = showExistingSessions(userName); else if (savedSessionsSupported) printf("<P>If you <A HREF=\"%s\">sign in</A>, " "you will also have the option to save named sessions.</P>\n", wikiLinkUserLoginUrl(cartSessionId(cart))); showSavingOptions(userName, existingSessionNames); showLoadingOptions(userName, savedSessionsSupported); printf("</FORM>\n"); } void showLinkingTemplates(char *userName) /* Explain how to create links to us for sharing sessions. */ { struct dyString *dyUrl = dyStringNew(1024); webNewSection("Sharing Sessions"); printf("There are several ways to share saved sessions with others.\n"); printf("<UL>\n"); if (userName != NULL) { printf("<LI>Each previously saved named session appears with " "Browser and Email links. " "The Email link invokes your email tool with a message " "containing the Genome Browser link. The Email link can " "be bookmarked in your web browser and/or shared with " "others. If you right-click and copy the Browser link, " "it will be the same as the Email link. However, if you " "click the Browser link it will take you to the Genome " "Browser and become a uniquely identified URL once the " "session loads, so that resulting link is not advised " "for sharing.</LI>\n" "<li>Each previously saved named session also appears with " "a checkbox to add the session to our " "<a href=\"../cgi-bin/hgPublicSessions?%s\">Public Sessions</a> " "listing. Adding a session to this listing allows other " "browser users to view the description and a thumbnail " "image of your session, and to load the session if they " "are interested.</li>\n", cartSidUrlString(cart)); } else if (loginSystemEnabled() || wikiLinkEnabled()) { printf("<LI>If you <A HREF=\"%s\">sign in</A>, you will be able " " to save named sessions which will be displayed with " " Browser and Email links.</LI>\n", wikiLinkUserLoginUrl(cartSessionId(cart))); } dyStringPrintf(dyUrl, "%shgTracks", hLocalHostCgiBinUrl()); printf("<LI>If you have saved your settings to a local file, you can send " "email to others with the file as an attachment and direct them to " "<A HREF=\"%s\">%s</A> .</LI>\n", dyUrl->string, dyUrl->string); dyStringPrintf(dyUrl, "?hgS_doLoadUrl=submit&hgS_loadUrlName="); printf("<LI>If a saved settings file is available from a web server, " "you can send email to others with a link such as " "%s<B>U</B> where <B>U</B> is the URL of your " "settings file, e.g. http://www.mysite.edu/~me/mySession.txt . " "In this type of link, you can replace " "\"hgSession\" with \"hgTracks\" in order to proceed directly to " "the Genome Browser. For an example page using such links " "please see the <A HREF=\"../goldenPath/help/sessions.html\" " "TARGET=_BLANK>Session Gallery</A>.</LI>\n", dyUrl->string); printf("</UL>\n"); dyStringFree(&dyUrl); } void doMainPage(char *userName, char *message) /* Login status/links and session controls. */ { if (sessionNewPageActive()) { doMainPageNew(userName, message); return; } cspWriteResponseHeader(); puts("Content-Type:text/html\n"); if (loginSystemEnabled() || wikiLinkEnabled()) { if (userName) welcomeUser(userName); else offerLogin(); if (isNotEmpty(message)) { if (cartVarExists(cart, hgsDoSessionDetail)) webNewSection("Session Details"); else webNewSection("Updated Session"); puts(message); } showSessionControls(userName, TRUE, TRUE); showLinkingTemplates(userName); } else { if (isNotEmpty(message)) { if (cartVarExists(cart, hgsDoSessionDetail)) webNewSection("Session Details"); else cartWebStart(cart, NULL, "Updated Session"); jsInit(); puts(message); showSessionControls(NULL, FALSE, TRUE); } else showSessionControls(NULL, FALSE, FALSE); showLinkingTemplates(NULL); } cartWebEnd(); } void cleanHgSessionFromCart(struct cart *cart) /* Remove hgSession action variables that should not stay in the cart. */ { char varName[256]; safef(varName, sizeof(varName), "%s%s", cgiBooleanShadowPrefix(), hgsSharePrefix); cartRemovePrefix(cart, varName); cartRemovePrefix(cart, hgsSharePrefix); safef(varName, sizeof(varName), "%s%s", cgiBooleanShadowPrefix(), hgsGalleryPrefix); cartRemovePrefix(cart, varName); cartRemovePrefix(cart, hgsGalleryPrefix); cartRemovePrefix(cart, hgsLoadPrefix); cartRemovePrefix(cart, hgsEditPrefix); cartRemovePrefix(cart, hgsLoadLocalFileName); cartRemovePrefix(cart, hgsDeletePrefix); cartRemovePrefix(cart, hgsShowDownloadPrefix); cartRemovePrefix(cart, hgsMakeDownloadPrefix); cartRemovePrefix(cart, hgsDoDownloadPrefix); cartRemovePrefix(cart, hgsDo); cartRemove(cart, hgsOldSessionName); cartRemove(cart, hgsCancel); + /* Two of the Save form's own inputs. If they stay in the cart they are stored inside every + * session saved afterwards, so one session's description travels in sessions that never had + * one. hgsNewSessionShare is left alone on purpose: it has the same problem, but it is also + * the only memory of the user's "Allow this session to be loaded by others" choice, and + * showSavingOptions() defaults that box to checked. Removing it here would quietly re-check + * the box for someone who keeps their sessions private. */ + cartRemove(cart, hgsNewSessionName); + cartRemove(cart, hgsNewSessionDescription); } static void outIfNotPresent(struct cart *cart, struct dyString *dy, char *track, int tdbVis) /* Output default trackDb visibility if it's not mentioned in the cart. */ { char *cartVis = cartOptionalString(cart, track); if (cartVis == NULL) { if (dy) dyStringPrintf(dy,"&%s=%s", track, hStringFromTv(tdbVis)); else printf("%s %s\n", track, hStringFromTv(tdbVis)); } } static void outAttachedHubUrls(struct cart *cart, struct dyString *dy) /* output the hubUrls for all attached hubs in the cart. */ { struct hubConnectStatus *statusList = hubConnectStatusListFromCart(cart, NULL); if (statusList == NULL) return; if (dy) dyStringPrintf(dy,"&assumesHub="); else printf("assumesHub "); for(; statusList; statusList = statusList->next) { if (dy) dyStringPrintf(dy,"%d=%s ", statusList->id, cgiEncode(statusList->hubUrl)); else printf("%d=%s ", statusList->id, statusList->hubUrl); } if (dy == NULL) printf("\n"); } static void outDefaultTracks(struct cart *cart, struct dyString *dy) /* Output the default trackDb visibility for all tracks * in trackDb if the track is not mentioned in the cart. */ { database = cartString(cart, "db"); struct trackDb *tdb = NULL; // Some old sessions reference databases that are no longer present, and that triggers an errAbort // when calling hgTrackDb. Just move on instead of errAborting. struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) tdb = hTrackDb(database); errCatchEnd(errCatch); if (errCatch->gotError) { fprintf(stderr, "outDefaultTracks: Error from hTrackDb: '%s'; Continuing...", errCatch->message->string); tdb = NULL; } errCatchFree(&errCatch); struct hash *parentHash = newHash(5); for(; tdb; tdb = tdb->next) { struct trackDb *parent = tdb->parent; if (parent) { if (hashLookup(parentHash, parent->track) == NULL) { hashStore(parentHash, parent->track); if (parent->isShow) outIfNotPresent(cart, dy, parent->track, tvShow); } } if (tdb->visibility != tvHide) outIfNotPresent(cart, dy, tdb->track, tdb->visibility); } // Put a variable in the cart that says we put the default // visibilities in it. if (dy) dyStringPrintf(dy,"&%s=on", CART_HAS_DEFAULT_VISIBILITY); else printf("%s on", CART_HAS_DEFAULT_VISIBILITY); } #define INITIAL_USE_COUNT 0 static int saveCartAsSession(struct sqlConnection *conn, char *encUserName, char *encSessionName, int sharingLevel) /* Save all settings in cart, either adding a new session or overwriting an existing session. * Return useCount so that the caller can distinguish between adding and overWriting. */ { struct sqlResult *sr = NULL; struct dyString *dy = dyStringNew(16 * 1024); char **row; char *firstUse = NULL; int useCount = INITIAL_USE_COUNT; char *settings = ""; boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); /* If this session already existed, preserve its firstUse, useCount, * and settings (if available). */ if (gotSettings) sqlDyStringPrintf(dy, "SELECT firstUse, useCount, settings FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); else sqlDyStringPrintf(dy, "SELECT firstUse, useCount FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); sr = sqlGetResult(conn, dy->string); if ((row = sqlNextRow(sr)) != NULL) { firstUse = cloneString(row[0]); useCount = atoi(row[1]) + 1; if (gotSettings) { settings = cloneString(row[2]); if (settings == NULL) settings = ""; } } sqlFreeResult(&sr); sessionDataSaveSession(cart, encUserName, encSessionName, cgiOptionalString(hgsSessionDataDbSuffix)); /* Remove pre-existing session (if any) before updating. */ dyStringClear(dy); sqlDyStringPrintf(dy, "DELETE FROM %s WHERE userName = '%s' AND " "sessionName = '%s';", namedSessionTable, encUserName, encSessionName); sqlUpdate(conn, dy->string); dyStringClear(dy); sqlDyStringPrintf(dy, "INSERT INTO %s ", namedSessionTable); sqlDyStringPrintf(dy, "(userName, sessionName, contents, shared, " "firstUse, lastUse, useCount"); if (gotSettings) sqlDyStringPrintf(dy, ", settings"); sqlDyStringPrintf(dy, ") VALUES ("); sqlDyStringPrintf(dy, "'%s', '%s', ", encUserName, encSessionName); sqlDyStringPrintf(dy, "'"); cleanHgSessionFromCart(cart); struct dyString *encoded = dyStringNew(4096); cartEncodeState(cart, encoded); // First output the hubStatus id's for attached trackHubs outAttachedHubUrls(cart, encoded); // Now add all the default visibilities to output. outDefaultTracks(cart, encoded); sqlDyAppendEscaped(dy, encoded->string); dyStringFree(&encoded); sqlDyStringPrintf(dy, "', "); sqlDyStringPrintf(dy, "%d, ", sharingLevel); if (firstUse) sqlDyStringPrintf(dy, "'%s', ", firstUse); else sqlDyStringPrintf(dy, "now(), "); sqlDyStringPrintf(dy, "now(), %d", useCount); if (gotSettings) sqlDyStringPrintf(dy, ", '%s'", settings); sqlDyStringPrintf(dy, ")"); sqlUpdate(conn, dy->string); dyStringFree(&dy); /* Prevent modification of custom track collections or quickLifts just saved to namedSessionDb: */ cartCopyLocalHubs(cart); return useCount; } char *doNewSession(char *userName) /* Save