b1c2fdec9a31078a56333427830a760757d22a51
angie
  Fri Jun 17 14:44:44 2016 -0700
Command line wrapper script for hgVai: hg/utils/vai.pl .  hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line.  Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not).
Has been tested somewhat on GBiB.  Needs documentation.
refs #12216

diff --git src/hg/hgVai/hgVai.c src/hg/hgVai/hgVai.c
index a96bad4..fbbd438 100644
--- src/hg/hgVai/hgVai.c
+++ src/hg/hgVai/hgVai.c
@@ -58,30 +58,34 @@
 
 // Null terminated list of CGI Variables we don't want to save permanently:
 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"
 #define hgvaSampleVariants "hgva_internally_generated_sample_variants"
 #define hgvaSampleVariantsLabel "Artificial Example Variants"
 #define hgvaUseVariantIds "hgva_useVariantIds"
 #define hgvaVariantIdsLabel "Variant Identifiers"
 #define hgvaVariantIds "hgva_variantIds"
+#define hgvaUseVariantFileOrUrl "hgva_useVariantFileOrUrl"
+#define hgvaVariantFileOrUrlLabel "from file"
+#define hgvaVariantFileOrUrl "hgva_variantFileOrUrl"
+#define hgvaVariantFileOrUrlType "hgva_variantFileOrUrlType"
 #define hgvaVariantPasteContainer "variantPasteContainer"
 
 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"
 	".sectionLiteHeader { font-weight: bold; font-size:larger; color:#000000;"
 	"  text-align:left; vertical-align:bottom; white-space:nowrap; }\n"
 	"div.sectionLiteHeader.noReorderRemove { padding-bottom:5px; }\n"
 	"div.sourceFilter { padding-top: 5px; padding-bottom: 5px }\n"
 	"</style>\n");
 }
@@ -2563,66 +2567,76 @@
     char *column = annoStreamDbColumnNameFromDtf(database, geneTrack, txStatDtf);
     annoFormatVepAddExtraItem(vepOut, (struct annoStreamer *)gpVarGrator,
                               tag, description, column, isBoolean);
     }
 }
 
 void doQuery()
 /* Translate simple form inputs into anno* components and execute query. */
 {
 dyInfo = dyStringNew(0);
 char *chrom = NULL;
 uint start = 0, end = 0;
 if (sameString(regionType, hgvaRegionTypeRange))
     getCartPosOrDie(&chrom, &start, &end);
 struct annoAssembly *assembly = hAnnoGetAssembly(database);
+boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL);
 
 char *geneTrack = cartString(cart, "hgva_geneTrack");
 struct trackDb *geneTdb = tdbForTrack(database, geneTrack, &fullTrackList);
 if (geneTdb == NULL)
     {
     warn("Can't find tdb for gene track %s", geneTrack);
+    if (! isCommandLine)
         doUi();
     return;
     }
 
 int maxVarRows = cartUsualInt(cart, "hgva_variantLimit", 10);
 struct annoStreamer *primary = NULL;
 char *primaryLongLabel = NULL;
 char *variantTrack = cartString(cart, "hgva_variantTrack");
 struct slName *commentList = NULL;
 if (sameString(variantTrack, hgvaSampleVariants))
     {
     primary = makeSampleVariantsStreamer(assembly, geneTdb, maxVarRows);
     primaryLongLabel = hgvaSampleVariantsLabel;
     // Sample variants can't always be made within the currently selected position range,
     // so just for these, force search to be genome-wide.
     chrom = NULL;
     start = 0;
     end = 0;
     }
 else if (sameString(variantTrack, hgvaUseVariantIds))
     {
     // Override search position if cart position doesn't include all variants:
     primary = makeVariantIdStreamer(assembly, maxVarRows, &chrom, &start, &end, &commentList);
     primaryLongLabel = hgvaVariantIdsLabel;
     }
+else if (sameString(variantTrack, hgvaUseVariantFileOrUrl))
+    {
+    char *fileOrUrl = cartString(cart, hgvaVariantFileOrUrl);
+    char *type = cartOptionalString(cart, hgvaVariantFileOrUrlType);
+    primary = hAnnoStreamerFromBigFileUrl(fileOrUrl, assembly, maxVarRows, type);
+    primaryLongLabel = hgvaVariantFileOrUrlLabel;
+    }
 else
     {
     struct trackDb *varTdb = getVariantTrackDb(variantTrack);
     if (varTdb == NULL)
 	{
+        if (! isCommandLine)
             doUi();
 	return;
 	}
     primary = hAnnoStreamerFromTrackDb(assembly, varTdb->table, varTdb, chrom, maxVarRows, NULL);
     primaryLongLabel = varTdb->longLabel;
     }
 
