d3b3e61da56f4a9ea90e627e49cdddf73785a597 angie Wed Jul 17 13:12:23 2013 -0700 hgVai's disclaimer note was obscuring the submit button, so I changed itto a dialog box that requires the user to agree before it will submit the query. Then it remembers in the cart that the user clicked agree, so they don't have to click a dialog box before every query. refs #6152 diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c index 510cee6..779f794 100644 --- src/hg/hgVai/hgVai.c +++ src/hg/hgVai/hgVai.c @@ -27,31 +27,31 @@ #include "libifyMe.h" /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */ char *genome = NULL; /* Name of genome - mouse, human, etc. */ char *database = NULL; /* Current genome database - hg17, mm5, etc. */ char *regionType = NULL; /* genome, ENCODE pilot regions, or specific position range. */ struct grp *fullGroupList = NULL; /* List of all groups. */ struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */ static struct pipeline *compressPipeline = (struct pipeline *)NULL; // Null terminated list of CGI Variables we don't want to save permanently: -char *excludeVars[] = {"Submit", "submit", NULL,}; +char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", NULL,}; #define hgvaRange "position" #define hgvaRegionType "hgva_regionType" #define hgvaRegionTypeEncode "encode" #define hgvaRegionTypeGenome "genome" #define hgvaRegionTypeRange "range" #define hgvaPositionContainer "positionContainer" void addSomeCss() /*#*** This should go in a .css file of course. */ { printf("<style>\n" "div.sectionLite { border-width: 1px; border-color: #"HG_COL_BORDER"; border-style: solid;" " background-color: #"HG_COL_INSIDE"; padding-left: 10px; padding-right: 10px; " " padding-top: 8px; padding-bottom: 5px; margin-top: 5px; margin-bottom: 5px }\n" @@ -688,31 +688,31 @@ puts("<BR>"); endCollapsibleSection(); } void selectFiltersCons() /* Options to restrict output based on overlap with conserved elements. */ { struct slRef *elTrackRefList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isConsElTrack, NULL, NULL, &elTrackRefList); if (elTrackRefList == NULL) return; startCollapsibleSection("filtersCons", "Conservation", FALSE); // Use a little table to indent radio buttons (if we do those) past checkbox: puts("<TABLE><TR><TD>"); cartMakeCheckBox(cart, "hgva_require_consEl", FALSE); -printf("</TD><TD>Include only the variants that overlap"); +printf("</TD><TD>Include only the variants that overlap:"); if (slCount(elTrackRefList) == 1) { struct trackDb *tdb = elTrackRefList->val; printf(" %s<BR>\n", tdb->longLabel); cgiMakeHiddenVar("hgva_require_consEl_track", tdb->track); puts("</TD></TR></TABLE>"); } else { puts("</TD></TR>"); char *selected = cartUsualString(cart, "hgva_require_consEl_track", ""); struct slRef *ref; for (ref = elTrackRefList; ref != NULL; ref = ref->next) { printf("<TR><TD></TD><TD>"); @@ -756,76 +756,73 @@ printf("<B>output file:</B> "); cgiMakeTextVar("hgva_outFile", fileName, 29); printf(" (leave blank to keep output in browser)<BR>\n"); printf("<B>file type returned: </B>"); cgiMakeRadioButton("hgva_compressType", textOutCompressNone, sameWord(textOutCompressNone, compressType)); printf(" plain text  "); cgiMakeRadioButton("hgva_compressType", textOutCompressGzip, sameWord(textOutCompressGzip, compressType)); printf(" gzip compressed (ignored if output file is blank)"); puts("<BR>"); } void submitAndDisclaimer() { -puts("<BR>"); -puts("<div class='warn-note' style='border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;'>"); -puts("<p><span style='font-weight: bold; color: #c70000;'>NOTE:</span><br>"); -if (hIsPrivateHost()) - puts("<span style='font-weight: bold; color: #c70000;'>THIS IS UNTESTED SOFTWARE. " - "We are still working out the bugs. Feel free to play with this and tell us " - "about the bugs, but treat results with extra skepticism.