e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/hgc/variomeClick.c src/hg/hgc/variomeClick.c index e84c7a2..d370e0c 100644 --- src/hg/hgc/variomeClick.c +++ src/hg/hgc/variomeClick.c @@ -1,444 +1,447 @@ /* Do clicks for the wiki track of variation for microattribution reviews */ +/* Copyright (C) 2010 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #include "common.h" #include "cart.h" #include "cheapcgi.h" #include "web.h" #include "hPrint.h" #include "obscure.h" #include "hgConfig.h" #include "hgc.h" #include "hCommon.h" #include "hgColors.h" #include "binRange.h" #include "web.h" #include "net.h" #include "grp.h" #include "hui.h" #include "htmlPage.h" #include "htmshell.h" #include "bedDetail.h" #include "wikiLink.h" #include "wikiTrack.h" #include "variome.h" void displayVariomeItem (struct variome *item, char *userName); static void startForm(char *name, char *actionType) { hPrintf("<FORM ID=\"%s\" NAME=\"%s\" ACTION=\"%s\">\n\n", name, name, hgcName()); cartSaveSession(cart); /* put actionType in place of table name */ cgiMakeHiddenVar("g", actionType); cgiContinueHiddenVar("c"); cgiContinueHiddenVar("o"); hPrintf("\n"); cgiContinueHiddenVar("l"); cgiContinueHiddenVar("r"); hPrintf("\n"); } void doVariome (char *wikiItemId, char *chrom, int winStart, int winEnd) /* handle item clicks on variome - may create new items */ { char *userName = NULL; if (wikiTrackEnabled(database, &userName) && sameWord("0", wikiItemId)) { cartWebStart(cart, database, "%s", "Variome track: Create new item"); if (NULL == userName) { offerLogin(0, "add new items to", "variome"); cartHtmlEnd(); return; } if (emailVerified(TRUE)) /* prints message when not verified */ { // outputJavaScript(); startForm("createItem", "variome.create"); /* passes hidden params */ webPrintLinkTableStart(); /* first row is a title line */ char label[256]; safef(label, ArraySize(label), "Create new item, owner: '%s'\n", userName); webPrintWideLabelCell(label, 2); webPrintLinkTableNewRow(); /* second row is classification pull-down menu */ //webPrintWideCellStart(2, HG_COL_TABLE); //puts("<B>classification: </B>"); //cgiMakeDropList(NEW_ITEM_CLASS, variomeClassList, variomeClassCnt, //cartUsualString(cart,NEW_ITEM_CLASS,ITEM_NOT_CLASSIFIED)); //cgiMakeDropList("variome.loc", gvLocationDbValue, gvLocationSize, //cartUsualString(cart, "variome.loc", //"not within known transcription unit")); //cgiMakeDropList("variome.coor", variomeCoorList, 2, //cartUsualString(cart, "variome.coor", "exact coordinates")); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); /* third row is position entry box */ webPrintWideCellStart(2, HG_COL_TABLE); puts("<B>position: </B>"); savePosInTextBox(seqName, winStart+1, winEnd); hPrintf(" (size: "); printLongWithCommas(stdout, (long long)(winEnd - winStart)); hPrintf(")"); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); /* fourth row is strand selection radio box */ webPrintWideCellStart(2, HG_COL_TABLE); char *strand = cartUsualString(cart, NEW_ITEM_STRAND, "plus"); boolean plusStrand = sameWord("plus",strand) ? TRUE : FALSE; hPrintf("<B>strand: "); cgiMakeRadioButton(NEW_ITEM_STRAND, "plus", plusStrand); hPrintf(" + "); cgiMakeRadioButton(NEW_ITEM_STRAND, "minus", ! plusStrand); hPrintf(" -</B>"); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); /* fifth row is item name text entry */ webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>item name (<A HREF=\"http://www.hgvs.org/mutnomen/\" TARGET=\"_BLANK\">HGVS mutation nomenclature</A>): </B>"); cgiMakeTextVar("i", "required", 25); webPrintLinkCellEnd(); /* add more fields to encourage consistancy but put together in comment before adding to wiki */ webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B><A HREF=\"http://www.researcherid.com/\" TARGET=\"_BLANK\">Researcher ID</A></B> "); cgiMakeTextVar("variome.rid", "required", 18); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>Associated