 enum annoGratorOverlap geneOverlapRule = agoMustOverlap;
 struct joinerDtf *txStatusExtras = getTxStatusExtras(database, geneTrack);
 struct jsonElement *gpConfig = configForStreamer(database, geneTdb, txStatusExtras);
 struct annoGrator *gpVarGrator = hAnnoGratorFromTrackDb(assembly, geneTdb->table, geneTdb, chrom,
                                                         ANNO_NO_LIMIT, primary->asObj,
                                                         geneOverlapRule, gpConfig);
 setGpVarFuncFilter(gpVarGrator);
 
@@ -2654,101 +2668,110 @@
 						(struct annoStreamer *)snpGrator,
 						snpDesc, assembly);
 addTxStatusExtras(vepOut, geneTrack, gpVarGrator, txStatusExtras);
 boolean haveRegulatory = FALSE;
 addOutputTracks(&gratorList, gratorsByName, vepOut, assembly, chrom, doHtml, &haveRegulatory);
 adjustGpVarOverlapRule(gpVarGrator, haveRegulatory);
 
 addFilterTracks(&gratorList, gratorsByName, assembly, chrom);
 
 slReverse(&gratorList);
 
 if (doHtml)
     {
     webStart(cart, database, "Annotated Variants in VEP/HTML format");
     }
-else
+else if (! isCommandLine)
     {
     // Undo the htmlPushEarlyHandlers() because after this point they make ugly text:
     popWarnHandler();
     popAbortHandler();
     textOpen();
     webStartText();
     }
 if (isNotEmpty(dyInfo->string))
     puts(dyInfo->string);
 struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
 struct slName *comment;
 for (comment = commentList;  comment != NULL;  comment = comment->next)
     vepOut->comment(vepOut, comment->name);
 if (chrom != NULL)
     annoGratorQuerySetRegion(query, chrom, start, end);
 annoGratorQueryExecute(query);
 annoGratorQueryFree(&query);
 
 if (doHtml)
     webEnd();
-else
+else if (! isCommandLine)
     textOutClose(&compressPipeline, NULL);
 }
 
 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);
+boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL);
+if (!isCommandLine)
+    htmlPushEarlyHandlers(); /* Make errors legible during initialization. */
 oldVars = hashNew(10);
 setUdcCacheDir();
 boolean startQuery = (cgiUsualString("hgva_startQuery", NULL) != NULL);
 if (startQuery)
+    {
+    if (isCommandLine)
+        // No HTTP header for command-line use.
+        cart = cartForSession(hUserCookie(), excludeVars, oldVars);
+    else
         cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars);
+    }
 else
     cart = cartAndCookie(hUserCookie(), excludeVars, oldVars);
 
 // Try to deal with virt chrom position used by hgTracks.
 if (startsWith("virt:", cartUsualString(cart, "position", "")))
     cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", ""));
 
 /* Set up global variables. */
 getDbAndGenome(cart, &database, &genome, oldVars);
 initGenbankTableNames(database);
 regionType = cartUsualString(cart, hgvaRegionType, hgvaRegionTypeGenome);
 if (isEmpty(cartOptionalString(cart, hgvaRange)))
     cartSetString(cart, hgvaRange, hDefaultPos(database));
 
 int timeout = cartUsualInt(cart, "udcTimeout", 300);
 if (udcCacheTimeout() < timeout)
     udcSetCacheTimeout(timeout);
 knetUdcInstall();
 
 cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE);
 if (lookupPosition(cart, hgvaRange))
     {
     if (startQuery)
 	doQuery();
-    else
+    else if (! isCommandLine)
 	doUi();
     }
 else
     {
     // Revert to lastPosition if we have multiple matches or warnings,
     // especially in case user manually edits browser location as in #13009:
     char *position = cartUsualString(cart, "lastPosition", hDefaultPos(database));
     cartSetString(cart, hgvaRange, position);
     if (webGotWarnings())
 	{
 	// We land here when lookupPosition pops up a warning box.
 	// Reset the problematic position and show the main page.
 	doMainPage();
 	}
     // If lookupPosition returned FALSE and didn't report warnings,
     // then it wrote HTML showing multiple position matches & links.
     }
 
 cartCheckout(&cart);
+if (! isCommandLine)
     cgiExitTime("hgVai", enteredMainTime);
 return 0;
 }