current settings in a new named session. * Return a message confirming what we did. */ { if (userName == NULL) return "Unable to save session -- please log in and try again."; struct dyString *dyMessage = dyStringNew(2048); - char *sessionName = trimSpaces(cartString(cart, hgsNewSessionName)); + /* Clone: saveCartAsSession() removes this cart variable, which frees the cart's own copy. */ + char *sessionName = trimSpaces(cloneString(cartString(cart, hgsNewSessionName))); if (isEmpty(sessionName)) return "Error: Unable to save a session without a name. Please add one and try again."; char *encSessionName = cgiEncodeFull(sessionName); boolean shareSession = cartBoolean(cart, hgsNewSessionShare); char *encUserName = cgiEncodeFull(userName); struct sqlConnection *conn = hConnectCentral(); if (sqlTableExists(conn, namedSessionTable)) { int useCount = saveCartAsSession(conn, encUserName, encSessionName, shareSession); if (useCount > INITIAL_USE_COUNT) dyStringPrintf(dyMessage, "Overwrote the contents of session <B>%s</B> " "(that %s be shared with other users). " "%s %s", htmlEncode(sessionName), (shareSession ? "may" : "may not"), getSessionLink(encUserName, encSessionName), getSessionEmailLink(encUserName, encSessionName)); else dyStringPrintf(dyMessage, "Added a new session <B>%s</B> that %s be shared with other users. " "%s %s", htmlEncode(sessionName), (shareSession ? "may" : "may not"), getSessionLink(encUserName, encSessionName), getSessionEmailLink(encUserName, encSessionName)); if (shareSession) { printShareMessage(dyMessage, encUserName, encSessionName, FALSE); } cartCheckForCustomTracks(cart, dyMessage); } else dyStringPrintf(dyMessage, "Sorry, required table %s does not exist yet in the central " "database (%s). Please ask a developer to create it using " "kent/src/hg/lib/namedSessionDb.sql .", namedSessionTable, sqlGetDatabase(conn)); hDisconnectCentral(&conn); return dyStringCannibalize(&dyMessage); } static void saveSessionJsonError(struct sqlConnection *conn, char *message) /* Emit a JSON error response for the "Share a link" AJAX endpoints and disconnect. */ { puts("Content-Type:application/json\n"); printf("{\"error\": \"%s\"}\n", jsonStringEscape(message)); hDisconnectCentral(&conn); } static void saveSessionJsonResult(struct sqlConnection *conn, char *encUserName, char *encSessionName, char *sessionName) /* Emit {"name": ..., "url": ...} for the "Share a link" AJAX endpoints and disconnect. * sessionName is the human-readable (decoded) name; the client uses it as the rename "old name". */ { struct dyString *dyUrl = dyStringNew(0); addSessionLink(dyUrl, encUserName, encSessionName, FALSE, TRUE); puts("Content-Type:application/json\n"); printf("{\"name\": \"%s\", \"url\": \"%s\"}\n", jsonStringEscape(sessionName), jsonStringEscape(dyUrl->string)); dyStringFree(&dyUrl); hDisconnectCentral(&conn); } +void doAnonNameJson() +/* AJAX endpoint that reserves a fresh, guaranteed-unique anonymous snapshot name and returns it as + * JSON {"name": ...} WITHOUT saving anything. The top-right "Share a link" dialog calls this on open + * so it can show the exact link as a preview before the user commits, while keeping name generation + * server-side (unique, crypto-strong) for every anonymous link. */ +{ +struct sqlConnection *conn = hConnectCentral(); +cartRemove(cart, hgsDoAnonName); +if (!sqlTableExists(conn, namedSessionTable)) + { + saveSessionJsonError(conn, "Required session table does not exist in the central database."); + return; + } +char *name = snapshotNewName(conn, "l"); +puts("Content-Type:application/json\n"); +printf("{\"name\": \"%s\"}\n", jsonStringEscape(name)); +hDisconnectCentral(&conn); +} + void doSaveSessionJson(char *userName) /* AJAX endpoint behind the "Share a link" menu button. Save the current cart as a named session * and print JSON {"name": <session name>, "url": <shareable link>}. When the user is not logged * in (or hgsShareAnon is set), save under the reserved anonymous user "l" with a random token - * name. When logged in with no name given, generate a short random name. Saved shared by link so - * the link works for anyone. Reuses saveCartAsSession() and addSessionLink(). */ + * name. When logged in, the caller supplies the name (a typed name, or a random internal + * "_XXXXXXXX" name generated client-side). Saved shared by link so the link works for anyone. + * Reuses saveCartAsSession() and addSessionLink(). */ { struct sqlConnection *conn = hConnectCentral(); if (!sqlTableExists(conn, namedSessionTable)) { saveSessionJsonError(conn, "Required session table does not exist in the central database."); return; } boolean anon = isEmpty(userName) || cgiBoolean(hgsShareAnon); +boolean failIfExists = cgiBoolean(hgsFailIfExists); +// A registered snapshot type (e.g. "blat") means: save a lightweight snapshot holding only that +// feature's declared cart vars, not the whole cart (see lib/snapshotSession.c). +char *snapshotType = cgiOptionalString(hgsSnapshotType); - // Read the requested name from the request, not the cart (hgSession's Save form leaves a sticky - // value in the cart under this same variable that would otherwise shadow ours). + // Read the requested name from the request, not the cart. cleanHgSessionFromCart() now takes + // this variable back out, but carts written before that still hold a sticky value from + // hgSession's Save form, and it would otherwise shadow ours. char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsNewSessionName, ""))); /* Keep our control variables out of the saved session contents and the user's own cart. */ cartRemove(cart, hgsDoSaveSessionJson); cartRemove(cart, hgsShareAnon); +cartRemove(cart, hgsFailIfExists); +cartRemove(cart, hgsSnapshotType); cartRemove(cart, hgsNewSessionName); cartRemove(cart, hgsNewSessionShare); +/* Snapshot path: a lightweight session holding only the feature's declared cart vars, under a + * server-generated, guaranteed-unique "__"-prefixed name (share tokens must never collide and + * silently overwrite one another). Handled before the normal full-session logic because its + * naming rules differ. Works for both anonymous ("l") and logged-in owners. */ +if (isNotEmpty(snapshotType)) + { + if (snapshotTypeFind(snapshotType) == NULL) + { + saveSessionJsonError(conn, "Unknown snapshot type."); + return; + } + char *snapUser = anon ? "l" : cgiEncodeFull(userName); + char *snapName; + if (isEmpty(sessionName)) + snapName = snapshotNewName(conn, snapUser); /* server-generated, unique */ + else if (startsWith(snapshotNamePrefix, sessionName)) + snapName = cgiEncodeFull(sessionName); + else + snapName = catTwoStrings(snapshotNamePrefix, cgiEncodeFull(sessionName)); + saveSnapshotSession(conn, snapshotType, snapUser, snapName, cart); + char *snapDecoded = cgiDecodeClone(snapName); + saveSessionJsonResult(conn, snapUser, snapName, snapDecoded); + return; + } + char *encUserName = NULL; char *encSessionName = NULL; if (anon) { encUserName = "l"; /* reserved anonymous user -> short link /s/l/<token> */ - sessionName = makeRandomKey(96); /* 16 URL-safe alphanumeric chars; no encoding needed */ - encSessionName = sessionName; + /* Every anonymous share uses the shared snapshot naming: a server-generated, guaranteed-unique + * "__"-token, so tokens never collide/overwrite and the reaper can garbage-collect abandoned + * ones. The top-right Share dialog passes a name it just reserved (for its live preview); we + * force the "__" prefix either way so the link stays reap-eligible. */ + if (isEmpty(sessionName)) + encSessionName = snapshotNewName(conn, encUserName); + else if (startsWith(snapshotNamePrefix, sessionName)) + encSessionName = cgiEncodeFull(sessionName); + else + encSessionName = catTwoStrings(snapshotNamePrefix, cgiEncodeFull(sessionName)); + sessionName = cgiDecodeClone(encSessionName); // keep decoded name in sync for the JSON result } else { + /* Logged-in callers always supply a name: the caller either typed one or generated a random + * internal "_XXXXXXXX" name client-side (sessRandomShareName in hgSession.js, shared by the + * top-right "Share a link" menu in topLinks.js), so we no longer auto-name here. */ if (isEmpty(sessionName)) { - /* One-click share: auto-name the session. "_" is kept verbatim by cgiEncodeFull (unlike - * "-"), so the short link /s/<user>/<name> stays clean. */ - char randName[32]; - char *rk = makeRandomKey(48); /* 8 URL-safe alphanumeric chars */ - safef(randName, sizeof randName, "share_%s", rk); - freeMem(rk); - sessionName = cloneString(randName); + saveSessionJsonError(conn, "Please provide a name for this session."); + return; } encUserName = cgiEncodeFull(userName); encSessionName = cgiEncodeFull(sessionName); + /* The Share dialog sets failIfExists when the user typed a custom name, so it can warn before + * clobbering an existing session of theirs. Report the clash instead of overwriting. */ + if (failIfExists) + { + char query[1024]; + sqlSafef(query, sizeof query, + "select count(*) from %s where userName = '%s' and sessionName = '%s'", + namedSessionTable, encUserName, encSessionName); + if (sqlQuickNum(conn, query) > 0) + { + puts("Content-Type:application/json\n"); + printf("{\"exists\": true}\n"); + hDisconnectCentral(&conn); + return; + } + } } saveCartAsSession(conn, encUserName, encSessionName, 1); /* shared by link */ saveSessionJsonResult(conn, encUserName, encSessionName, sessionName); } void doRenameSessionJson(char *userName) /* AJAX endpoint for the "Specify name" step of the Share dialog: rename an existing session * (hgsOldSessionName -> hgsNewSessionName) under the current user. Logged-in only. Rejects a * name already in use rather than overwriting it. Returns {"name","url"} or {"error"}. */ { struct sqlConnection *conn = hConnectCentral(); // Read the names from the request, not the cart: hgSession's Save form also uses these variables // and leaves a sticky value (e.g. the username) in the cart that would otherwise shadow ours. char *oldName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); char *newName = trimSpaces(cloneString(cgiUsualString(hgsNewSessionName, ""))); cartRemove(cart, hgsDoRenameSessionJson); cartRemove(cart, hgsOldSessionName); cartRemove(cart, hgsNewSessionName); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in to name this link."); return; } if (isEmpty(oldName) || isEmpty(newName)) { saveSessionJsonError(conn, "Please enter a name."); return; } char *encUserName = cgiEncodeFull(userName); char *encOldName = cgiEncodeFull(oldName); char *encNewName = cgiEncodeFull(newName); char query[1024]; if (sameString(oldName, newName)) { saveSessionJsonResult(conn, encUserName, encNewName, newName); return; } /* Reject a name the user is already using (don't clobber an existing saved session). */ sqlSafef(query, sizeof query, "select count(*) from %s where userName = '%s' and sessionName = '%s'", namedSessionTable, encUserName, encNewName); if (sqlQuickNum(conn, query) > 0) { saveSessionJsonError(conn, "You already have a session with that name. Please pick another."); return; } sqlSafef(query, sizeof query, "select count(*) from %s where userName = '%s' and sessionName = '%s'", namedSessionTable, encUserName, encOldName); if (sqlQuickNum(conn, query) == 0) { saveSessionJsonError(conn, "Could not find the link to rename."); return; } /* Same UPDATE that doSessionChange uses to rename a session. */ sqlSafef(query, sizeof query, "UPDATE %s set sessionName = '%s' WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encNewName, encUserName, encOldName); sqlUpdate(conn, query); saveSessionJsonResult(conn, encUserName, encNewName, newName); } int thumbnailAdd(char *encUserName, char *encSessionName, struct sqlConnection *conn, struct dyString *dyMessage) /* Create a thumbnail image for the gallery. If the necessary tools can't be found, * add a warning message to dyMessage unless the hg.conf setting * sessionThumbnail.suppressWarning is set to "on". * Leaks memory from a generated filename string, plus a couple of dyStrings. * Returns without determining if image creation succeeded (it happens in a separate * thread); the return value is 0 if a message was added to dyMessage, otherwise it's 1. */ { char query[4096]; char *suppressConvert = cfgOption("sessionThumbnail.suppress"); if (suppressConvert != NULL && sameString(suppressConvert, "on")) return 1; char *convertPath = cfgOption("sessionThumbnail.convertPath"); if (convertPath == NULL) convertPath = cloneString("convert"); char *whichCmd[] = {"which", convertPath, NULL}; struct pipeline *pl = pipelineOpen1(whichCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0); int convertTestResult = pipelineWait(pl); if (convertTestResult != 0) { dyStringPrintf(dyMessage, "Note: A thumbnail image for this session was not created because the ImageMagick convert " "tool could not be found. Please contact your mirror administrator to resolve this " "issue, either by installing convert so that it is part of the webserver's PATH, " "by adding the \"sessionThumbnail.convertPath\" option to the mirror's hg.conf file " "to specify the path to that program, or by adding \"sessionThumbnail.suppress=on\" to " "the mirror's hg.conf file to suppress this warning.<br>"); return 0; } sqlSafef(query, sizeof(query), "select firstUse from %s where userName = \"%s\" and sessionName = \"%s\"", namedSessionTable, encUserName, encSessionName); char *firstUse = sqlNeedQuickString(conn, query); sqlSafef(query, sizeof(query), "select idx from gbMembers where userName = '%s'", encUserName); char *userIdx = sqlQuickString(conn, query); char *userIdentifier = sessionThumbnailGetUserIdentifier(encUserName, userIdx); char *destFile = sessionThumbnailFilePath(userIdentifier, encSessionName, firstUse); if (destFile != NULL) { struct dyString *hgTracksUrl = dyStringNew(0); addSessionLink(hgTracksUrl, encUserName, encSessionName, FALSE, FALSE); struct dyString *renderUrl = dyStringSub(hgTracksUrl->string, "cgi-bin/hgTracks", "cgi-bin/hgRenderTracks"); dyStringAppend(renderUrl, "&pix=640"); char *renderCmd[] = {"wget", "-q", "-O", "-", renderUrl->string, NULL}; char *convertCmd[] = {convertPath, "-", "-resize", "320", "-crop", "320x240+0+0", destFile, NULL}; char **cmdsImg[] = {renderCmd, convertCmd, NULL}; pipelineOpen(cmdsImg, pipelineWrite, "/dev/null", NULL, 0); } return 1; } void thumbnailRemove(char *encUserName, char *encSessionName, struct sqlConnection *conn) /* Unlink thumbnail image for the gallery. Leaks memory from a generated filename string. */ { char query[4096]; sqlSafef(query, sizeof(query), "select firstUse from %s where userName = \"%s\" and sessionName = \"%s\"", namedSessionTable, encUserName, encSessionName); char *firstUse = sqlNeedQuickString(conn, query); sqlSafef(query, sizeof(query), "select idx from gbMembers where userName = '%s'", encUserName); char *userIdx = sqlQuickString(conn, query); char *userIdentifier = sessionThumbnailGetUserIdentifier(encUserName, userIdx); char *filePath = sessionThumbnailFilePath(userIdentifier, encSessionName, firstUse); if (filePath != NULL) unlink(filePath); } static struct slName *getUserSessionNames(char *encUserName) /* Return a list of unencoded session names belonging to user. */ { struct slName *existingSessionNames = NULL; struct sqlConnection *conn = hConnectCentral(); char query[1024]; sqlSafef(query, sizeof(query), "select sessionName from %s where userName = '%s';", namedSessionTable, encUserName); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { char *encSessionName = row[0]; char *sessionName = cgiDecodeClone(encSessionName); slNameAddHead(&existingSessionNames, sessionName); } sqlFreeResult(&sr); hDisconnectCentral(&conn); return existingSessionNames; } char *doSessionDetail(char *userName, char *sessionName) /* Show details about a particular session. */ { if (userName == NULL) return "Sorry, please log in again."; struct dyString *dyMessage = dyStringNew(4096); char *encSessionName = cgiEncodeFull(sessionName); char *encUserName = cgiEncodeFull(userName); struct sqlConnection *conn = hConnectCentral(); struct sqlResult *sr = NULL; char **row = NULL; char query[512]; webPushErrHandlersCartDb(cart, cartUsualString(cart, "db", NULL)); boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); if (gotSettings) sqlSafef(query, sizeof(query), "SELECT shared, firstUse, settings from %s " "WHERE userName = '%s' AND sessionName = '%s'", namedSessionTable, encUserName, encSessionName); else sqlSafef(query, sizeof(query), "SELECT shared, firstUse from %s " "WHERE userName = '%s' AND sessionName = '%s'", namedSessionTable, encUserName, encSessionName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { int shared = atoi(row[0]); char *firstUse = row[1]; char *settings = NULL; if (gotSettings) settings = row[2]; char *description = getSetting(settings, "description"); if (description == NULL) description = ""; dyStringPrintf(dyMessage, "<A HREF=\"../goldenPath/help/hgSessionHelp.html#Details\" " "TARGET=_BLANK>Session Details Help</A><P/>\n"); #define highlightAccChanges " var b = document.getElementById('" hgsDoSessionChange "'); " \ " if (b) { b.style.background = '#ff9999'; }" #define toggleGalleryDisable \ " var c = document.getElementById('detailsSharedCheckbox'); " \ " var d = document.getElementById('detailsGalleryCheckbox'); " \ " if (c.checked)" \ " {d.disabled = false;} " \ " else" \ " {d.disabled = true; " \ " d.checked = false; }" dyStringPrintf(dyMessage, "<B>%s</B><P>\n" "<FORM ACTION=\"%s\" NAME=\"detailForm\" METHOD=GET>\n" "<INPUT TYPE=HIDDEN NAME=\"%s\" VALUE=%s>" "<INPUT TYPE=HIDDEN NAME=\"%s\" VALUE=\"%s\">" "Session Name: " "<INPUT TYPE=TEXT NAME=\"%s\" id='%s' SIZE=%d VALUE=\"%s\" >\n", sessionName, hgSessionName(), cartSessionVarName(cart), cartSessionId(cart), hgsOldSessionName, sessionName, hgsNewSessionName, hgsNewSessionName, 32, sessionName); jsOnEventById("change" , hgsNewSessionName, highlightAccChanges); jsOnEventById("keydown", hgsNewSessionName, highlightAccChanges); dyStringPrintf(dyMessage, " <INPUT TYPE=SUBMIT ID=\"%s\" NAME=\"%s\" VALUE=\"Accept changes\">" " <INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"Cancel\"> " "<BR>\n", hgsDoSessionChange, hgsDoSessionChange, hgsCancel); struct slName *existingSessionNames = getUserSessionNames(encUserName); struct dyString *checkExistingNameJs = dyPrintCheckExistingSessionJs( existingSessionNames, sessionName); struct dyString *onClickJs = dyStringCreate( "var pattern = /^\\s*$/;" "if (document.getElementById(\"detailsGalleryCheckbox\").checked &&" " pattern.test(document.getElementById(\"%s\").value)) {" " warn('Please add a description to allow this session to be included in the Public Gallery');" " event.preventDefault();" "} else {" " %s" "}", hgsNewSessionDescription, checkExistingNameJs->string); jsOnEventById("click", hgsDoSessionChange, onClickJs->string); dyStringFree(&onClickJs); dyStringFree(&checkExistingNameJs); dyStringPrintf(dyMessage, "Share with others? <INPUT TYPE=CHECKBOX NAME=\"%s%s\"%s VALUE=on " "id=\"detailsSharedCheckbox\">\n" "<INPUT TYPE=HIDDEN NAME=\"%s%s%s\" VALUE=0><BR>\n", hgsSharePrefix, encSessionName, (shared>0 ? " CHECKED" : ""), cgiBooleanShadowPrefix(), hgsSharePrefix, encSessionName); jsOnEventByIdF("change", "detailsSharedCheckbox", "{%s %s}", highlightAccChanges, toggleGalleryDisable); jsOnEventByIdF("click" , "detailsSharedCheckbox", "{%s %s}", highlightAccChanges, toggleGalleryDisable); dyStringPrintf(dyMessage, "List in Public Sessions? <INPUT TYPE=CHECKBOX NAME=\"%s%s\"%s VALUE=on " "id=\"detailsGalleryCheckbox\">\n" "<INPUT TYPE=HIDDEN NAME=\"%s%s%s\" VALUE=0><BR>\n", hgsGalleryPrefix, encSessionName, (shared>=2 ? " CHECKED" : ""), cgiBooleanShadowPrefix(), hgsGalleryPrefix, encSessionName); jsOnEventById("change", "detailsGalleryCheckbox", highlightAccChanges); jsOnEventById("click" , "detailsGalleryCheckbox", highlightAccChanges); /* Set initial disabled state of the gallery checkbox */ jsInline(toggleGalleryDisable); dyStringPrintf(dyMessage, "Created on %s.