</span><br>"); +puts("<div id=disclaimerDialog title='NOTE'>"); puts("This tool is for research use only. While this tool is open to the " "public, users seeking information about a personal medical or genetic " "condition are urged to consult with a qualified physician for " "diagnosis and for answers to personal questions."); -puts("</p></div><BR>"); -printf(" <img id='loadingImg' src='../images/loading.gif' />\n"); -printf("<span id='loadingMsg'></span>\n"); -cgiMakeButtonWithOnClick("startQuery", "Go!", - "get the results of your query", - "loadingImage.run(); return true;"); +puts("</div><BR>"); +printf("<div><img id='loadingImg' src='../images/loading.gif' />\n"); +printf("<span id='loadingMsg'></span></div>\n"); +cgiMakeOnClickButton("hgva.submitQueryIfDisclaimerAgreed();", "Get results"); +puts("<BR><BR>"); } /* * When user clicks submit, we need to roll a JSON querySpec from form selections, * and show data from a submission to hgAnnoGrator. redirect from this CGI? * or have javascript submit directly? * * primary: variants, from custom track * * if there are genes, those w/annoGratorGpVar * * if there are {dbSNP, dbNsfp, regulatory, cons} selections, grator for each of those * * vep output config * * If we get bold & offer 1000Genomes VCF, will def. need handling of split chroms. * Are we really going to offer genome-wide in hgVai? * Up-front limit on #rows of input ? * * Eventually, we might want a FormatVep that produces structs that are passed * forward to multiple output writers... I would want to send it lots of gratorData * like a formatter, but it would produce rows like an annoGrator. * Maybe annoGrators should accept a bunch of input rows like formatters? * or would this grator wrap all the input grators inside? */ void doMainPage() /* Print out initial HTML of control page. */ { jsInit(); jsIncludeFile("jquery-ui.js", NULL); webIncludeResourceFile("jquery-ui.css"); jsIncludeFile("hgVarAnnogrator.js", NULL); +boolean alreadyAgreed = cartUsualBoolean(cart, "hgva_agreedToDisclaimer", FALSE); +printf("<script>\n" + "$(document).ready(function() { hgva.disclaimer.init(%s, hgva.userClickedAgree); });\n" + "</script>\n", alreadyAgreed ? "true" : "false"); addSomeCss(); printAssemblySection(); /* Check for variant custom tracks. If there are none, tell user they need to * upload at least one. */ struct slRef *varTrackList = NULL, *varGroupList = NULL; tdbFilterGroupTrack(fullTrackList, fullGroupList, isVariantCustomTrack, NULL, &varGroupList, &varTrackList); if (varTrackList == NULL) { askUserForVariantCustomTrack(); } else { @@ -1236,31 +1233,31 @@ else textOutClose(&compressPipeline); } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); if (hIsPrivateHost()) pushCarefulMemHandler(LIMIT_2or6GB); htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ cgiSpoof(&argc, argv); oldVars = hashNew(10); setUdcCacheDir(); -boolean startQuery = (cgiUsualString("startQuery", NULL) != NULL); +boolean startQuery = (cgiUsualString("hgva_startQuery", NULL) != NULL); if (startQuery) cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars); else cart = cartAndCookie(hUserCookie(), excludeVars, oldVars); /* Set up global variables. */ getDbAndGenome(cart, &database, &genome, oldVars); if (trackHubDatabase(database)) errAbort("Assembly Data Hubs not yet supported by the Variant Annotaion Integrator"); regionType = cartUsualString(cart, hgvaRegionType, hgvaRegionTypeGenome); if (isEmpty(cartOptionalString(cart, hgvaRange))) cartSetString(cart, hgvaRange, hDefaultPos(database)); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout)