1a2011f25ac0bd4ce02ed0eb093ff169724f9047
angie
  Mon May 2 16:39:23 2016 -0700
Added trackDb setting "tableBrowser noGenome", which allows tables to appear in TB and DI menus,
unlike "tableBrowser off", but does not allow genome-wide queries on the tables.  The new "noGenome"
setting is used for OMIM tracks -- OMIM gave the OK for non-genome-wide queries on their tables.

See #4458#note-53 for details of UI & functional changes to the TB and DI for noGenome tracks.

hg/lib/cartTrackDb.c handles access control based on trackDb tableBrowser settings (and the
seldom-used tableAccessControl database tables that restrict tables to be viewed only by
certain hosts).  As before, 'tableBrowser off' means that the track is removed from the
trackList so the TB & DI don't even know that it exists.  'tableBrowser noGenome' tracks are
included in the trackList, but the tracks and any tables listed after 'noGenome' are hashed
for later use by cartTrackDbIsNoGenome().  The hash used to contain permitted-host lists,
but now contains structs that combine the permitted-host lists with a noGenome flag.

hgIntegrator.c now includes a 'noGenome' flag in the JSONified groupedTrackDb, which the JS
code uses to identify noGenome tracks.  When executing a query, if the query region is genome
but hgi_querySpec has noGenome related tables left over from past position-only queries, those
related table settings are removed from the parsed JSON querySpec->config->relatedTables that is
passed down into annoStreamDb.  If one of the dataSources is noGenome but the region is genome
(should be possible only by URL-tweaking), the region is forced to position.

In hgTables, when region is genome, correlation and intersection track menu options for
noGenome tracks are disabled.  On the main page, JS code controls whether options are disabled
depending on the current region.  When listing related tables for filtering or selected fields
output, if region is genome then the checkboxes for noGenome tables are disabled.  If the cart
has noGenome related table or intersection settings left over from past searches, they are
ignored.  If a noGenome query URL is tweaked to have hgta_region=genome, the TB errors out.

hgIntegratorModel.js handles disabling of menu options and related table field settings for
noGenome tracks when region is genome.

refs #4458

diff --git src/hg/inc/jsHelper.h src/hg/inc/jsHelper.h
index 5c99cff..5398b9d 100644
--- src/hg/inc/jsHelper.h
+++ src/hg/inc/jsHelper.h
@@ -1,166 +1,171 @@
 // jsHelper.c - helper routines for interface between CGIs and client-side javascript
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #ifndef JSHELPER_H
 #define JSHELPER_H
 
 #include "cart.h"
 #include <regex.h>
 #include "jsonParse.h"
 
 #define JS_CLEAR_ALL_BUTTON_LABEL    "Clear all"
 #define JS_SET_ALL_BUTTON_LABEL  "Set all"
 #define JS_DEFAULTS_BUTTON_LABEL "Set defaults"
 
 // Make toggle and [+][-] buttons without image gifs.
 // Not ready for this release.
 //#define BUTTONS_BY_CSS
 
 void jsCreateHiddenForm(struct cart *cart, char *scriptName,
 	char **vars, int varCount);
 /* Create a hidden form with the given variables.  Must be
  * called. */
 
 void jsInit();
 /* If this is the first call, set window.onload to the operations
  * performed upon loading a page and print supporting javascript.
  * Currently this just sets the page vertical position if specified on
  * CGI, and includes jsHelper.js.
  * Subsequent calls do nothing, so this can be called many times. */
 
 struct dyString *jsOnChangeStart();
 /* Start up an onChange string */
 
 char *jsOnChangeEnd(struct dyString **pDy);
 /* Finish up javascript onChange command. */
 
 void jsDropDownCarryOver(struct dyString *dy, char *var);
 /* Add statement to carry-over drop-down item to dy. */
 
 void jsTextCarryOver(struct dyString *dy, char *var);
 /* Add statement to carry-over text item to dy. */
 
 void jsTrackingVar(char *jsVar, char *val);
 /* Emit a little Javascript to keep track of a variable.
  * This helps especially with radio buttons. */
 
 void jsMakeTrackingRadioButton(char *cgiVar, char *jsVar,
 	char *val, char *selVal);
 /* Make a radio button that also sets tracking variable
  * in javascript. */
 
+void jsMakeTrackingRadioButtonExtraHtml(char *cgiVar, char *jsVar,
+                                        char *val, char *selVal, char *extraHtml);
+/* Make a radio button with extra HTML attributes that also sets tracking variable
+ * in javascript. */
+
 void jsMakeTrackingCheckBox(struct cart *cart, char *cgiVar,
 	char *jsVar, boolean usualVal);
 /* Make a check box filling in with existing value and
  * putting a javascript tracking variable on it. */
 
 void jsTrackedVarCarryOver(struct dyString *dy, char *cgiVar, char *jsVar);
 /* Carry over tracked variable (radio button?) to hidden form. */
 
 char *jsRadioUpdate(char *cgiVar, char *jsVar, char *val);
 /* Make a little javascript to check and uncheck radio buttons
  * according to new value.  To use this you must have called
  * jsInit somewhere, and also must use jsMakeTrackingRadioButton
  * to make the buttons. */
 