<BR>\n", firstUse); /* Print custom track counts per assembly */ struct cart *tmpCart = cartNew(NULL,NULL,NULL,NULL); struct sqlConnection *conn2 = hConnectCentral(); cartLoadUserSession(conn2, userName, sessionName, tmpCart, NULL, NULL); hDisconnectCentral(&conn2); hubConnectLoadHubs(tmpCart); cartCheckForCustomTracks(tmpCart, dyMessage); if (gotSettings) { description = replaceChars(description, "\\\\", "\\__ESC__"); description = replaceChars(description, "\\r", "\r"); description = replaceChars(description, "\\n", "\n"); description = replaceChars(description, "\\__ESC__", "\\"); char *encDescription = htmlEncode(description); dyStringPrintf(dyMessage, "Description:<BR>\n" "<TEXTAREA NAME=\"%s\" id='%s' ROWS=%d COLS=%d " ">%s</TEXTAREA><BR>\n", hgsNewSessionDescription, hgsNewSessionDescription, 5, 80, encDescription); jsOnEventById("change" , hgsNewSessionDescription, highlightAccChanges); jsOnEventById("keypress" , hgsNewSessionDescription, highlightAccChanges); } dyStringAppend(dyMessage, "</FORM>\n"); sqlFreeResult(&sr); } else errAbort("doSessionDetail: got no results from query:<BR>\n%s\n", query); return dyStringCannibalize(&dyMessage); } char *doUpdateSessions(char *userName) /* Look for cart variables matching prefixes for sharing/unsharing, * loading or deleting a previously saved session. * Return a message confirming what we did, or NULL if no such variables * were in the cart. */ { if (userName == NULL) return NULL; struct dyString *dyMessage = dyStringNew(1024); struct hashEl *cartHelList = NULL, *hel = NULL; struct sqlConnection *conn = hConnectCentral(); char *encUserName = cgiEncodeFull(userName); boolean didSomething = FALSE; char query[512]; cartHelList = cartFindPrefix(cart, hgsGalleryPrefix); if (cartHelList != NULL) { struct hash *galleryHash = hashNew(0); char **row; struct sqlResult *sr; sqlSafef(query, sizeof(query), "select sessionName,shared from %s where userName = '%s'", namedSessionTable, encUserName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) hashAddInt(galleryHash, row[0], atoi(row[1])); sqlFreeResult(&sr); for (hel = cartHelList; hel != NULL; hel = hel->next) { char *encSessionName = hel->name + strlen(hgsGalleryPrefix); char *sessionName = cgiDecodeClone(encSessionName); boolean inGallery = hashIntVal(galleryHash, encSessionName) >= 2 ? TRUE : FALSE; boolean newGallery = cartUsualInt(cart, hel->name, 0) > 0 ? TRUE : FALSE; if (newGallery != inGallery) { sqlSafef(query, sizeof(query), "UPDATE %s SET shared = %d " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, newGallery == TRUE ? 2 : 1, encUserName, encSessionName); sqlUpdate(conn, query); sessionTouchLastUse(conn, encUserName, encSessionName); dyStringPrintf(dyMessage, "Marked session <B>%s</B> as %s.<BR>\n", htmlEncode(sessionName), (newGallery == TRUE ? "added to gallery" : "removed from public listing")); if (newGallery == FALSE) thumbnailRemove(encUserName, encSessionName, conn); if (newGallery == TRUE) thumbnailAdd(encUserName, encSessionName, conn, dyMessage); didSomething = TRUE; } } hashFree(&galleryHash); } cartHelList = cartFindPrefix(cart, hgsSharePrefix); if (cartHelList != NULL) { struct hash *sharedHash = hashNew(0); char **row; struct sqlResult *sr; sqlSafef(query, sizeof(query), "select sessionName,shared from %s where userName = '%s'", namedSessionTable, encUserName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) hashAddInt(sharedHash, row[0], atoi(row[1])); sqlFreeResult(&sr); for (hel = cartHelList; hel != NULL; hel = hel->next) { char *encSessionName = hel->name + strlen(hgsSharePrefix); char *sessionName = cgiDecodeClone(encSessionName); boolean alreadyShared = hashIntVal(sharedHash, encSessionName) > 0 ? TRUE : FALSE; boolean inGallery = hashIntVal(sharedHash, encSessionName) >= 2 ? TRUE : FALSE; boolean newShared = cartUsualInt(cart, hel->name, 1) ? TRUE : FALSE; if (newShared != alreadyShared) { sqlSafef(query, sizeof(query), "UPDATE %s SET shared = %d " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, newShared, encUserName, encSessionName); sqlUpdate(conn, query); sessionTouchLastUse(conn, encUserName, encSessionName); dyStringPrintf(dyMessage, "Marked session <B>%s</B> as %s.<BR>\n", htmlEncode(sessionName), (newShared == TRUE ? "shared" : "unshared")); if (newShared == FALSE && inGallery == TRUE) thumbnailRemove(encUserName, encSessionName, conn); didSomething = TRUE; } } hashFree(&sharedHash); } hel = cartFindPrefix(cart, hgsEditPrefix); if (hel != NULL) { char *encSessionName = hel->name + strlen(hgsEditPrefix); char *sessionName = cgiDecodeClone(encSessionName); dyStringPrintf(dyMessage, "%s", doSessionDetail(userName, sessionName)); didSomething = TRUE; } hel = cartFindPrefix(cart, hgsLoadPrefix); if (hel != NULL) { char *encSessionName = hel->name + strlen(hgsLoadPrefix); char *sessionName = cgiDecodeClone(encSessionName); char wildStr[256]; safef(wildStr, sizeof(wildStr), "%s*", hgsLoadPrefix); dyStringPrintf(dyMessage, "Loaded settings from session <B>%s</B>. %s %s<BR>\n", htmlEncode(sessionName), getSessionLink(encUserName, encSessionName), getSessionEmailLink(encUserName, encSessionName)); cartLoadUserSession(conn, userName, sessionName, cart, NULL, wildStr); cartCopyLocalHubs(cart); hubConnectLoadHubs(cart); cartHideDefaultTracks(cart); cartCheckForCustomTracks(cart, dyMessage); didSomething = TRUE; } cartHelList = cartFindPrefix(cart, hgsDeletePrefix); for (hel = cartHelList; hel != NULL; hel = hel->next) { char *encSessionName = hel->name + strlen(hgsDeletePrefix); char *sessionName = cgiDecodeClone(encSessionName); sqlSafef(query, sizeof(query), "select shared from %s " "where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); int shared = sqlQuickNum(conn, query); if (shared >= 2) thumbnailRemove(encUserName, encSessionName, conn); sqlSafef(query, sizeof(query), "DELETE FROM %s " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); sqlUpdate(conn, query); dyStringPrintf(dyMessage, "Deleted session <B>%s</B>.<BR>\n", htmlEncode(sessionName)); didSomething = TRUE; } hDisconnectCentral(&conn); if (didSomething) return(dyStringCannibalize(&dyMessage)); else { dyStringFree(&dyMessage); return NULL; } } char *doOtherUser(char *actionVar) /* Load settings from another user's named session. * Return a message confirming what we did. */ { struct sqlConnection *conn = hConnectCentral(); struct dyString *dyMessage = dyStringNew(1024); char *otherUser = trimSpaces(cartString(cart, hgsOtherUserName)); char *sessionName = trimSpaces(cartString(cart, hgsOtherUserSessionName)); char *encOtherUser = cgiEncodeFull(otherUser); char *encSessionName = cgiEncodeFull(sessionName); dyStringPrintf(dyMessage, "Loaded settings from user <B>%s</B>'s session <B>%s</B>. %s %s", htmlEncode(otherUser), htmlEncode(sessionName), getSessionLink(encOtherUser, encSessionName), getSessionEmailLink(encOtherUser, encSessionName)); cartLoadUserSession(conn, otherUser, sessionName, cart, NULL, actionVar); cartCopyLocalHubs(cart); hubConnectLoadHubs(cart); cartHideDefaultTracks(cart); cartCheckForCustomTracks(cart, dyMessage); hDisconnectCentral(&conn); return dyStringCannibalize(&dyMessage); } void doSaveLocal() /* Output current settings to be saved as a file on the user's machine. * Return a message confirming what we did. */ { char *fileName = textOutSanitizeHttpFileName(cartString(cart, hgsSaveLocalFileName)); char *compressType = cartString(cart, hgsSaveLocalFileCompress); struct pipeline *compressPipe = textOutInit(fileName, compressType, NULL); cleanHgSessionFromCart(cart); cartDumpHgSession(cart); // First output the hubStatus id's for attached trackHubs outAttachedHubUrls(cart, NULL); // Now add all the default visibilities to output. outDefaultTracks(cart, NULL); textOutClose(&compressPipe, NULL); } char *doLoad(boolean fromUrl, char *actionVar) /* Load settings from a file or URL sent by the user. * Return a message confirming what we did. */ { struct dyString *dyMessage = dyStringNew(1024); struct lineFile *lf = NULL; webPushErrHandlersCartDb(cart, cartUsualString(cart, "db", NULL)); if (fromUrl) { char *url = trimSpaces(cartString(cart, hgsLoadUrlName)); if (isEmpty(url)) errAbort("Please go back and enter the URL (http://..., ftp://...) " "of a file that contains " "previously saved browser settings, and then click " "\"submit\" again."); if (!startsWith("http://",url) && !startsWith("https://",url) && !startsWith("ftp://",url)) errAbort("Unsupported protocol for loading a file via URL. Please use http, https, or ftp"); lf = netLineFileOpen(url); dyStringPrintf(dyMessage, "Loaded settings from URL %s . %s %s", htmlEncode(url), getUrlLink(url), getUrlEmailLink(url)); } else { char *filePlainContents = cartOptionalString(cart, hgsLoadLocalFileName); char *fileBinaryCoords = cartOptionalString(cart, hgsLoadLocalFileName "__binary"); char *fileName = cartOptionalString(cart, hgsLoadLocalFileName "__filename"); if (isNotEmpty(filePlainContents)) { char *settings = trimSpaces(filePlainContents); dyStringAppend(dyMessage, "Loaded settings from local file "); if (isNotEmpty(fileName)) dyStringPrintf(dyMessage, "<B>%s</B> ", fileName); dyStringPrintf(dyMessage, "(%lu bytes).", (unsigned long)strlen(settings)); lf = lineFileOnString("settingsFromFile", TRUE, cloneString(settings)); } else if (isNotEmpty(fileBinaryCoords)) { /* The cart holds the address and size of the uploaded bytes, but any * request can set that variable, so only use a block cheapcgi * handed out. */ unsigned long size = 0; char *mem = cgiMemBlobFind(fileBinaryCoords, &size); lf = (mem == NULL) ? NULL : lineFileDecompressMem(TRUE, mem, size); if (lf != NULL) { dyStringAppend(dyMessage, "Loaded settings from local file "); if (isNotEmpty(fileName)) dyStringPrintf(dyMessage, "<B>%s</B> ", fileName); dyStringPrintf(dyMessage, "(%lu bytes).", size); } else dyStringPrintf(dyMessage, "Sorry, I don't recognize the file type of " "<B>%s</B>. Please submit plain text or " "compressed text in one of the formats offered in " "<B>Save Settings</B>.", fileName); } else { dyStringAppend(dyMessage, "Sorry, your web browser seems to have " "posted no data"); if (isNotEmpty(fileName)) dyStringPrintf(dyMessage, ", only the filename <B>%s</B>", fileName); dyStringAppend(dyMessage, " (empty file?). Your settings have not been changed."); lf = NULL; } dyStringPrintf(dyMessage, " " "<A HREF=\"%shgTracks?