gene or locus</B> "); cgiMakeTextVar("variome.gene", "required", 18); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>dbSNP rs#</B> "); cgiMakeTextVar("variome.rs", "", 18); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>dbSNP ss#</B> "); cgiMakeTextVar("variome.ss", "", 18); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>Phenotype</B> "); cgiMakeTextVar("variome.pheno", "", 25); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>OMIM variant ID</B> "); cgiMakeTextVar("variome.omim", "", 18); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); /* sixth is score which is not used */ /* seventh row is item color pull-down menu, not used */ /* eighth row is initial comment/description text entry */ webPrintWideCellStart(2, HG_COL_TABLE); hPrintf("<B>Comments:</B><BR>"); cgiMakeTextArea(NEW_ITEM_COMMENT, NEW_ITEM_COMMENT_DEFAULT, 5, 40); webPrintLinkCellEnd(); webPrintLinkTableNewRow(); /* ninth row is the submit and cancel buttons */ /*webPrintLinkCellStart(); more careful explicit alignment */ hPrintf("<TD BGCOLOR=\"#%s\" ALIGN=\"CENTER\" VALIGN=\"TOP\">", HG_COL_TABLE); cgiMakeButton("submit", "create new item"); hPrintf("\n</FORM>\n"); webPrintLinkCellEnd(); /*webPrintLinkCellStart(); doesn't valign center properly */ hPrintf("<TD BGCOLOR=\"#%s\" ALIGN=\"CENTER\" VALIGN=\"TOP\">", HG_COL_TABLE); hPrintf("\n<FORM ID=\"cancel\" NAME=\"cancel\" ACTION=\"%s\">", hgTracksName()); cgiMakeButton("cancel", "cancel"); hPrintf("\n</FORM>\n"); webPrintLinkCellEnd(); webPrintLinkTableEnd(); } } else { struct variome *item = findVariomeItemId(database, wikiItemId); cartWebStart(cart, database, "%s (%s)", "User Annotation Track", item->name); displayVariomeItem(item, userName); } cartHtmlEnd(); } /* void doVariome() */ void displayVariomeItem (struct variome *item, char *userName) /* given an already fetched item, get the item description from * the wiki. Put up edit form(s) if userName is not NULL */ { char *url = cfgOptionDefault(CFG_WIKI_URL, NULL); //struct slName *class = slNameListFromString(item->class, ','); if (isNotEmpty(item->geneSymbol) && differentWord(item->geneSymbol,"0")) { hPrintf("<B>Gene symbol: </B><A " "HREF=\"../cgi-bin/hgGene?hgg_gene=%s\" TARGET=_blank>%s</A><BR>\n", item->geneSymbol, item->geneSymbol); } printPosOnChrom(item->chrom, item->chromStart, item->chromEnd, item->strand, FALSE, item->name); hPrintf("<B>Created </B>%s<B> by: </B>", item->creationDate); hPrintf("<A HREF=\"%s/index.php/User:%s\" TARGET=_blank>%s</A><BR>\n", url, item->owner, item->owner); hPrintf("<B>Last update: </B>%s<BR>\n", item->lastModifiedDate); char *editors = cfgOptionDefault(CFG_WIKI_EDITORS, NULL); char *editor = NULL; if ((NULL != userName) && editors) { int i; int wordCount = chopByChar(editors, ',', NULL, 0); char **words = (char **)needMem((size_t)(wordCount * sizeof(char *))); chopByChar(editors, ',', words, wordCount); for (i = 0; i < wordCount; ++i) { if (sameWord(userName, words[i])) { editor = words[i]; break; } } } if ((NULL != userName) && (editor || (sameWord(userName, item->owner)))) { startForm("deleteForm", "variome.delete"); char idString[128]; safef(idString, ArraySize(idString), "%d", item->id); cgiMakeHiddenVar("i", idString); hPrintf("\n"); webPrintLinkTableStart(); webPrintLinkCellStart(); if (editor && (differentWord(userName, item->owner))) hPrintf("Editor '%s' has deletion rights ", editor); else hPrintf("Owner '%s' has deletion rights ", item->owner); webPrintLinkCellEnd(); webPrintLinkCellStart(); cgiMakeButton("submit", "DELETE"); webPrintLinkCellEnd(); webPrintLinkCellStart(); hPrintf(" (no questions asked)"); webPrintLinkCellEnd(); webPrintLinkTableEnd(); hPrintf("\n</FORM>\n"); } if (NULL != userName) hPrintf("<B>Mark this wiki article as <em>" "<A HREF=\"%s/index.php/%s?action=watch\" TARGET=_blank>watched</A>" "</em> to receive email notices of any comment additions.