53a520d17d725ceacf50f5eecead0c75470ce48a
braney
Sat Jul 29 16:13:58 2017 -0700
adding hgCollection, a tool to build custom collections of tracks
diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c
new file mode 100644
index 0000000..ac765cf
--- /dev/null
+++ src/hg/hgCollection/hgCollection.c
@@ -0,0 +1,821 @@
+/* hgVai - Variant Annotation Integrator. */
+
+/* Copyright (C) 2014 The Regents of the University of California
+ * See README in this or parent directory for licensing information. */
+#include "common.h"
+#include "linefile.h"
+#include "hash.h"
+#include "options.h"
+#include "jksql.h"
+#include "htmshell.h"
+#include "web.h"
+#include "cheapcgi.h"
+#include "cart.h"
+#include "cartTrackDb.h"
+#include "genbank.h"
+#include "hgConfig.h"
+#include "hgHgvs.h"
+#include "hui.h"
+#include "grp.h"
+#include "hCommon.h"
+#include "hgFind.h"
+#include "hPrint.h"
+#include "jsHelper.h"
+#include "memalloc.h"
+#include "textOut.h"
+#include "trackHub.h"
+#include "hubConnect.h"
+#include "twoBit.h"
+#include "gpFx.h"
+#include "bigGenePred.h"
+#include "udc.h"
+#include "knetUdc.h"
+#include "md5.h"
+#include "regexHelper.h"
+#include "hAnno.h"
+#include "trashDir.h"
+#include "api.h"
+#include "customComposite.h"
+
+//#include "libifyMe.h"
+
+
+/* Global Variables */
+struct cart *cart; /* CGI and other variables */
+struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */
+char *genome = NULL; /* Name of genome - mouse, human, etc. */
+char *database = NULL; /* Current genome database - hg17, mm5, etc. */
+char *regionType = NULL; /* genome, ENCODE pilot regions, or specific position range. */
+struct grp *fullGroupList = NULL; /* List of all groups. */
+struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */
+ struct pipeline *compressPipeline = (struct pipeline *)NULL;
+
+
+// Null terminated list of CGI Variables we don't want to save permanently:
+char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", NULL,};
+
+struct track
+{
+struct track *next;
+struct track *trackList;
+struct trackDb *tdb;
+char *name;
+char *shortLabel;
+char *longLabel;
+char *visibility;
+};
+
+static char *getString(char **input)
+{
+char *ptr = *input;
+
+if (*ptr != '"')
+ errAbort("string must start with \"");
+ptr++;
+char *ret = ptr;
+for(; *ptr != '"'; ptr++)
+ ;
+*ptr = 0;
+ptr++;
+
+if (*ptr == ',')
+ ptr++;
+
+*input = ptr;
+
+return ret;
+}
+
+char *makeUnique(struct hash *nameHash, char *name)
+// Make the name of this track unique.
+{
+char *skipHub = trackHubSkipHubName(name);
+if (hashLookup(nameHash, skipHub) == NULL)
+ {
+ hashStore(nameHash, name);
+ return skipHub;
+ }
+
+unsigned count = 0;
+char buffer[4096];
+
+for(;; count++)
+ {
+ safef(buffer, sizeof buffer, "%s%d", skipHub, count);
+ if (hashLookup(nameHash, buffer) == NULL)
+ {
+ hashStore(nameHash, buffer);
+ return cloneString(buffer);
+ }
+ }
+
+return NULL;
+}
+
+static boolean trackCanBeAdded(struct trackDb *tdb)
+{
+return (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) && (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type)) ;
+}
+
+static void printGroup(char *parent, struct trackDb *tdb, boolean folder, boolean user)
+{
+printf("| %s | ", parent, trackHubSkipHubName(tdb->track), user ? "class='user'" : "", folder ? "folder" : "file", tdb->shortLabel );
+printf("%s |
\n", tdb->longLabel);
+
+
+if (tdb->subtracks)
+ {
+ struct trackDb *subTdb;
+
+ for(subTdb = tdb->subtracks; subTdb; subTdb = subTdb->next)
+ printGroup(trackHubSkipHubName(tdb->track), subTdb, FALSE, user);
+ }
+}
+
+static void outHubHeader(FILE *f, char *db, char *hubName)
+{
+char *hubFile = strrchr(hubName, '/') + 1;
+
+fprintf(f,"hub hub1\n\
+shortLabel User Composite\n\
+longLabel User Composite\n\
+genomesFile %s\n\
+email braney@soe.ucsc.edu\n\
+descriptionUrl hub.html\n\n", hubFile);
+fprintf(f,"genome %s\n\
+trackDb %s\n\n", db, hubFile);
+}
+
+
+static char *getHubName(char *db)
+{
+struct tempName hubTn;
+char buffer[4096];
+safef(buffer, sizeof buffer, "%s-%s", customCompositeCartName, db);
+char *hubName = cartOptionalString(cart, buffer);
+
+if (hubName == NULL)
+ {
+ trashDirDateFile(&hubTn, "hgComposite", "hub", ".txt");
+ hubName = cloneString(hubTn.forCgi);
+ cartSetString(cart, buffer, hubName);
+ FILE *f = mustOpen(hubName, "a");
+ outHubHeader(f, db, hubName);
+ fclose(f);
+ cartSetString(cart, "hubUrl", hubName);
+ cartSetString(cart, hgHubConnectRemakeTrackHub, hubName);
+ }
+return hubName;
+}
+
+static bool subtrackEnabledInTdb(struct trackDb *subTdb)
+/* Return TRUE unless the subtrack was declared with "subTrack ... off". */
+{
+bool enabled = TRUE;
+char *words[2];
+char *setting;
+if ((setting = trackDbLocalSetting(subTdb, "parent")) != NULL)
+ {
+ if (chopLine(cloneString(setting), words) >= 2)
+ if (sameString(words[1], "off"))
+ enabled = FALSE;
+ }
+else
+ return subTdb->visibility != tvHide;
+
+return enabled;
+}
+
+bool isSubtrackVisible(struct trackDb *tdb)
+/* Has this subtrack not been deselected in hgTrackUi or declared with
+ * * "subTrack ... off"? -- assumes composite track is visible. */
+{
+boolean overrideComposite = (NULL != cartOptionalString(cart, tdb->track));
+bool enabledInTdb = subtrackEnabledInTdb(tdb);
+char option[1024];
+safef(option, sizeof(option), "%s_sel", tdb->track);
+boolean enabled = cartUsualBoolean(cart, option, enabledInTdb);
+if (overrideComposite)
+ enabled = TRUE;
+return enabled;
+}
+
+
+bool isParentVisible( struct trackDb *tdb)
+// Are this track's parents visible?
