32c0818813157d38ca7581b1e2eb6288c6ddfef7 max Tue Apr 30 11:31:44 2013 -0700 moving the publication track code into its own .h/.c files diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c index 9e31b3b..70f60a4 100644 --- src/hg/hgTracks/simpleTracks.c +++ src/hg/hgTracks/simpleTracks.c @@ -112,30 +112,31 @@ #include "oregannoUi.h" #include "pgSnp.h" #include "bedDetail.h" #include "bed12Source.h" #include "dbRIP.h" #include "wikiLink.h" #include "wikiTrack.h" #include "dnaMotif.h" #include "hapmapTrack.h" #include "omicia.h" #include "nonCodingUi.h" #include "transMapTracks.h" #include "retroTracks.h" #include "pcrResult.h" #include "variome.h" +#include "pubsTracks.h" #endif /* GBROWSE */ #ifdef LOWELAB #include "loweLabTracks.h" #include "rnaPLFoldTrack.h" #endif /* LOWELAB */ #ifdef LOWELAB_WIKI #include "wiki.h" #endif /* LOWELAB_WIKI */ #define CHROM_COLORS 26 int colorBin[MAXPIXELS][256]; /* count of colors for each pixel for each color */ /* Declare our color gradients and the the number of colors in them */ Color shadesOfGreen[EXPR_DATA_SHADES]; @@ -12040,509 +12041,30 @@ // end stuff copied from hgTracks.c enum trackVisibility trackVis = track->tdb->visibility; if (s != NULL) trackVis = hTvFromString(s); if (trackVis != tvHide) { track->visibility = tvDense; track->limitedVis = tvDense; track->limitedVisSet = TRUE; } track->nextItemButtonable = track->nextExonButtonable = FALSE; track->nextPrevItem = NULL; track->nextPrevExon = NULL; } -char* pubsArticleTable(struct track *tg) -/* return the name of the pubs articleTable, either - * the value from the trackDb statement 'articleTable' - * or the default value: <trackName>Article */ -{ -char *articleTable = trackDbSettingClosestToHome(tg->tdb, "pubsArticleTable"); -if (isEmpty(articleTable)) - { - char buf[256]; - safef(buf, sizeof(buf), "%sArticle", tg->track); - articleTable = cloneString(buf); - } -return articleTable; -} - -static char *makeMysqlMatchStr(char *str) -{ -// return a string with all words prefixed with a '+' to force a boolean AND query; -// we also strip leading/trailing spaces. -char *matchStr = needMem(strlen(str) * 2 + 1); -int i = 0; -for(;*str && isspace(*str);str++) - ; while(*str) - { - matchStr[i++] = '+'; - for(; *str && !isspace(*str);str++) - matchStr[i++] = *str; - for(;*str && isspace(*str);str++) - ; - } -matchStr[i++] = 0; -return matchStr; -} - -struct pubsExtra -/* additional info needed for publication blat linked features: author+year and title */ -{ - char *label; // usually author+year - char *mouseOver; // usually title of article - char *class; // class of article, usually a curated database - // color depends on cart settings, either based on topic, impact or year - // support to ways to color: either by shade (year, impact) or directly with rgb values - int shade; // year or impact are shades which we can't resolve to rgb easily - struct rgbColor *color; -}; - -/* assignment of pubs classes to colors */ -static struct hash* pubsClassColors = NULL; - -static void pubsParseClassColors() -/* parse class colors from hgFixed.pubsClassColors into the hash pubsClassColors */ -{ -if (pubsClassColors!=NULL) - return; - -pubsClassColors = hashNew(0); -struct sqlConnection *conn = hAllocConn(database); -if (!sqlTableExists(conn, "hgFixed.pubsClassColors")) - { - return; - } -char *query = "SELECT class, rgbColor FROM hgFixed.pubsClassColors"; -struct sqlResult *sr = sqlGetResult(conn, query); -char **row = NULL; -while ((row = sqlNextRow(sr)) != NULL) - { - char *class = row[0]; - char *colStr = row[1]; - // copied from genePredItemClassColor - is there no function for this? - // convert comma sep rgb string to array - char *rgbVals[5]; - chopString(colStr, ",", rgbVals, sizeof(rgbVals)); - struct rgbColor *rgb; - AllocVar(rgb); - rgb->r = (sqlUnsigned(rgbVals[0])); - rgb->g = (sqlUnsigned(rgbVals[1])); - rgb->b = (sqlUnsigned(rgbVals[2])); - //printf("Adding hash: %s -> %d,%d,%d", class, rgb->r, rgb->g, rgb->b); - hashAdd(pubsClassColors, cloneString(class), rgb); - } -sqlFreeResult(&sr); -} - -static char* pubsFeatureLabel(char* author, char* year) -/* create