%s=%s\">Browser</A>", hLocalHostCgiBinUrl(), cartSessionVarName(), cartSessionId(cart)); } if (lf != NULL) { lineFileCarefulNewlines(lf); struct dyString *dyLoadMessage = dyStringNew(0); boolean ok = cartLoadSettingsFromUserInput(lf, cart, NULL, actionVar, dyLoadMessage); lineFileClose(&lf); if (ok) { dyStringAppend(dyMessage, dyLoadMessage->string); cartCopyLocalHubs(cart); hubConnectLoadHubs(cart); cartHideDefaultTracks(cart); cartCheckForCustomTracks(cart, dyMessage); } else { dyStringClear(dyMessage); dyStringAppend(dyMessage, "<span style='color: red;'><b>" "Unable to load session: </b></span>"); dyStringAppend(dyMessage, dyLoadMessage->string); dyStringAppend(dyMessage, "The uploaded file needs to have been previously saved from the " "<b>Save Settings</b> section.\n"); // Looking for the words "custom track" in an error string is hokey, returning an enum // from cartLoadSettings would be better, but IMO that isn't worth a big refactoring. if (stringIn("custom track", dyLoadMessage->string)) { dyStringPrintf(dyMessage, "If you would like to upload a custom track, please use the " "<a href='%s?%s'>" "Custom Tracks</a> tool.\n", hgCustomName(), cartSidUrlString(cart)); } dyStringAppend(dyMessage, "If you feel you have reached this " "message in error, please contact the " "<A HREF=\"mailto:genome-www@soe.ucsc.edu?subject=Session file upload failed&" "body=Hello Genome Browser team,%0AMy session file failed to upload. " "The error message was:%0A"); dyStringAppend(dyMessage, cgiEncodeFull(dyLoadMessage->string)); dyStringAppend(dyMessage, "%0ACan you help me upload the data?\">" "UCSC Genome Browser team</A> for assistance.\n"); } dyStringFree(&dyLoadMessage); } return dyStringCannibalize(&dyMessage); } void renamePrefixedCartVar(char *prefix, char *oldName, char *newName) /* If cart has prefix+oldName, replace it with prefix+newName = submit. */ { char varName[256]; safef(varName, sizeof(varName), "%s%s", prefix, oldName); if (cartVarExists(cart, varName)) { cartRemove(cart, varName); safef(varName, sizeof(varName), "%s%s", prefix, newName); cartSetString(cart, varName, "submit"); } } char *doSessionChange(char *userName, char *oldSessionName) /* Process changes to session from session details page. */ { if (userName == NULL) return "Unable to make changes to session. Please log in again."; struct dyString *dyMessage = dyStringNew(1024); webPushErrHandlersCartDb(cart, cartUsualString(cart, "db", NULL)); char *sessionName = oldSessionName; char *encSessionName = cgiEncodeFull(sessionName); char *encOldSessionName = encSessionName; char *encUserName = cgiEncodeFull(userName); struct sqlConnection *conn = hConnectCentral(); struct sqlResult *sr = NULL; char **row = NULL; char query[512]; int shared = 1; char *settings = NULL; boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); if (gotSettings) sqlSafef(query, sizeof(query), "SELECT shared, settings from %s " "WHERE userName = '%s' AND sessionName = '%s'", namedSessionTable, encUserName, encSessionName); else sqlSafef(query, sizeof(query), "SELECT shared from %s " "WHERE userName = '%s' AND sessionName = '%s'", namedSessionTable, encUserName, encSessionName); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) { shared = atoi(row[0]); if (gotSettings) settings = cloneString(row[1]); sqlFreeResult(&sr); } else errAbort("doSessionChange: got no results from query:<BR>\n%s\n", query); char *newName = trimSpaces(cartOptionalString(cart, hgsNewSessionName)); if (isNotEmpty(newName) && !sameString(sessionName, newName)) { char *encNewName = cgiEncodeFull(newName); // In case the user has clicked to confirm that they want to overwrite an existing session, // delete the existing row before updating the row that will overwrite it. sqlSafef(query, sizeof(query), "delete from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encNewName); sqlUpdate(conn, query); sqlSafef(query, sizeof(query), "UPDATE %s set sessionName = '%s' WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encNewName, encUserName, encSessionName); sqlUpdate(conn, query); dyStringPrintf(dyMessage, "Changed session name from %s to <B>%s</B>.\n", sessionName, newName); sessionName = newName; encSessionName = encNewName; renamePrefixedCartVar(hgsEditPrefix , encOldSessionName, encNewName); renamePrefixedCartVar(hgsLoadPrefix , encOldSessionName, encNewName); renamePrefixedCartVar(hgsDeletePrefix , encOldSessionName, encNewName); renamePrefixedCartVar(hgsShowDownloadPrefix , encOldSessionName, encNewName); renamePrefixedCartVar(hgsMakeDownloadPrefix , encOldSessionName, encNewName); renamePrefixedCartVar(hgsDoDownloadPrefix , encOldSessionName, encNewName); if (shared >= 2) { thumbnailRemove(encUserName, encSessionName, conn); thumbnailAdd(encUserName, encNewName, conn, dyMessage); } } char sharedVarName[256]; char galleryVarName[256]; safef(sharedVarName, sizeof(sharedVarName), hgsSharePrefix "%s", encOldSessionName); safef(galleryVarName, sizeof(galleryVarName), hgsGalleryPrefix "%s", encOldSessionName); if (cgiBooleanDefined(sharedVarName) || cgiBooleanDefined(galleryVarName)) { int newShared = shared; if (cgiBooleanDefined(sharedVarName)) newShared = cartBoolean(cart, sharedVarName) ? 1 : 0; if (cgiBooleanDefined(galleryVarName)) newShared = cartBoolean(cart, galleryVarName) ? 2 : newShared; if (newShared != shared) { sqlSafef(query, sizeof(query), "UPDATE %s set shared = %d WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, newShared, encUserName, encSessionName); sqlUpdate(conn, query); dyStringPrintf(dyMessage, "Marked session <B>%s</B> as %s.<BR>\n", htmlEncode(sessionName), (newShared>0 ? newShared>=2 ? "shared in public listing" : "shared, but not in public listing" : "unshared")); if (shared >= 2 && newShared < 2) thumbnailRemove(encUserName, encSessionName, conn); if (shared < 2 && newShared >= 2) thumbnailAdd(encUserName, encSessionName, conn, dyMessage); } cartRemove(cart, sharedVarName); cartRemove(cart, galleryVarName); char shadowVarName[512]; safef(shadowVarName, sizeof(shadowVarName), "%s%s", cgiBooleanShadowPrefix(), sharedVarName); cartRemove(cart, shadowVarName); safef(shadowVarName, sizeof(shadowVarName), "%s%s", cgiBooleanShadowPrefix(), galleryVarName); cartRemove(cart, shadowVarName); } if (gotSettings) { struct hash *settingsHash = raFromString(settings); char *description = hashFindVal(settingsHash, "description"); char *newDescription = cartOptionalString(cart, hgsNewSessionDescription); if (newDescription != NULL) { // newline escaping of \n is needed for ra syntax. // not sure why \r and \ are being escaped, but it may be too late to change // since there are probably records in the database that way now. newDescription = replaceChars(newDescription, "\\", "\\\\"); newDescription = replaceChars(newDescription, "\r", "\\r"); newDescription = replaceChars(newDescription, "\n", "\\n"); } else newDescription = ""; if (description == NULL) description = ""; if (!sameString(description, newDescription)) { hashRemove(settingsHash, "description"); hashAdd(settingsHash, "description", newDescription); struct dyString *dyRa = dyStringNew(512); struct hashEl *hel = hashElListHash(settingsHash); while (hel != NULL) { dyStringPrintf(dyRa, "%s %s\n", hel->name, (char *)hel->val); hel = hel->next; } struct dyString *dyQuery = dyStringNew(1024); sqlDyStringPrintf(dyQuery, "UPDATE %s set settings = '%s' " "WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, dyRa->string, encUserName, encSessionName); sqlUpdate(conn, dyQuery->string); dyStringPrintf(dyMessage, "Updated description of <B>%s</B>.\n", sessionName); } } if (isEmpty(dyMessage->string)) dyStringPrintf(dyMessage, "No changes to session <B>%s</B>.\n", sessionName); dyStringPrintf(dyMessage, "%s %s", getSessionLink(encUserName, encSessionName), getSessionEmailLink(encUserName, encSessionName)); if (shared) printShareMessage(dyMessage, encUserName, encSessionName, FALSE); return dyStringCannibalize(&dyMessage); } static int getSharingLevel(struct sqlConnection *conn, char *encUserName, char *encSessionName) /* Return the value of 'shared' from the namedSessionDb row for user & session; * errAbort if there is no such session. (0 = not shared, 1 = shared by link, 2 = public session) */ { char query[2048]; sqlSafef(query, sizeof(query), "select shared from %s where userName='%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); char buf[256]; char *sharedStr = sqlQuickQuery(conn, query, buf, sizeof buf); if (sharedStr == NULL) errAbort("Unable to find session for userName='%s' and sessionName='%s'; no result from query '%s'", encUserName, encSessionName, query); return atoi(sharedStr); } char *doReSaveSession(char *userName, char *actionVar) /* Load a session (which may have old trash and customTrash references) and re-save it * so that customTrash tables will be moved to customData* databases and trash paths * will be replaced with userdata (hg.conf sessionDataDir) paths. * NOTE: this is not intended to be reachable by the UI; it is for a script to update * old sessions to use the new sessionData locations. */ { if (userName == NULL) return "Unable to re-save session -- please log in and try again."; struct sqlConnection *conn = hConnectCentral(); - char *sessionName = trimSpaces(cartString(cart, hgsNewSessionName)); + /* Clone: cartLoadUserSession() and saveCartAsSession() both free the cart's own copy. */ + char *sessionName = trimSpaces(cloneString(cartString(cart, hgsNewSessionName))); if (isEmpty(sessionName)) return "Error: Unable to save a session without a name. Please add one and try again."; char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); int sharingLevel = getSharingLevel(conn, encUserName, encSessionName); cartLoadUserSession(conn, userName, sessionName, cart, NULL, actionVar); // Don't cartCopyLocalHubs because we're not going to make any track collection changes