8ba9695dd0a51b772a5a0f826027f313d7c3d21a angie Fri Jan 23 14:21:11 2015 -0800 Added header comments as suggested by Kate. refs #14698 diff --git src/hg/hgAi/hgAi.c src/hg/hgAi/hgAi.c index 7a7693d..d15ddaf 100644 --- src/hg/hgAi/hgAi.c +++ src/hg/hgAi/hgAi.c @@ -1,336 +1,346 @@ -/* hgAi - General annotation integrator interface. */ +/* hgAi - bootstrapper / back end for the Annotation Integrator user interface + * This CGI has three modes of operation: + * - HTML output for minimal main page with a <div> container to be filled in by javascript + * (default, in the absence of special CGI params) + * - JSON responses to ajax requests from javascript (using hg/lib/cartJson.c) + * (if CGI param CARTJSON_COMMAND exists) + * - text output for annoGrator queries on track data + * (if CGI param DO_QUERY exists) + * The UI view top level is in ../js/react/hgAi/hgAi.jsx + * The UI model top level is in ../js/model/hgAi/hgAiModel.js + */ #include "common.h" #include "cart.h" #include "cartJson.h" #include "cartTrackDb.h" #include "cheapcgi.h" #include "hAnno.h" #include "hCommon.h" #include "hdb.h" #include "hgColors.h" #include "hui.h" #include "jsonParse.h" #include "textOut.h" #include "trackHub.h" #include "web.h" #include "annoFormatTab.h" #include "annoGratorQuery.h" /* Global Variables */ struct cart *cart = NULL; /* CGI and other variables */ #define QUERY_SPEC "hgai_querySpec" #define DO_QUERY "hgai_doQuery" //#*** duplicated from hgVai... put in some anno*.h? #define NO_MAXROWS 0 static void writeDbMetadata(struct cartJson *cj, struct hash *paramHash) /* Send all the info that we'll need for working with a specific assembly db. */ { cartJsonGetGroupsTracksTables(cj, paramHash); //#*** TODO: move jsonStringEscape inside jsonWriteString char *encoded = jsonStringEscape(cartOptionalString(cart, QUERY_SPEC)); jsonWriteString(cj->jw, QUERY_SPEC, encoded); } static void changeDb(struct cartJson *cj, struct hash *paramHash) /* The user has changed db; send groups, tracks, tables etc. for the new db. */ { cartJsonChangeDb(cj, paramHash); writeDbMetadata(cj, paramHash); } static void changeOrg(struct cartJson *cj, struct hash *paramHash) /* The user has changed org/genome; send groups, tracks, tables etc. for the new default db. */ { cartJsonChangeOrg(cj, paramHash); writeDbMetadata(cj, paramHash); } static void changeClade(struct cartJson *cj, struct hash *paramHash) /* The user has changed clade; send groups, tracks, tables etc. for the new default db. */ { cartJsonChangeClade(cj, paramHash); writeDbMetadata(cj, paramHash); } static void makeTrackLabel(struct trackDb *tdb, char *table, char *label, size_t labelSize) /* Write tdb->shortLabel into label if table is the same as tdb->track; otherwise, write shortLabel * followed by table name in parens. */ { if (sameString(table, tdb->track)) safecpy(label, labelSize, tdb->shortLabel); else safef(label, labelSize, "%s (%s)", tdb->shortLabel, table); } static void getFields(struct cartJson *cj, struct hash *paramHash) /* Print out the fields of the tables in comma-sep tables param. */ { char *tableStr = cartJsonRequiredParam(paramHash, "tables", cj->jw, "getFields"); if (! tableStr) return; char *db = cartString(cart, "db"); struct slName *table, *tables = slNameListFromComma(tableStr); jsonWriteObjectStart(cj->jw, "tableFields"); struct trackDb *fullTrackList = NULL; struct grp *fullGroupList = NULL; cartTrackDbInit(cj->cart, &fullTrackList, &fullGroupList, /* useAccessControl= */TRUE); for (table = tables; table != NULL; table = table->next) { struct trackDb *tdb = tdbForTrack(NULL, table->name, &fullTrackList); if (tdb) { struct asObject *asObj = hAnnoGetAutoSqlForTdb(db, hDefaultChrom(db), tdb); if (asObj) { jsonWriteObjectStart(cj->jw, table->name); char label[strlen(tdb->shortLabel) + strlen(table->name) + PATH_LEN]; makeTrackLabel(tdb, table->name, label, sizeof(label)); jsonWriteString(cj->jw, "label", label); jsonWriteListStart(cj->jw, "fields"); struct asColumn *col; for (col = asObj->columnList; col != NULL; col = col->next) jsonWriteString(cj->jw, NULL, col->name); jsonWriteListEnd(cj->jw); jsonWriteObjectEnd(cj->jw); } } } jsonWriteObjectEnd(cj->jw); slFreeList(&tables); } void