label <author><year> given authors and year strings */ -{ -char* authorYear = NULL; - -if (isEmpty(author)) - author = "NoAuthor"; -if (isEmpty(year)) - year = "NoYear"; -authorYear = catTwoStrings(author, year); - -return authorYear; -} - -static struct pubsExtra *pubsMakeExtra(struct track* tg, char* articleTable, - struct sqlConnection* conn, struct linkedFeatures* lf) -/* bad solution: a function that is called before the extra field is - * accessed and that fills it from a sql query. Will need to redo this like gencode, - * drawing from atom, variome and bedLoadN or bedDetails */ -{ -char query[LARGEBUF]; -struct sqlResult *sr = NULL; -char **row = NULL; -struct pubsExtra *extra = NULL; - -/* support two different storage places for article data: either the bed table directly - * includes the title + author of the article or we have to look it up from the articles - * table. Having a copy of the title in the bed table is faster */ -bool newFormat = false; -if (sqlColumnExists(conn, tg->table, "title")) - { - safef(query, sizeof(query), "SELECT firstAuthor, year, title, impact, classes FROM %s " - "WHERE chrom = '%s' and chromStart = '%d' and name='%s'", tg->table, chromName, lf->start, lf->name); - newFormat = true; - } -else - { - safef(query, sizeof(query), "SELECT firstAuthor, year, title FROM %s WHERE articleId = '%s'", - articleTable, lf->name); - newFormat = false; - } - -sr = sqlGetResult(conn, query); -if ((row = sqlNextRow(sr)) != NULL) - { - char* firstAuthor = row[0]; - char* year = row[1]; - char* title = row[2]; - char* impact = NULL; - char* classes = NULL; - - - extra = needMem(sizeof(struct pubsExtra)); - extra->label = pubsFeatureLabel(firstAuthor, year); - if (isEmpty(title)) - extra->mouseOver = extra->label; - else - extra->mouseOver = cloneString(title); - extra->color = NULL; - extra->shade = -1; - - if (newFormat) - { - impact = row[3]; - classes = row[4]; - if (!isEmpty(impact)) - { - char *colorBy = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsColorBy"); - if ((colorBy==NULL) || strcmp(colorBy,"topic")==0) - { - char *classCopy = classes; - char* mainClass = cloneNextWordByDelimiter(&classes, ','); - classes = classCopy; - if (mainClass!=NULL) - { - struct rgbColor *col = (struct rgbColor*) hashFindVal(pubsClassColors, mainClass); - extra->color = col; - // add class to mouseover text - struct dyString *mo = dyStringNew(0); - dyStringAppend(mo, extra->mouseOver); - dyStringAppend(mo, " (categories: "); - dyStringAppend(mo, classes); - dyStringAppend(mo, ")"); - freeMem(extra->mouseOver); - extra->mouseOver = dyStringContents(mo); - } - } - else - { - if (strcmp(colorBy,"impact")==0) - { - char impInt = atoi(impact); - extra->shade = impInt/25; - } - if (strcmp(colorBy,"year")==0) - { - int relYear = (atoi(year)-1990); - extra->shade = min(relYear/3, 10); - //extra->color = shadesOfGray[yearShade]; - } - } - } - } - } - - -sqlFreeResult(&sr); -return extra; -} - -static void pubsAddExtra(struct track* tg, struct linkedFeatures* lf) -/* add authorYear and title to linkedFeatures->extra */ -{ -char *articleTable = trackDbSettingClosestToHome(tg->tdb, "pubsArticleTable"); -if(isEmpty(articleTable)) - return; -if (lf->extra != NULL) { - return; - } - -struct sqlConnection *conn = hAllocConn(database); -struct pubsExtra* extra = pubsMakeExtra(tg, articleTable, conn, lf); -lf->extra = extra; -hFreeConn(&conn); -} - -static void pubsLoadKeywordYearItems(struct track *tg) -/* load items that fulfill keyword and year filter */ -{ -pubsParseClassColors(); -struct sqlConnection *conn = hAllocConn(database); -char *keywords = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsKeywords"); -char *yearFilter = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsYear"); -char *articleTable = pubsArticleTable(tg); - -if(yearFilter == NULL || sameWord(yearFilter, "anytime")) - yearFilter = NULL; - -if(isNotEmpty(keywords)) - keywords = makeMysqlMatchStr(sqlEscapeString(keywords)); - -if(isEmpty(yearFilter) && isEmpty(keywords)) -{ - loadGappedBed(tg); -} -else - { - char* oldLabel = tg->longLabel; - tg->longLabel = catTwoStrings(oldLabel, " (filter activated)"); - freeMem(oldLabel); - - char extra[2048], yearWhere[256], keywordsWhere[1024], prefix[256]; - char **row; - struct linkedFeatures *lfList = NULL; - struct trackDb *tdb = tg->tdb; - int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0")); - int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMax", "1000")); - boolean useItemRgb = bedItemRgb(tdb); - - safef(prefix, sizeof(prefix), "name IN (SELECT articleId FROM %s WHERE", articleTable); - if(isNotEmpty(keywords)) - safef(keywordsWhere, sizeof(keywordsWhere), \ - "MATCH (citation, title, authors, abstract) AGAINST ('%s' IN BOOLEAN MODE)", keywords); - if(isNotEmpty(yearFilter)) - safef(yearWhere, sizeof(yearWhere), "year >= '%s'", sqlEscapeString(yearFilter)); - - if(isEmpty(keywords)) - safef(extra, sizeof(extra), "%s %s)", prefix, yearWhere); - else if(isEmpty(yearFilter)) - safef(extra, sizeof(extra), "%s %s)", prefix, keywordsWhere); - else - safef(extra, sizeof(extra), "%s %s AND %s)", prefix, yearWhere, keywordsWhere); - - int rowOffset = 0; - struct sqlResult *sr = hExtendedRangeQuery(conn, tg->table, chromName, winStart, winEnd, extra, - FALSE, NULL, &rowOffset); - while ((row = sqlNextRow(sr)) != NULL) - { - struct bed *bed = bedLoad12(row+rowOffset); - slAddHead(&lfList, bedMungToLinkedFeatures(&bed, tdb, 12, scoreMin, scoreMax, useItemRgb)); - } - sqlFreeResult(&sr); - slReverse(&lfList); - slSort(&lfList, linkedFeaturesCmp); - tg->items = lfList; - } -hFreeConn(&conn); -} - -#define PUBSFILTERNAME "pubsFilterArticleId" - -static void activatePslTrackIfCgi(struct track *tg) -/* the publications hgc creates links back to the browser with - * the cgi param pubsFilterArticleId to show only a single type - * of feature for the pubsBlatPsl track. - * If the parameter was supplied, we save this parameter here - * into the cart and activate the track. - */ -{ -char *articleId = cgiOptionalString(PUBSFILTERNAME); -//if (articleId==NULL) - //articleId = cartOptionalString(cart, PUBSFILTERNAME); - -if (articleId!=NULL) -{ - cartSetString(cart, PUBSFILTERNAME, articleId); - tdbSetCartVisibility(tg->tdb, cart, hCarefulTrackOpenVis(database, tg->track)); - tg->visibility=tvPack; -} -} - -Color pubsItemColor(struct track *tg, void *item, struct hvGfx *hvg) -/* get color from extra field */ -{ -//pubsParseClassColors(); -struct linkedFeatures *lf = item; -pubsAddExtra(tg, lf); - -struct pubsExtra* extra = lf->extra; -if (extra==NULL || (extra->color==NULL && extra->shade==-1)) - return MG_BLACK; - -if (extra->shade != -1) - return shadesOfBlue[extra->shade]; -else - { - //printf("got item color %d", extra->color->r); - return hvGfxFindRgb(hvg, extra->color); - } -} - -char *pubsItemName(struct track *tg, void *item) -/* get author/year from extra field */ -{ -struct linkedFeatures *lf = item; -pubsAddExtra(tg, lf); - -struct pubsExtra* extra = lf->extra; -if (extra!=NULL) - return extra->label; -else - return lf->name; - -} - -static void pubsMapItem(struct track *tg, struct hvGfx *hvg, void *item, - char *itemName, char *mapItemName, int start, int end, - int x, int y, int width, int height) -/* create mouse over with title for pubs blat features. */ -{ -if (!theImgBox || tg->limitedVis != tvDense || !tdbIsCompositeChild(tg->tdb)) -{ - struct linkedFeatures *lf = item; - pubsAddExtra(tg, lf); - struct pubsExtra* extra = lf->extra; - char* mouseOver = NULL; - if (extra != NULL) - mouseOver = extra->mouseOver; - else - mouseOver = itemName; - - mapBoxHc(hvg, start, end, x, y, width, height, tg->track, mapItemName, mouseOver); -} -} - -char *pubsMarkerItemName(struct track *tg, void *item) -/* retrieve article count from score field and return.