hubConnectLoadHubs(cart); // Some old sessions reference databases that are no longer present, and that triggers an errAbort // when cartHideDefaultTracks calls hgTrackDb. Don't let that stop the process of updating other // stuff in the session. struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) cartHideDefaultTracks(cart); errCatchEnd(errCatch); if (errCatch->gotError) fprintf(stderr, "doReSaveSession: Error from cartHideDefaultTracks: '%s'; Continuing...", errCatch->message->string); errCatchFree(&errCatch); struct dyString *dyMessage = dyStringNew(1024); dyStringPrintf(dyMessage, "Re-saved settings from user <B>%s</B>'s session <B>%s</B> " "that %s be shared with others. %s %s", htmlEncode(userName), htmlEncode(sessionName), (sharingLevel ? "may" : "may not"), getSessionLink(encUserName, encSessionName), getSessionEmailLink(encUserName, encSessionName)); cartCheckForCustomTracks(cart, dyMessage); int useCount = saveCartAsSession(conn, encUserName, encSessionName, sharingLevel); if (useCount <= INITIAL_USE_COUNT) errAbort("Expected useCount of at least %d after re-saving session for " "userName='%s', sessionName='%s', but got %d", INITIAL_USE_COUNT+1, encUserName, encSessionName, useCount); hDisconnectCentral(&conn); return dyStringCannibalize(&dyMessage); } // ====================================== void prepBackGroundCall(char **pBackgroundProgress, char *cleanPrefix) /* fix cart and save state */ { *pBackgroundProgress = cloneString(cgiUsualString("backgroundProgress", NULL)); cartRemove(cart, "backgroundExec"); cartRemove(cart, "backgroundProgress"); cartRemovePrefix(cart, cleanPrefix); cartSaveState(cart); // in case it crashes } void launchForeAndBackGround(char *operation) /* update cart, launch background and foreground */ { char cmd[1024]; safef(cmd, sizeof cmd, "./hgSession backgroundExec=%s", operation); // allow child to see variables loaded from CGI. // because CGI settings have not been saved back to the cart yet cartSaveState(cart); char *workUrl = NULL; // automatically adds hgsid // automatically adds backGroundProgress=%s url.progress for separate channel // Have to pass the userName manually since background exec will not get cookie, // but we are no longer using userName which was needed with saved-sessions. startBackgroundWork(cmd, &workUrl); htmlOpen("Background Status"); jsInlineF( "setTimeout(function(){location = 'hgSession?backgroundStatus=%s&hgsid=%s';},2000);\n", cgiEncode(workUrl), cartSessionId(cart)); htmlClose(); fflush(stdout); } void passSubmittedBinaryAsTrashFile(struct hashEl *list) /* fetch the binary file submitted in memory, * and save it to temp trash location, * saving the name in the cart. * This is necessary to pass the file to the background process.*/ { // List should have these two // hgS_extractUpload_hub_9614_Anc11__binary // hgS_extractUpload_hub_9614_Anc11__filename // can have a third __filepath if crashes leaving in the cart. char *binaryParam = NULL; struct hashEl *hel = NULL; for (hel = list; hel; hel = hel->next) { if (endsWith(hel->name, "__binary")) binaryParam = cloneString(hel->name); } if (!binaryParam) { htmlOpen("No file selected"); printf("Please choose a saved session custom tracks local backup archive file (.tar.gz) to upload"); htmlClose(); exit(0); } char *binaryValue = cartOptionalString(cart, binaryParam); /* The cart holds the address and size of the uploaded bytes, but any request * can set that variable, so only use a block cheapcgi handed out. */ unsigned long size = 0; char *mem = cgiMemBlobFind(binaryValue, &size); if (mem == NULL) errAbort("The contents of the uploaded file are no longer available. " "Please choose the file again."); struct tempName tn; trashDirFile(&tn, "backGround", cartSessionId(cart), ".bin"); writeGulp(tn.forCgi, mem, size); // add new cart var with trash path // hgS_extractUpload_hub_9614_Anc11__filepath char *varName = replaceChars(binaryParam, "__binary", "__filepath"); cartRemove(cart, varName); // just in case cartSetString(cart, varName, tn.forCgi); // update the cart } /* --------------------------------------------------------------------------------------------- * Experimental client-rendered "Sessions" page (hgSession.js). * * An opt-in modern alternative to the classic server-rendered page, applying hgBlat's facelift * strategy (#37996): hgSession.c stays the data/action backend, emits the session list and page * config as an inline JSON global (hgSessionData) into an empty container, and hgSession.js builds * the UI. Gated exactly like hgBlat's blatNewForm/blatNewFormBanner: * - sessionNewPage (hg.conf bool, default off; also a cart var so a user's choice sticks * and the banner links can flip it) selects which UI is the default. * - sessionNewPageBanner (hg.conf bool, default = sessionNewPage) turns on the old<->new notes. * The inline table actions (delete/share/gallery/overwrite/describe) each POST to a small JSON * endpoint below that runs the same SQL the classic full-page handlers do, but returns JSON so the * table can update in place. Navigation actions (load, load from URL/file, save-local, backup, * reset) stay as ordinary form submits/links that hgSession.js builds against the existing actions. * --------------------------------------------------------------------------------------------- */ static boolean sessionNewPageActive() /* TRUE when the experimental client-rendered Sessions page should be shown. Cart variable * sessionNewPage (set by the banner links) wins, defaulting to the hg.conf flag of the same name. */ { return cartUsualBoolean(cart, "sessionNewPage", cfgOptionBooleanDefault("sessionNewPage", FALSE)); } static void printSessionNewPageBanner(boolean onNewPage) /* Emit the note that links between the classic and the experimental pages, so neither is a one-way * door. Shown wherever sessionNewPageBanner is on (defaulting to sessionNewPage), like hgBlat's * printNewFormBanner. On the new page gbModern.css supplies .gbBanner; the classic page does not * load it, so emit a small inline style there. */ { if (!cfgOptionBooleanDefault("sessionNewPageBanner", cfgOptionBooleanDefault("sessionNewPage", FALSE))) return; if (onNewPage) printf("<div class='gbBanner'>You are using the new experimental Sessions page. " "<a href='hgSession?sessionNewPage=0&%s=%s'>Return to the classic page</a>. " "If you have feedback, please let us know at " "<a href='mailto:genome@soe.ucsc.edu'>genome@soe.ucsc.edu</a>.</div>\n", cartSessionVarName(), cartSessionId(cart)); else { printf("<style>.gbBannerClassic{background:#fbf3e2;border:1px solid #d9bd82;padding:10px 14px;" "margin:12px 0;font-size:14px;}</style>\n"); printf("<div class='gbBannerClassic'>We are testing a new Sessions page, with a searchable, " "sortable table and one-click sharing. " "<a href='hgSession?sessionNewPage=1&%s=%s'>Try the new page</a>.</div>\n", cartSessionVarName(), cartSessionId(cart)); } } static char *sessionValFromContents(char *contents, char *var) /* Extract the value of var (e.g. "db" or "position") from a saved session's CGI-encoded cart * contents string, CGI-decoded, or NULL if not present. */ { if (isEmpty(contents)) return NULL; char pfx[64]; char *valIdx = NULL; safef(pfx, sizeof(pfx), "%s=", var); if (startsWith(pfx, contents)) valIdx = contents + strlen(pfx); else { char ampPfx[66]; safef(ampPfx, sizeof(ampPfx), "&%s", pfx); char *p = strstr(contents, ampPfx); if (p != NULL) valIdx = p + strlen(ampPfx); } if (valIdx == NULL) return NULL; char *valEnd = strchr(valIdx, '&'); char *enc = valEnd ? cloneStringZ(valIdx, valEnd - valIdx) : cloneString(valIdx); char *dec = cgiDecodeClone(enc); freez(&enc); return dec; } static int countShownTracks(struct cart *cart) /* Rough count of tracks turned on in the current cart: cart entries whose value is a display * visibility other than hide. A proxy for "tracks currently shown" for the save-summary line * (may over/undercount some composite subtracks); good enough for a hint. */ { int n = 0; struct hashEl *list = hashElListHash(cart->hash), *el; for (el = list; el != NULL; el = el->next) { char *v = (char *)el->val; if (v && (sameString(v, "dense") || sameString(v, "squish") || sameString(v, "pack") || sameString(v, "full") || sameString(v, "show"))) n++; } hashElFreeList(&list); return n; } static void sessionDataToJson(char *userName, struct jsonWrite *jw) /* Fill jw (an open object) with { config:{...}, sessions:[...] } for the experimental page. */ { boolean loggedIn = isNotEmpty(userName); boolean loginAvail = (loginSystemEnabled() || wikiLinkEnabled()); jsonWriteObjectStart(jw, "config"); jsonWriteBoolean(jw, "loggedIn", loggedIn); jsonWriteBoolean(jw, "loginAvail", loginAvail); if (loggedIn) jsonWriteString(jw, "userName", userName); jsonWriteString(jw, "hgsid", cartSessionId(cart)); jsonWriteString(jw, "cartVar", cartSessionVarName()); /* Current view being saved, for the save-summary line. Show the assembly accession, not the * internal "hub_<id>_<acc>" name, for assembly hubs (trackHubSkipHubName). */ char *db = cartUsualString(cart, "db", NULL); if (isNotEmpty(db)) jsonWriteString(jw, "db", trackHubSkipHubName(db)); char *pos = cartUsualString(cart, "position", NULL); if (isNotEmpty(pos)) jsonWriteString(jw, "position", pos); int trackCount = countShownTracks(cart); if (trackCount > 0) jsonWriteNumber(jw, "trackCount", trackCount); /* Login / account URLs so the JS can render a compact account line. */ if (loginAvail) { if (!loggedIn) jsonWriteString(jw, "loginUrl", wikiLinkUserLoginUrl(cartSessionId(cart))); else { jsonWriteString(jw, "logoutUrl", wikiLinkUserLogoutUrl(cartSessionId(cart))); if (!loginUseBasicAuth()) jsonWriteString(jw, "changePasswordUrl", wikiLinkChangePasswordUrl(cartSessionId(cart))); } jsonWriteString(jw, "signupUrl", wikiLinkUserSignupUrl(cartSessionId(cart))); } jsonWriteStringf(jw, "classicUrl", "hgSession?sessionNewPage=0&%s=%s", cartSessionVarName(), cartSessionId(cart)); jsonWriteString(jw, "helpUrl", "../goldenPath/help/hgSessionHelp.html"); jsonWriteString(jw, "galleryUrl", "../goldenPath/help/sessions.html"); jsonWriteStringf(jw, "publicSessionsUrl", "../cgi-bin/hgPublicSessions?