 char *jsSetVerticalPosition(char *form);
 /* Returns a javascript statement for storing the vertical position of the
  * page; typically this would go just before a document submit.
  * jsInit must be called first.
  * Do not free return value!   */
 
 void jsMakeCheckboxGroupSetClearButton(char *buttonVar, boolean isSet);
 /* Make a button for setting or clearing a set of checkboxes with the same name.
  * Uses only javascript to change the checkboxes, no resubmit. */
 
 void jsMakeSetClearContainer();
 /* Begin a wrapper div with class setClearContainer, plus 'Set all' and 'Clear all' buttons.
  * This should be followed by a bunch of checkboxes, and then a call to jsEndContainer. */
 
 void jsEndContainer();
 /* End a wrapper div. */
 
 char *jsPressOnEnter(char *button);
 /* Returns a javascript statement that clicks button when the Enter key
  * has been pressed; typically this would go in a text input.
  * jsInit must be called first.
  * Do not free return value!  */
 
 void jsIncludeFile(char *fileName, char *noScriptMsg);
 /* Prints out html to include given javascript file from the js directory; suppresses redundant
  *  <script ...> tags if called repeatedly.
  * <noscript>...</noscript> tags are provided automatically. The noscript message may be specified via
  * the noScriptMsg parameter (the string may contain HTML markup). A default msg is provided
  * if noScriptMsg == NULL; noscript msg is suppressed if noScriptMsg == "" (this is useful
  * if you want to more carefully control where the message will appear on the page). */
 
 void jsIncludeReactLibs();
 /* Prints out <script src="..."> tags for external libraries including ReactJS & ImmutableJS
  * and our own model libs, React mixins and components. */
 
 char *jsCheckAllOnClickHandler(char *idPrefix, boolean state);
 /* Returns javascript for use as an onclick attribute value to apply "check all"/"uncheck all"
  * to all checkboxes with given idPrefix.
  * state parameter determines whether to "check all" or "uncheck all" (TRUE means "check all"). */
 
 void cgiMakeCheckAllSubmitButton(char *name, char *value, char *id, char *idPrefix, boolean state);
 /* Make submit button which uses javascript to apply check all or uncheck all to all
  * checkboxes with given idPrefix.
  * state parameter determines whether to "check all" or "uncheck all" (TRUE means "check all").
  * id parameter may be NULL */
 
 char *jsStripJavascript(char *str);
 /* Strip out anything that looks like javascript in html string.
    This function is designed to cleanup user input (e.g. to avoid XSS attacks).
    Returned string should be free'ed after use. */
 
 char *stripRegEx(char *str, char *regEx, int flags);
 /* Strip out text matching regEx from str.
    flags is passed through to regcomp as the cflags argument.
    Returned string should be free'ed after use. */
 
 char *replaceRegEx(char *str, char *replace, char *regEx, int flags);
 /* Replace text matching regEx in str with replace string.
    flags is passed through to regcomp as the cflags argument.
    Returned string should be free'ed after use. */
 
 void jsBeginCollapsibleSection(struct cart *cart, char *track, char *section, char *sectionTitle,
 			       boolean isOpenDefault);
 /* Make the hidden input, collapse/expand button and <TR id=...> needed for utils.js's
  * setTableRowVisibility().  Caller needs to have already created a <TABLE> and <FORM>. */
 
 void jsBeginCollapsibleSectionFontSize(struct cart *cart, char *track, char *section,
 				       char *sectionTitle, boolean isOpenDefault, char *fontSize);
 /* Make the hidden input, collapse/expand button and <TR id=...> needed for utils.js's
  * setTableRowVisibility().  Caller needs to have already created a <TABLE> and <FORM>. */
 
 void jsBeginCollapsibleSectionOldStyle(struct cart *cart, char *track, char *section,
 				       char *sectionTitle, boolean isOpenDefault);
 /* Make the hidden input, collapse/expand button and <TR id=...> needed for utils.js's
  * setTableRowVisibility().  Caller needs to have already created a <TABLE> and <FORM>. 
  * With support for varying font size */
 
 void jsEndCollapsibleSection();
 /* End the collapsible <TR id=...>. */
 
 void jsReloadOnBackButton(struct cart *cart);
 /* Add some javascript to detect that the back button (or reload) has been pressed,
  * and to resubmit in that case to redraw the page with the latest cart contents. */
 
 // --- Genome browser specific json stuff - see also inc/json.h for more generic stuff 
 
 void jsonPrint(struct jsonElement *json, char *name, int indentLevel);
 // print out a jsonElement and children using hPrintf, and for indentLevel >=0
 // bracketing with comments.  See also jsonPrintToFile.
 
 void jsonErrPrintf(struct dyString *ds, char *format, ...)
 //  Printf a json error to a dyString for communicating with ajax code; format is:
 //  {"error": error message here}
 #if defined(__GNUC__)
 __attribute__((format(printf, 2, 3)))
 #endif
 ;
 
 #endif /* JSHELPER_H */