+{
+if (tdb->parent == NULL)
+ return TRUE;
+
+if (!isParentVisible(tdb->parent))
+ return FALSE;
+
+char *cartVis = cartOptionalString(cart, tdb->parent->track);
+boolean vis;
+if (cartVis != NULL)
+ vis = differentString(cartVis, "hide");
+else if (tdbIsSuperTrack(tdb->parent))
+ vis = tdb->parent->isShow;
+else
+ vis = tdb->parent->visibility != tvHide;
+
+return vis;
+}
+
+
+void addVisibleTracks()
+{
+printf("| All Visible | All the tracks visible in hgTracks |
\n");
+struct trackDb *tdb;
+for(tdb = fullTrackList; tdb; tdb = tdb->next)
+ {
+ if (isParentVisible(tdb) && isSubtrackVisible(tdb))
+ {
+ printGroup("visible", tdb, FALSE, FALSE);
+ }
+ }
+}
+
+static void doHeader()
+{
+puts(
+"\n"
+" \n"
+"
\n"
+);
+printf(
+"
\n"
+" My Collections \n"
+" "
+"
Build Custom Collections of Tracks \n" );
+puts(
+"\n"
+"
\n"
+" \n"
+" \n"
+" \n"
+" \n"
+"
\n"
+"
\n"
+
+"
\n"
+"
\n"
+"
\n"
+
+"
Save
\n"
+"
Discard Changes
\n"
+"
\n" );
+puts(
+"
\n"
+"
\n"
+"
All Tracks
\n"
+"
\n");
+
+puts(
+"
\n"
+"
Make New Collection
\n"
+"
\n"
+);
+puts(
+"
\n"
+"
\n");
+struct grp *curGroup;
+printf("| My Collections | ");
+printf("Your collected tracks. |
\n");
+for(curGroup = fullGroupList; curGroup; curGroup = curGroup->next)
+ {
+ if ((hubName != NULL) && sameString(curGroup->name, hubName))
+ break;
+ }
+if (curGroup != NULL)
+ {
+ // print out all the tracks in this group
+ struct trackDb *tdb;
+ for(tdb = fullTrackList; tdb; tdb = tdb->next)
+ {
+ if (sameString(tdb->grp, hubName))
+ printGroup("collections", tdb, TRUE, TRUE);
+ }
+ }
+//addVisibleTracks();
+for(curGroup = fullGroupList; curGroup; curGroup = curGroup->next)
+ {
+ if ((hubName != NULL) && sameString(curGroup->name, hubName))
+ continue;
+ printf("| %s | |
\n", curGroup->name, curGroup->label );
+ struct trackDb *tdb;
+ for(tdb = fullTrackList; tdb; tdb = tdb->next)
+ {
+ if ( sameString(tdb->grp, curGroup->name))
+ {
+ printGroup(curGroup->name, tdb, FALSE, FALSE);
+ }
+ }
+ }
+printf("
\n");
+}
+
+static void doAttributes()
+{
+puts(
+" \n"
+" \n"
+"
Set Attributes
\n"
+"
\n");
+puts(
+"
\n"
+);
+puts(
+"
\n"
+"
Discard Changes
\n"
+"
\n"
+);
+puts(
+"
"
+"Drag to custom composite to copy to Collections"
+"
"
+);
+
+// mathwig options
+puts(
+"\n"
+);
+
+// custom composite options
+puts(
+""
+""
+"\n"
+"\n"
+"\n"
+""
+"\n"
+"\n"
+"
\n"
+);
+
+// custom track options
+puts(
+"\n"
+
+);
+
+}
+
+static void onclickJumpToTop(char *id)
+/* CSP-safe click handler arrows that cause scroll to top */
+{
+jsOnEventById("click", id, "$('html,body').scrollTop(0);");
+}
+
+static void printHelp()
+{
+puts(
+"\n"
+" \n"
+"
Help
\n"
+"
\n"
+);
+#define DATA_INFO_JUMP_ARROW_ID "hgGtexDataInfo_jumpArrow"
+printf(
+" \n",
+DATA_INFO_JUMP_ARROW_ID
+);
+onclickJumpToTop(DATA_INFO_JUMP_ARROW_ID);
+puts(
+"
\n"
+"
\n"
+"
\n");
+puts("
");
+puts("
");
+webIncludeHelpFileSubst("hgCompositeHelp", NULL, FALSE);
+
+puts("
");
+puts("
");
+
+puts(
+"
\n"
+"