doCartJson() /* Perform UI commands to update the cart and/or retrieve cart vars & metadata. */ { struct cartJson *cj = cartJsonNew(cart); cartJsonRegisterHandler(cj, "changeDb", changeDb); cartJsonRegisterHandler(cj, "changeOrg", changeOrg); cartJsonRegisterHandler(cj, "changeClade", changeClade); cartJsonRegisterHandler(cj, "getFields", getFields); cartJsonExecute(cj); } static struct pipeline *configTextOut(struct jsonElement *queryObj, int *pSavedStdout) // Set up a textOut pipeline according to output file options in queryObj. { char *fileName = ""; char *compressType = textOutCompressNone; struct jsonElement *outFileOptions = jsonFindNamedField(queryObj, QUERY_SPEC, "outFileOptions"); if (outFileOptions) { boolean doFile = jsonOptionalBooleanField(outFileOptions, "doFile", FALSE); if (doFile) { fileName = jsonOptionalStringField(outFileOptions, "fileName", "hgAiResults"); boolean doGzip = jsonOptionalBooleanField(outFileOptions, "doGzip", FALSE); if (doGzip) compressType = textOutCompressGzip; } } return textOutInit(fileName, compressType, pSavedStdout); } static struct annoFormatter *makeTabFormatter(struct jsonElement *queryObj) // Create and configure an annoFormatter subclass as specified by queryObj. { struct annoFormatter *tabOut = annoFormatTabNew("stdout"); // Look for fields that have been deselected by the user struct jsonElement *outFileOptions = jsonFindNamedField(queryObj, QUERY_SPEC, "outFileOptions"); if (outFileOptions) { struct jsonElement *tableFieldsObj = jsonFindNamedField(outFileOptions, "outFileOptions", "tableFields"); if (tableFieldsObj) { struct hash *tableFields = jsonObjectVal(tableFieldsObj, "tableFields"); // Iterate over names which are tables which had better end up being annoStreamer names... //#*** Hmmm, annoStreamer uses complete file path for big and we don't have that info //#*** here. Better find a way to pass in names to streamers for consistency! struct hashEl *hel; struct hashCookie cookie = hashFirst(tableFields); while ((hel = hashNext(&cookie)) != NULL) { char *sourceName = hel->name; struct jsonElement *tableObj = hel->val; struct hash *fieldVals = jsonObjectVal(tableObj, sourceName); // Now iterate over field/column names to see which ones are explicitly deselected: struct hashEl *innerHel; struct hashCookie innerCookie = hashFirst(fieldVals); while ((innerHel = hashNext(&innerCookie)) != NULL) { char *colName = innerHel->name; struct jsonElement *enabledEl = innerHel->val; boolean enabled = jsonBooleanVal(enabledEl, colName); if (! enabled) annoFormatTabSetColumnVis(tabOut, sourceName, colName, enabled); } } } } return tabOut; } void doQuery() /* Execute a query that has been built up by the UI. */ { // Make sure we have either genome-wide search or a valid position char *db = cartString(cart, "db"); char *chrom = NULL; uint start = 0, end = 0; char *regionType = cartUsualString(cart, "hgai_range", "position"); if (sameString(regionType, "position")) { char *position = cartUsualString(cart, "position", hDefaultPos(db)); if (! parsePosition(position, &chrom, &start, &end)) errAbort("doQuery: Expected position to be chrom:start-end but got '%s'", position); } struct annoAssembly *assembly = hAnnoGetAssembly(db); // Decode and parse CGI-encoded querySpec. char *querySpec = cartString(cart, QUERY_SPEC); int len = strlen(querySpec); char querySpecDecoded[len+1]; cgiDecodeFull(querySpec, querySpecDecoded, len); struct jsonElement *queryObj = jsonParse(querySpecDecoded); // Set up output. int savedStdout = -1; struct pipeline *textOutPipe = configTextOut(queryObj, &savedStdout); webStartText(); // Build annoGrator query. struct slRef *dataSources = jsonListVal(jsonFindNamedField(queryObj, "queryObj", "dataSources"), "dataSources"); struct grp *fullGroupList = NULL; struct trackDb *fullTrackList = NULL; cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); struct annoStreamer *primary = NULL; struct annoGrator *gratorList = NULL; struct slRef *dsRef; int i; for (i = 0, dsRef = dataSources; dsRef != NULL; i++, dsRef = dsRef->next) { struct jsonElement *dsObj = dsRef->val; char *table = jsonStringField(dsObj, "table"); char *track = jsonStringField(dsObj, "track"); struct