%s", cartSidUrlString(cart)); /* Reset-to-defaults link, same as showCartLinks(). */ char returnAddress[512]; safef(returnAddress, sizeof(returnAddress), "%s?%s", hgSessionName(), cartSidUrlString(cart)); jsonWriteStringf(jw, "resetUrl", "../cgi-bin/cartReset?%s&destination=%s", cartSidUrlString(cart), cgiEncodeFull(returnAddress)); jsonWriteObjectEnd(jw); // config perfTimerStep(hgSessionTiming, "page header + config"); jsonWriteListStart(jw, "sessions"); if (loggedIn) { struct sqlConnection *conn = hConnectCentral(); if (sqlTableExists(conn, namedSessionTable)) { char *encUserName = cgiEncodeFull(userName); boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); char query[512]; if (gotSettings) sqlSafef(query, sizeof(query), "SELECT sessionName, shared, firstUse, useCount, contents, settings, lastUse FROM %s " "WHERE userName = '%s' ORDER BY sessionName;", namedSessionTable, encUserName); else sqlSafef(query, sizeof(query), "SELECT sessionName, shared, firstUse, useCount, contents, lastUse FROM %s " "WHERE userName = '%s' ORDER BY sessionName;", namedSessionTable, encUserName); struct sqlResult *sr = sqlGetResult(conn, query); perfTimerStep(hgSessionTiming, "load sessions from MySQL"); char **row; /* Cache one connection per assembly db so the per-session band/locus lookups don't * re-open a connection for every row when many sessions share an assembly. */ struct hash *dbConnCache = hashNew(0); while ((row = sqlNextRow(sr)) != NULL) { char *encSessionName = row[0]; char *sessionName = cgiDecodeClone(encSessionName); int shared = atoi(row[1]); char *firstUse = cloneString(row[2]); struct tm firstUseTm; ZeroVar(&firstUseTm); strptime(firstUse, "%Y-%m-%d %T", &firstUseTm); long epoch = (long)mktime(&firstUseTm); /* created = date only for display; createdFull = date+minute for the hover. */ char *dateOnly = cloneString(firstUse); char *spacePt = strchr(dateOnly, ' '); if (spacePt != NULL) *spacePt = '\0'; char *createdFull = cloneString(firstUse); if (strlen(createdFull) == 19) createdFull[16] = '\0'; char *db2 = sessionValFromContents(row[4], "db"); char *pos2 = sessionValFromContents(row[4], "position"); char *description = gotSettings ? getSetting(row[5], "description") : NULL; /* lastUse (last time the session was saved/overwritten/loaded) drives the "most * recently saved session" quick-update shortcut on the client. */ char *lastUse = cloneString(row[gotSettings ? 6 : 5]); struct tm lastUseTm; ZeroVar(&lastUseTm); strptime(lastUse, "%Y-%m-%d %T", &lastUseTm); long lastUseEpoch = (long)mktime(&lastUseTm); char *lastUseDate = cloneString(lastUse); /* date only for display */ char *sp2 = strchr(lastUseDate, ' '); if (sp2 != NULL) *sp2 = '\0'; /* Trim the seconds off the full value shown on hover: "...10:29:25" -> "...10:29". */ if (strlen(lastUse) == 19) lastUse[16] = '\0'; /* Band (from cytoBand) and locus (from locusName) for the saved position, looked up in * the session's own assembly. Skips hub assemblies and missing tables. For a very * large region there are too many genes to name, so say so instead. */ char *band = NULL, *locus = NULL; if (isNotEmpty(db2) && isNotEmpty(pos2) && !trackHubDatabase(db2)) { char *posClone = cloneString(pos2); stripChar(posClone, ','); char *colon = strrchr(posClone, ':'); char *chrom = NULL; int start = 0, end = 0; boolean parsed = FALSE; if (colon != NULL) { *colon = '\0'; chrom = posClone; char *dash = strchr(colon + 1, '-'); if (dash != NULL) { *dash = '\0'; start = atoi(colon + 1) - 1; /* display is 1-based; tables are 0-based */ if (start < 0) start = 0; end = atoi(dash + 1); parsed = (end > start); } } if (parsed) { struct sqlConnection *dbConn = hashFindVal(dbConnCache, db2); if (dbConn == NULL && sqlDatabaseExists(db2)) { dbConn = hAllocConn(db2); hashAdd(dbConnCache, db2, dbConn); } if (dbConn != NULL) { if (sqlTableExists(dbConn, "cytoBand")) { char bandBuf[HDB_MAX_BAND_STRING]; if (hChromBandConn(dbConn, chrom, start, bandBuf) && bandBuf[0]) band = cloneString(bandBuf); } if ((end - start) > 10000000) locus = cloneString("Too large for the genes"); else locus = hLocusName(dbConn, chrom, start, end); } } freez(&posClone); } struct dyString *dyUrl = dyStringNew(0); addSessionLink(dyUrl, encUserName, encSessionName, FALSE, TRUE); jsonWriteObjectStart(jw, NULL); jsonWriteString(jw, "name", sessionName); jsonWriteString(jw, "encName", encSessionName); jsonWriteNumber(jw, "shared", shared); jsonWriteString(jw, "created", dateOnly); jsonWriteString(jw, "createdFull", createdFull); jsonWriteNumber(jw, "createdEpoch", epoch); jsonWriteString(jw, "lastUse", lastUse); jsonWriteString(jw, "lastUseDate", lastUseDate); jsonWriteNumber(jw, "lastUseEpoch", lastUseEpoch); jsonWriteNumber(jw, "useCount", atoll(row[3])); if (isNotEmpty(db2)) jsonWriteString(jw, "db", trackHubSkipHubName(db2)); if (isNotEmpty(pos2)) jsonWriteString(jw, "position", pos2); if (isNotEmpty(band)) jsonWriteString(jw, "band", band); if (isNotEmpty(locus)) jsonWriteString(jw, "locus", locus); if (isNotEmpty(description)) jsonWriteString(jw, "description", description); jsonWriteString(jw, "shareUrl", dyUrl->string); jsonWriteObjectEnd(jw); dyStringFree(&dyUrl); freez(&band); freez(&locus); freez(&firstUse); freez(&dateOnly); freez(&createdFull); freez(&lastUse); freez(&lastUseDate); freez(&sessionName); } sqlFreeResult(&sr); perfTimerStep(hgSessionTiming, "annotate positions (band + locus) + build JSON"); /* Release the cached per-assembly connections. */ struct hashEl *hel, *helList = hashElListHash(dbConnCache); for (hel = helList; hel != NULL; hel = hel->next) { struct sqlConnection *dbConn = hel->val; hFreeConn(&dbConn); } hashElFreeList(&helList); hashFree(&dbConnCache); } hDisconnectCentral(&conn); } jsonWriteListEnd(jw); // sessions } void doMainPageNew(char *userName, char *message) /* Render the experimental client-rendered Sessions page: framework header (gold "My Sessions" * band), the experimental banner, an empty #sessionApp container, and the hgSessionData JSON that * hgSession.js reads to build the UI. */ { if (isNotEmpty(cartOptionalString(cart, "measureTiming"))) hgSessionTiming = perfTimerNew(); /* times the page; emitted as hgSessionData.timing */ cspWriteResponseHeader(); puts("Content-Type:text/html\n"); cartWebStart(cart, NULL, "My Sessions"); jsInit(); jsIncludeDataTablesLibs(); webIncludeResourceFile("gbModern.css"); webIncludeResourceFile("hgSession.css"); jsIncludeFile("hgSession.js", NULL); printSessionNewPageBanner(TRUE); if (isNotEmpty(message)) printf("<div class='gbBanner'>%s</div>\n", message); printf("<div id='sessionApp' class='gbApp'></div>\n"); struct jsonWrite *jw = jsonWriteNew(); jsonWriteObjectStart(jw, NULL); sessionDataToJson(userName, jw); /* When &measureTiming is set, hand the per-phase timings to hgSession.js (it shows them in a * dialog). Emitted at the top level as hgSessionData.timing. */ perfTimerJson(hgSessionTiming, jw, "timing"); jsonWriteObjectEnd(jw); jsInlineF("var hgSessionData = %s;\n", jw->dy->string); jsonWriteFree(&jw); perfTimerFree(&hgSessionTiming); cartWebEnd(); } /* ---- JSON action endpoints for the experimental page's inline table actions ---- */ static void saveSessionJsonOk(struct sqlConnection *conn, char *extraFields) /* Emit {"success": true[, <extraFields>]} and disconnect. extraFields (may be NULL) is inserted * verbatim after "success": true, e.g. ", \"shared\": 2". */ { puts("Content-Type:application/json\n"); printf("{\"success\": true%s}\n", extraFields ? extraFields : ""); hDisconnectCentral(&conn); } void doDeleteSessionJson(char *userName) /* AJAX: delete the session named by hgsOldSessionName under the current user. */ { struct sqlConnection *conn = hConnectCentral(); char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in and try again."); return; } if (isEmpty(sessionName)) { saveSessionJsonError(conn, "No session was specified."); return; } char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); char query[512]; sqlSafef(query, sizeof(query), "select shared from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); int shared = sqlQuickNum(conn, query); if (shared >= 2) thumbnailRemove(encUserName, encSessionName, conn); sqlSafef(query, sizeof(query), "DELETE FROM %s WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, encUserName, encSessionName); sqlUpdate(conn, query); saveSessionJsonOk(conn, NULL); } void doShareSessionJson(char *userName) /* AJAX: set the "shared by link" flag (0<->1) on hgsOldSessionName. Desired state in * hgsNewSessionShare (0/1). Does not touch the gallery (shared==2) except to unshare. */ { struct sqlConnection *conn = hConnectCentral(); char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); int desired = cgiUsualInt(hgsNewSessionShare, 0); cartRemove(cart, hgsNewSessionShare); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in and try again."); return; } if (isEmpty(sessionName)) { saveSessionJsonError(conn, "No session was specified."); return; } char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); char query[512]; sqlSafef(query, sizeof(query), "select shared from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); int shared = sqlQuickNum(conn, query); int newShared = desired ? 