</B><BR>\n", url, item->descriptionKey); hPrintf("<HR>\n"); displayComments((struct wikiTrack *)item); hPrintf("<HR>\n"); //DELETE this? //if (NULL == userName) //{ //offerLogin(item->id, "add comments to items on", "variome"); //} //else if (emailVerified(TRUE)) /* prints message when not verified */ //{ //startForm("addComments", "variome.addComments"); //char idString[128]; //safef(idString, ArraySize(idString), "%d", item->id); //cgiMakeHiddenVar("i", idString); //hPrintf("\n"); //webPrintLinkTableStart(); ///* first row is a title line */ //char label[256]; //safef(label, ArraySize(label), //"'%s' adding comments to item '%s'\n", userName, item->name); //webPrintWideLabelCell(label, 2); //webPrintLinkTableNewRow(); ///* second row is initial comment/description text entry */ //webPrintWideCellStart(2, HG_COL_TABLE); //cgiMakeTextArea(NEW_ITEM_COMMENT, ADD_ITEM_COMMENT_DEFAULT, 3, 40); //webPrintLinkCellEnd(); //webPrintLinkTableNewRow(); ///*webPrintLinkCellStart(); more careful explicit alignment */ //hPrintf("<TD BGCOLOR=\"#%s\" ALIGN=\"CENTER\" VALIGN=\"TOP\">", //HG_COL_TABLE); //cgiMakeButton("submit", "add comments"); //hPrintf("\n</FORM>\n"); //webPrintLinkCellEnd(); //hPrintf("<TD BGCOLOR=\"#%s\" ALIGN=\"CENTER\" VALIGN=\"TOP\">", //HG_COL_TABLE); //hPrintf("\n<FORM ID=\"cancel\" NAME=\"cancel\" ACTION=\"%s\">", hgTracksName()); //cgiMakeButton("cancel", "return to tracks display"); //hPrintf("\n</FORM>\n"); //webPrintLinkCellEnd(); //webPrintLinkTableEnd(); //Only allow edits through wiki? hPrintf("Editing should be done using the "); hPrintf("wiki article <A HREF=\"%s/index.php/%s\" TARGET=_blank>%s</A> " "for this item's description.<BR>", url, item->descriptionKey, item->descriptionKey); //} } /* displayVariomeItem() */ void makeCommentFromFields () /* works with cart variables, puts fields in form together as a html dl and puts it into the NEW_ITEM_COMMENT variable for the wiki */ { /* HGVS name is also the item name */ char *hgvs = cartCgiUsualString(cart, "i", NULL); char *rid = cartCgiUsualString(cart, "variome.rid", NULL); char *gene = cartCgiUsualString(cart, "variome.gene", NULL); char *rs = cartCgiUsualString(cart, "variome.rs", NULL); char *ss = cartCgiUsualString(cart, "variome.ss", NULL); char *omim = cartCgiUsualString(cart, "variome.omim", NULL); char *phen = cartCgiUsualString(cart, "variome.pheno", NULL); char *comm = cartCgiUsualString(cart, NEW_ITEM_COMMENT, NULL); char *pos = cartCgiUsualString(cart, "getDnaPos", NULL); char *strand = cartCgiUsualString(cart, NEW_ITEM_STRAND, NULL); struct dyString *dy = newDyString(512); /* make sure defined & defaults have changed for required fields */ if (hgvs == NULL || sameString(hgvs, "required")) errAbort("The HGVS name is a required field\n"); if (rid == NULL || sameString(rid, "required")) errAbort("The Researcher ID is a required field\n"); if (gene == NULL || sameString(gene, "required")) errAbort("The associated gene or locus is required, it can be a HUGO gene name, LRG ID, or GenBank accession.\n"); dyStringPrintf(dy, "{{Variome_entry\n|hgvs=%s\n|rid=%s|position=%s\n", hgvs, rid, pos); dyStringPrintf(dy, "|gene=%s\n", gene); /* required */ //dyStringPrintf(dy, "<dl><dt>HGVS name<dd>%s<dt>Researcher ID<dd>%s", //hgvs, rid); if (strand != NULL && differentString(strand, "")) { if (sameString(strand, "+")) dyStringPrintf(dy, "|strand=+\n"); else dyStringPrintf(dy, "|strand=-\n"); } if (rs != NULL && differentString(rs, "")) dyStringPrintf(dy, "|rs=%s\n", rs); //dyStringPrintf(dy, "<dt>dbSNP rs#<dd>%s", rs); if (ss != NULL && differentString(ss, "")) dyStringPrintf(dy, "|ss=%s\n", ss); //dyStringPrintf(dy, "<dt>dbSNP ss#<dd>%s", ss); if (omim != NULL && differentString(omim, "")) dyStringPrintf(dy, "|omim=%s\n", omim); //dyStringPrintf(dy, "<dt>OMIM variant ID<dd>%s", omim); if (phen != NULL && differentString(phen, "")) dyStringPrintf(dy, "|pheno=%s\n", phen); //dyStringPrintf(dy, "<dt>Phenotype<dd>%s", phen); if (comm != NULL && differentString(comm, NEW_ITEM_COMMENT_DEFAULT)) dyStringPrintf(dy, "|comment=%s\n", comm); //dyStringPrintf(dy, "<dt>Comment<dd>%s", comm); dyStringPrintf(dy, "}}\n"); //dyStringPrintf(dy, "</dl>"); cartSetString(cart, NEW_ITEM_COMMENT, dy->string); } void doCreateVariomeItem (char *itemName, char *chrom, int winStart, int winEnd) /* handle create item clicks for variome */ { int id = 0, itemStart = 0, itemEnd = 0; char *chrName = NULL; char *pos = NULL; char *strand = cartUsualString(cart, NEW_ITEM_STRAND, "plus"); char *class = cloneString("varRep"); /* section of browser belongs in */ char *color = cartUsualString(cart, NEW_ITEM_COLOR, "#000000"); char *userName = NULL; if (! wikiTrackEnabled(database, &userName)) errAbort("create new wiki item: wiki track not enabled"); if (NULL == userName) errAbort("create new wiki item: user not logged in ?"); pos = stripCommas(cartOptionalString(cart, "getDnaPos")); if (NULL == pos) errAbort("create new wiki item: called incorrectly, without getDnaPos"); hgParseChromRange(database, pos, &chrName, &itemStart, &itemEnd); id = addVariomeItem(database, chrName, itemStart, itemEnd, itemName, 1000, strand, userName, class, color, "Variome", "0", NULL); /* char *db, char *chrom, int start, int end, char *name, int score, char *strand, char *owner, char *class, char *color, char *category, char *geneSymbol, char *wikiKey */ cartWebStart(cart, database, "%s %s", "Variome Track, created new item: ", itemName); char wikiItemId[64]; safef(wikiItemId,ArraySize(wikiItemId),"%d", id); struct variome *item = findVariomeItemId(database, wikiItemId); makeCommentFromFields(); /* gets comment from cart, NEW_ITEM_COMMENT */ addDescription((struct wikiTrack *)item, userName, seqName, winStart, winEnd, cart, database, NULL, NULL, "[[Category:Variome]]"); displayVariomeItem(item, userName); cartHtmlEnd(); } //DELETE this? force to use wiki to edit? void doAddVariomeComments(char *wikiItemId, char *chrom, int winStart, int winEnd) /* handle add comment item clicks for Variome Track */ { char *userName = NULL; struct variome *item = findVariomeItemId(database, wikiItemId); cartWebStart(cart, database, "%s (%s)", "Variome Track", item->name); if (NULL == wikiItemId) errAbort("add wiki comments: NULL wikiItemId"); if (! wikiTrackEnabled(database, &userName)) errAbort("add wiki comments: wiki track not enabled"); if (NULL == userName) errAbort("add wiki comments: user not logged in ?"); /* gets comment from cart, NEW_ITEM_COMMENT */ addDescription((struct wikiTrack *)item, userName, seqName, winStart, winEnd, cart, database, NULL, NULL, "[[Category:Variome]]"); updateVariomeLastModifiedDate(database, sqlSigned(wikiItemId)); displayVariomeItem(item, userName); cartHtmlEnd(); } void doDeleteVariomeItem(char *wikiItemId, char *chrom, int winStart, int winEnd) /* handle delete item clicks for Variome Track */ { char *userName = NULL; struct variome *item = findVariomeItemId(database, wikiItemId); cartWebStart(cart, database, "%s (%s)", "Variome Track, deleted item: ", item->name); if (NULL == wikiItemId) errAbort("delete wiki item: NULL wikiItemId"); if (! wikiTrackEnabled(database, &userName)) errAbort("delete wiki item: wiki track not enabled"); char comments[1024]; safef(comments,ArraySize(comments), "This item '''%s''' on assembly %s " "at %s:%d-%d has been deleted from the wiki track\n\n", item->db, item->name, item->chrom, item->chromStart, item->chromEnd); prefixComments((struct wikiTrack *)item, comments, userName, seqName, winStart, winEnd, database, NULL, "(deleted item)", "[[Category:Variome]]"); deleteVariomeItem(database, sqlSigned(wikiItemId)); hPrintf("<BR>\n"); hPrintf("<FORM ID=\"delete\" NAME=\"delete\" ACTION=\"%s\">", hgTracksName()); cgiMakeButton("submit", "return to tracks display"); hPrintf("\n</FORM>\n"); hPrintf("<BR>\n"); cartHtmlEnd(); }