trackDb *tdb = tdbForTrack(db, table, &fullTrackList); if (!tdb) tdb = tdbForTrack(db, track, &fullTrackList); if (!tdb) errAbort("doQuery: no tdb for track %s, table %s", track, table); if (i == 0) { primary = hAnnoStreamerFromTrackDb(assembly, table, tdb, chrom, NO_MAXROWS); annoStreamerSetName(primary, table); } else { struct annoGrator *grator = hAnnoGratorFromTrackDb(assembly, table, tdb, chrom, NO_MAXROWS, NULL, agoNoConstraint); if (grator) { annoStreamerSetName((struct annoStreamer *)grator, table); slAddHead(&gratorList, grator); } else errAbort("doQuery: no grator for track %s, table %s", track, table); } } slReverse(&gratorList); // Make an annoFormatter to print output. // For now, tab-separated output is it. struct annoFormatter *formatter = makeTabFormatter(queryObj); // Set up and execute query. struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, formatter); if (chrom != NULL) annoGratorQuerySetRegion(query, chrom, start, end); annoGratorQueryExecute(query); annoGratorQueryFree(&query); textOutClose(&textOutPipe, &savedStdout); } void doMainPage() /* Send HTML with javascript to bootstrap the user interface. */ { char *db = cartUsualString(cart, "db", hDefaultDb()); webStartWrapperDetailedNoArgs(cart, trackHubSkipHubName(db), "", "Annotation Integrator", TRUE, FALSE, TRUE, TRUE); // Ideally these would go in the <HEAD> puts("<link rel=\"stylesheet\" href=\"//code.jquery.com/ui/1.10.3/themes/smoothness/jquery-ui.css\">"); puts("<link rel=\"stylesheet\" href=\"//netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css\">"); puts("<div id=\"appContainer\">Loading...</div>"); // Set a global JS variable hgsid. // Plain old "var ..." doesn't work (other scripts can't see it), it has to belong to window. printf("<script>window.%s='%s';</script>\n", cartSessionVarName(), cartSessionId(cart)); // We need a package manager and require-handling system... bower and browserify? puts("<script src=\"../js/es5-shim.4.0.3.min.js\"></script>"); puts("<script src=\"../js/es5-sham.4.0.3.min.js\"></script>"); puts("<script src=\"../js/lodash.2.4.1.compat.min.js\"></script>"); puts("<script src=\"//code.jquery.com/jquery-1.9.1.min.js\"></script>"); puts("<script src=\"//code.jquery.com/ui/1.10.3/jquery-ui.min.js\"></script>"); puts("<script src=\"//fb.me/react-with-addons-0.12.2.min.js\"></script>"); puts("<script src=\"../js/immutable.3.2.1.min.js\"></script>"); puts("<script src=\"../js/BackboneExtend.js\"></script>"); puts("<script src=\"../js/cart.js\"></script>"); puts("<script src=\"../js/ImModel.js\"></script>"); puts("<script src=\"../js/CladeOrgDbMixin.js\"></script>"); puts("<script src=\"../js/PositionSearchMixin.js\"></script>"); puts("<script src=\"../js/PathUpdate.js\"></script>"); puts("<script src=\"../js/PathUpdateOptional.js\"></script>"); puts("<script src=\"../js/ImmutableUpdate.js\"></script>"); puts("<script src=\"../js/reactLibBundle.js\"></script>"); puts("<script src=\"../js/reactHgAi.js\"></script>"); puts("<script src=\"../js/hgAiModel.js\"></script>"); // Invisible form for submitting a query printf("\n<form action=\"%s\" method=%s id='queryForm'>\n", hgAiName(), cartUsualString(cart, "formMethod", "GET")); cartSaveSession(cart); cgiMakeHiddenVar(QUERY_SPEC, cartUsualString(cart, QUERY_SPEC, "")); cgiMakeHiddenVar(DO_QUERY, "go"); puts("</form>"); // Invisible form for jumping to another CGI printf("\n<form method=%s id='jumpForm'>\n", cartUsualString(cart, "formMethod", "GET")); cartSaveSession(cart); puts("</form>"); webEnd(); } void doMiddle(struct cart *theCart) /* Depending on invocation, either perform a query and print out results, * serve up JSON for the UI, or display the main page. */ { cart = theCart; if (cgiOptionalString(CARTJSON_COMMAND)) doCartJson(); else if (cgiOptionalString(DO_QUERY)) doQuery(); else doMainPage(); } int main(int argc, char *argv[]) /* Process CGI / command line. */ { /* Null terminated list of CGI Variables we don't want to save * permanently. */ char *excludeVars[] = {DO_QUERY, CARTJSON_COMMAND, NULL,}; struct hash *oldVars = NULL; cgiSpoof(&argc, argv); setUdcCacheDir(); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); return 0; }