1 : 0; sqlSafef(query, sizeof(query), "UPDATE %s SET shared = %d WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, newShared, encUserName, encSessionName); sqlUpdate(conn, query); sessionTouchLastUse(conn, encUserName, encSessionName); if (newShared == 0 && shared >= 2) thumbnailRemove(encUserName, encSessionName, conn); char extra[32]; safef(extra, sizeof(extra), ", \"shared\": %d", newShared); saveSessionJsonOk(conn, extra); } void doGallerySessionJson(char *userName) /* AJAX: add/remove hgsOldSessionName to/from the public gallery (shared 2<->1). Desired state in * hgsNewSessionShare (0/1). Adding requires a non-empty description, like the classic page. */ { struct sqlConnection *conn = hConnectCentral(); char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); int desired = cgiUsualInt(hgsNewSessionShare, 0); cartRemove(cart, hgsNewSessionShare); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in and try again."); return; } if (isEmpty(sessionName)) { saveSessionJsonError(conn, "No session was specified."); return; } char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); char query[512]; if (desired) { if (!gotSettings) { saveSessionJsonError(conn, "This server does not support the public listing."); return; } sqlSafef(query, sizeof(query), "select settings from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); char *settings = sqlQuickString(conn, query); char *description = getSetting(settings, "description"); if (isEmpty(description)) { saveSessionJsonError(conn, "Please add a description (with the Edit button) before posting " "this session to the public listing."); return; } } sqlSafef(query, sizeof(query), "select shared from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); int shared = sqlQuickNum(conn, query); int newShared = desired ? 2 : 1; sqlSafef(query, sizeof(query), "UPDATE %s SET shared = %d WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, newShared, encUserName, encSessionName); sqlUpdate(conn, query); sessionTouchLastUse(conn, encUserName, encSessionName); struct dyString *dyMsg = dyStringNew(256); if (desired && shared < 2) thumbnailAdd(encUserName, encSessionName, conn, dyMsg); if (!desired && shared >= 2) thumbnailRemove(encUserName, encSessionName, conn); dyStringFree(&dyMsg); char extra[32]; safef(extra, sizeof(extra), ", \"shared\": %d", newShared); saveSessionJsonOk(conn, extra); } void doOverwriteSessionJson(char *userName) /* AJAX: re-save the current cart over an existing session (hgsOldSessionName), preserving its * sharing level. Returns the refreshed created date, view count and assembly. */ { struct sqlConnection *conn = hConnectCentral(); char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in and try again."); return; } if (isEmpty(sessionName)) { saveSessionJsonError(conn, "No session was specified."); return; } if (!sqlTableExists(conn, namedSessionTable)) { saveSessionJsonError(conn, "Required session table does not exist."); return; } char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); char query[1024]; sqlSafef(query, sizeof(query), "select count(*) from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); if (sqlQuickNum(conn, query) == 0) { saveSessionJsonError(conn, "Could not find that session to overwrite."); return; } sqlSafef(query, sizeof(query), "select shared from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); int shared = sqlQuickNum(conn, query); int useCount = saveCartAsSession(conn, encUserName, encSessionName, shared); /* Report the refreshed values so the table row can update in place. */ boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); (void)gotSettings; sqlSafef(query, sizeof(query), "select firstUse, contents from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); struct sqlResult *sr = sqlGetResult(conn, query); char **row = sqlNextRow(sr); char *dateOnly = NULL, *db2 = NULL; if (row != NULL) { dateOnly = cloneString(row[0]); char *spacePt = strchr(dateOnly, ' '); if (spacePt != NULL) *spacePt = '\0'; db2 = sessionValFromContents(row[1], "db"); } sqlFreeResult(&sr); struct dyString *extra = dyStringNew(256); dyStringPrintf(extra, ", \"useCount\": %d", useCount); if (isNotEmpty(dateOnly)) dyStringPrintf(extra, ", \"created\": \"%s\"", jsonStringEscape(dateOnly)); if (isNotEmpty(db2)) dyStringPrintf(extra, ", \"db\": \"%s\"", jsonStringEscape(db2)); saveSessionJsonOk(conn, extra->string); dyStringFree(&extra); } void doDescribeSessionJson(char *userName) /* AJAX: set the description in the settings ra of hgsOldSessionName (from hgsNewSessionDescription). * Mirrors the description-editing branch of doSessionChange. */ { struct sqlConnection *conn = hConnectCentral(); char *sessionName = trimSpaces(cloneString(cgiUsualString(hgsOldSessionName, ""))); char *newDescription = cloneString(cgiUsualString(hgsNewSessionDescription, "")); cartRemove(cart, hgsNewSessionDescription); if (isEmpty(userName)) { saveSessionJsonError(conn, "Please log in and try again."); return; } if (isEmpty(sessionName)) { saveSessionJsonError(conn, "No session was specified."); return; } boolean gotSettings = (sqlFieldIndex(conn, namedSessionTable, "settings") >= 0); if (!gotSettings) { saveSessionJsonError(conn, "This server does not support session descriptions."); return; } char *encUserName = cgiEncodeFull(userName); char *encSessionName = cgiEncodeFull(sessionName); char query[512]; sqlSafef(query, sizeof(query), "select settings from %s where userName = '%s' and sessionName = '%s';", namedSessionTable, encUserName, encSessionName); char *settings = sqlQuickString(conn, query); struct hash *settingsHash = raFromString(isEmpty(settings) ? "" : settings); /* ra syntax needs \n / \r / backslash escaped (kept compatible with doSessionChange). */ newDescription = replaceChars(newDescription, "\\", "\\\\"); newDescription = replaceChars(newDescription, "\r", "\\r"); newDescription = replaceChars(newDescription, "\n", "\\n"); hashRemove(settingsHash, "description"); hashAdd(settingsHash, "description", newDescription); struct dyString *dyRa = dyStringNew(512); struct hashEl *hel = hashElListHash(settingsHash); while (hel != NULL) { dyStringPrintf(dyRa, "%s %s\n", hel->name, (char *)hel->val); hel = hel->next; } struct dyString *dyQuery = dyStringNew(1024); sqlDyStringPrintf(dyQuery, "UPDATE %s set settings = '%s' WHERE userName = '%s' AND sessionName = '%s';", namedSessionTable, dyRa->string, encUserName, encSessionName); sqlUpdate(conn, dyQuery->string); dyStringFree(&dyQuery); dyStringFree(&dyRa); saveSessionJsonOk(conn, NULL); } void hgSession() /* hgSession - Interface with wiki login and do session saving/loading. * Here we set up cart and some global variables, dispatch the command, * and put away the cart when it is done. */ { struct hash *oldVars = hashNew(10); /* Sometimes we output HTML and sometimes plain text; let each outputter * take care of headers instead of using a fixed cart*Shell(). */ cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars); char *userName = (loginSystemEnabled() || wikiLinkEnabled()) ? wikiLinkUserName() : NULL; char *backgroundStatus = cloneString(cartUsualString(cart, "backgroundStatus", NULL)); if (backgroundStatus) { // clear backgroundStatus from the cart cartRemove(cart, "backgroundStatus"); /* Save cart variables. */ cartSaveState(cart); getBackgroundStatus(backgroundStatus); exit(0); } char *backgroundExec = cloneString(cgiUsualString("backgroundExec", NULL)); struct hashEl *showDownloadList = cartFindPrefix(cart, hgsShowDownloadPrefix); struct hashEl *makeDownloadList = cartFindPrefix(cart, hgsMakeDownloadPrefix); struct hashEl *doDownloadList = cartFindPrefix(cart, hgsDoDownloadPrefix); if (showDownloadList) showDownloadSessionCtData(showDownloadList); else if (makeDownloadList) { if (sameOk(backgroundExec,"makeDownloadSessionCtData")) { // only one, not a list. struct hashEl *hel = makeDownloadList; char *param1 = cloneString(hel->name); char *backgroundProgress = NULL; prepBackGroundCall(&backgroundProgress, hgsMakeDownloadPrefix); makeDownloadSessionCtData(param1, backgroundProgress); exit(0); // cannot return } else { launchForeAndBackGround("makeDownloadSessionCtData"); exit(0); } } else if (doDownloadList) doDownloadSessionCtData(doDownloadList); else if (cartVarExists(cart, hgsDoMainPage) || cartVarExists(cart, hgsCancel)) doMainPage(userName, NULL); else if (cartVarExists(cart, hgsDoNewSession)) { char *message = doNewSession(userName); doMainPage(userName, message); } +else if (cartVarExists(cart, hgsDoAnonName)) + { + doAnonNameJson(); + } else if (cartVarExists(cart, hgsDoSaveSessionJson)) { doSaveSessionJson(userName); } else if (cartVarExists(cart, hgsDoRenameSessionJson)) { doRenameSessionJson(userName); } else if (cartVarExists(cart, hgsDoDeleteJson)) { doDeleteSessionJson(userName); } else if (cartVarExists(cart, hgsDoShareJson)) { doShareSessionJson(userName); } else if (cartVarExists(cart, hgsDoGalleryJson)) { doGallerySessionJson(userName); } else if (cartVarExists(cart, hgsDoOverwriteJson)) { doOverwriteSessionJson(userName); } else if (cartVarExists(cart, hgsDoDescribeJson)) { doDescribeSessionJson(userName); } else if (cartVarExists(cart, hgsDoOtherUser)) { char *message = doOtherUser(hgsDoOtherUser); doMainPage(userName, message); } else if (cartVarExists(cart, hgsDoSaveLocal)) { doSaveLocal(); } else if (cartVarExists(cart, hgsDoLoadLocal)) { char *message = doLoad(FALSE, hgsDoLoadLocal); doMainPage(userName, message); } else if (cartVarExists(cart, hgsDoLoadUrl)) { char *message = doLoad(TRUE, hgsDoLoadUrl); doMainPage(userName, message); } else if (cartVarExists(cart, hgsDoSessionDetail)) { char *message = doSessionDetail(userName, cartString(cart, hgsDoSessionDetail)); doMainPage(userName, message); } else if (cartVarExists(cart, hgsDoSessionChange)) { char *message = doSessionChange(userName, cartString(cart, hgsOldSessionName)); doMainPage(userName, message); } else if (cartVarExists(cart, hgsOldSessionName)) { char *message1 = doSessionChange(userName, cartString(cart, hgsOldSessionName)); char *message2 = doUpdateSessions(userName); char *message = message2; if (!startsWith("No changes to session", message1)) { size_t len = (sizeof message1[0]) * (strlen(message1) + strlen(message2) + 1); message = needMem(len); safef(message, len, "%s%s", message1, message2); } doMainPage(userName, message); } else if (cartVarExists(cart, hgsDoReSaveSession)) { char *message = doReSaveSession(userName, hgsDoReSaveSession); printf("\n%s\n\n", message); } else { char *message = doUpdateSessions(userName); doMainPage(userName, message); } cleanHgSessionFromCart(cart); /* Save the cart state: */ cartCheckout(&cart); } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); htmlPushEarlyHandlers(); cgiSpoof(&argc, argv); hgSession(); cgiExitTime("hgSession", enteredMainTime); return 0; }