ae3969602106c0229160648f6ff6c87c3ad0de2d giardine Tue Dec 7 14:13:12 2010 -0800 Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project) diff --git src/hg/hgc/variomeClick.c src/hg/hgc/variomeClick.c new file mode 100644 index 0000000..e84c7a2 --- /dev/null +++ src/hg/hgc/variomeClick.c @@ -0,0 +1,444 @@ +/* Do clicks for the wiki track of variation for microattribution reviews */ + +#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(); +} +