*/ -{ -struct bed *bed = item; -char newName[64]; -safef(newName, sizeof(newName), "%d articles", (int) bed->score); -return cloneString(newName); -} - -static void pubsMarkerMapItem(struct track *tg, struct hvGfx *hvg, void *item, - char *itemName, char *mapItemName, int start, int end, - int x, int y, int width, int height) -{ -struct bed *bed = item; -genericMapItem(tg, hvg, item, bed->name, bed->name, start, end, x, y, width, height); -} - -static struct hash* pubsLookupSequences(struct track *tg, struct sqlConnection* conn, char* articleId, bool getSnippet) -/* create a hash with a mapping annotId -> snippet or annotId -> shortSeq for an articleId*/ -{ - char query[LARGEBUF]; - char *sequenceTable = trackDbRequiredSetting(tg->tdb, "pubsSequenceTable"); - char *selectValSql = NULL; - if (getSnippet) - selectValSql = "replace(replace(snippet, \"<B>\", \"\\n>>> \"), \"</B>\", \" <<<\\n\")"; - else - selectValSql = "concat(substr(sequence,1,4),\"...\",substr(sequence,-4))"; - - safef(query, sizeof(query), "SELECT annotId, %s FROM %s WHERE articleId='%s' ", - selectValSql, sequenceTable, articleId); - struct hash *seqIdHash = sqlQuickHash(conn, query); - //freeMem(sequenceTable); // XX Why does this crash?? - return seqIdHash; -} - -static char *pubsArticleDispId(struct track *tg, struct sqlConnection *conn, char* articleId) -/* given an articleId, lookup author and year and create <author><year> label for it */ -{ -char* dispLabel = NULL; -char *articleTable = pubsArticleTable(tg); -char query[LARGEBUF]; -safef(query, sizeof(query), "SELECT firstAuthor, year FROM %s WHERE articleId = '%s'", - articleTable, articleId); -struct sqlResult *sr = sqlGetResult(conn, query); -if (sr!=NULL) - { - char **row = NULL; - row = sqlNextRow(sr); - if (row != NULL) - dispLabel = pubsFeatureLabel(row[0], row[1]); - else - dispLabel = articleId; - } -else - dispLabel = articleId; -sqlFreeResult(&sr); -return dispLabel; -} - -static void pubsPslLoadItems(struct track *tg) -/* load only psl items from a single article */ -{ -// get articleId to filter on -char *articleId = cartOptionalString(cart, PUBSFILTERNAME); -if (articleId==NULL) - return; - -struct sqlConnection *conn = hAllocConn(database); -char* dispLabel = pubsArticleDispId(tg, conn, articleId); -struct hash *idToSnip = pubsLookupSequences(tg, conn, articleId, TRUE); -struct hash *idToSeq = pubsLookupSequences(tg, conn, articleId, FALSE); - -// change track label -char* oldLabel = tg->longLabel; -tg->longLabel = catTwoStrings("Individual matches for article ", dispLabel); -freeMem(oldLabel); - -// filter and load items for this articleId -char where[256]; -safef(where, sizeof(where), " articleId=%s ", articleId); - -int rowOffset = 0; -struct sqlResult *sr = NULL; -sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, where, &rowOffset); - -struct linkedFeatures *lfList = NULL; -char **row = NULL; -while ((row = sqlNextRow(sr)) != NULL) - { - struct psl *psl = pslLoad(row+rowOffset); - slAddHead(&lfList, lfFromPsl(psl, TRUE)); - char* shortSeq = hashFindVal(idToSeq, lfList->name); - char* snip = hashFindVal(idToSnip, lfList->name); - struct pubsExtra *extra = needMem(sizeof(struct pubsExtra)); - extra->mouseOver=snip; - extra->label=shortSeq; - lfList->extra = extra; - } -sqlFreeResult(&sr); -slReverse(&lfList); -slSort(&lfList, linkedFeaturesCmp); -tg->items = lfList; -hFreeConn(&conn); -} - -static void pubsBlatPslMethods(struct track *tg) -/* a track that shows only the indiv matches for one single article */ -{ -activatePslTrackIfCgi(tg); -tg->loadItems = pubsPslLoadItems; -tg->itemName = pubsItemName; -tg->mapItem = pubsMapItem; -} - -static void pubsBlatMethods(struct track *tg) -/* publication blat tracks are bed12+2 tracks of sequences in text, mapped with BLAT */ -{ -//bedMethods(tg); -tg->loadItems = pubsLoadKeywordYearItems; -tg->itemName = pubsItemName; -tg->itemColor = pubsItemColor; -tg->mapItem = pubsMapItem; -} - -static void pubsMarkerMethods(struct track *tg) -/* publication marker tracks are bed5 tracks of genome marker occurences like rsXXXX found in text*/ -{ -tg->mapItem = pubsMarkerMapItem; -tg->itemName = pubsMarkerItemName; -} - void fillInFromType(struct track *track, struct trackDb *tdb) /* Fill in various function pointers in track from type field of tdb. */ { char *typeLine = tdb->type, *words[8], *type; int wordCount; if (typeLine == NULL) return; wordCount = chopLine(cloneString(typeLine), words); if (wordCount <= 0) return; type = words[0]; #ifndef GBROWSE if (sameWord(type, "bed")) {