aab4f66a2aca5293f3536cc1d1438b17d2b09dfd
tdreszer
  Thu May 5 16:14:15 2011 -0700
A large set of tiny changes.  These fix a lot of discrepencies with bgcolor and font color declarations which were tripping up docttype 4.01.
diff --git src/hg/hgHubConnect/hgHubConnect.c src/hg/hgHubConnect/hgHubConnect.c
index c2e9964..caf7446 100644
--- src/hg/hgHubConnect/hgHubConnect.c
+++ src/hg/hgHubConnect/hgHubConnect.c
@@ -1,369 +1,369 @@
 /* hgHubConnect - the CGI web-based program to select track data hubs to connect with. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "errabort.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "cheapcgi.h"
 #include "htmshell.h"
 #include "hdb.h"
 #include "hui.h"
 #include "cart.h"
 #include "dbDb.h"
 #include "web.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "trashDir.h"
 #include "hPrint.h"
 
 #define TEXT_ENTRY_ROWS 7
 #define TEXT_ENTRY_COLS 73
 #define CONFIG_ENTRY_ROWS 3
 #define SAVED_LINE_COUNT  50
 
 #define HUB_CUSTOM_TEXT_ALT_VAR  "hghub_customText"
 #define HUB_CUSTOM_FILE_VAR      "hghub.customFile"
 #define HUB_UPDATED_ID           "hghub_updatedId"
 
 
 
 #define hgHubDataText      HUB_CUSTOM_TEXT_ALT_VAR
 #define hgHubDataFile      HUB_CUSTOM_FILE_VAR
 #define hgHubUpdatedId     HUB_UPDATED_ID
 
 #define hgHub             "hgHub_"  /* prefix for all control variables */
 #define hgHubDo            hgHub   "do_"    /* prefix for all commands */
 #define hgHubDoAdd         hgHubDo "add"
 
 
 struct cart *cart;	/* The user's ui state. */
 struct hash *oldVars = NULL;
 
 static char *destUrl = "../cgi-bin/hgTracks";
 static char *pageTitle = "Import Tracks from Data Hubs";
 char *database = NULL;
 char *organism = NULL;
 
 boolean nameInCommaList(char *name, char *commaList)
 /* Return TRUE if name is in comma separated list. */
 {
 if (commaList == NULL)
     return FALSE;
 int nameLen = strlen(name);
 for (;;)
     {
     char c = *commaList;
     if (c == 0)
         return FALSE;
     if (memcmp(name, commaList, nameLen) == 0)
         {
 	c = commaList[nameLen];
 	if (c == 0 || c == ',')
 	    return TRUE;
 	}
     commaList = strchr(commaList, ',');
     if (commaList == NULL)
         return FALSE;
     commaList += 1;
     }
 }
 
 void hgHubConnectPrivate()
 /* Put up the list of private hubs and other controls for the page. */
 {
 printf("<B>List of Private Hubs</B><BR>");
 struct hubConnectStatus *hub, *hubList =  hubConnectStatusListFromCart(cart);
 int count = 0;
 for(hub = hubList; hub; hub = hub->next)
     {
     if (hub->id > 0)
 	continue;
     if (count)
 	webPrintLinkTableNewRow();
     else
 	webPrintLinkTableStart();
     count++;
 
     if (isEmpty(hub->errorMessage))
 	{
 	webPrintLinkCellStart();
 	char hubName[32];
 	safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
 	cartMakeCheckBox(cart, hubName, FALSE);
 	webPrintLinkCellEnd();
 	}
     else
 	webPrintLinkCell("error");
     webPrintLinkCell(hub->shortLabel);
     if (isEmpty(hub->errorMessage))
 	webPrintLinkCell(hub->longLabel);
     else
 	webPrintLinkCell(hub->errorMessage);
     webPrintLinkCell(hub->hubUrl);
     }
 if (count)
     webPrintLinkTableEnd();
 else
     printf("No Private Track Hubs for this genome assembly<BR>");
 }
 
 static void makeNewHubButton()
 {
 printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"secondForm\">\n", "../cgi-bin/hgHubConnect");
 cartSaveSession(cart);
 cgiMakeHiddenVar(hgHubDoAdd, "on");
 cgiMakeButton("add", "Add new private hub");
 printf("</FORM>\n");
 }
 
 static void makeGenomePrint()
 {
 getDbAndGenome(cart, &database, &organism, oldVars);
 printf("<B>genome:</B> %s &nbsp;&nbsp;&nbsp;<B>assembly:</B> %s  ", 
 	organism, hFreezeDate(database));
 }
 
 void hgHubConnectPublic()
 /* Put up the list of external hubs and other controls for the page. */
 {
 printf("<B>List of Public Hubs</B><BR>");
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 safef(query, sizeof(query), "select id,shortLabel,longLabel,errorMessage,hubUrl,dbList from %s", 
 	hubConnectTableName); 
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row;
 
 boolean gotAnyRows = FALSE;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *id = row[0], *shortLabel = row[1], *longLabel = row[2], *errorMessage = row[3],
     	 *url = row[4], *dbList = row[5];
     if (nameInCommaList(database, dbList))
 	{
 	if (gotAnyRows)
 	    webPrintLinkTableNewRow();
 	else
 	    {
 	    webPrintLinkTableStart();
 	    gotAnyRows = TRUE;
 	    }
 	if (isEmpty(errorMessage))
 	    {
 	    webPrintLinkCellStart();
 	    char hubName[32];
 	    safef(hubName, sizeof(hubName), "%s%s", hgHubConnectHubVarPrefix, id);
 	    cartMakeCheckBox(cart, hubName, FALSE);
 	    webPrintLinkCellEnd();
 	    }
 	else
 	    webPrintLinkCell("error");
 	webPrintLinkCell(shortLabel);
 	if (isEmpty(errorMessage))
 	    webPrintLinkCell(longLabel);
 	else
 	    webPrintLinkCell(errorMessage);
 	webPrintLinkCell(url);
 	}
     }
 sqlFreeResult(&sr);
 if (gotAnyRows)
     webPrintLinkTableEnd();
 else
     printf("No Track Hubs for this genome assembly");
 hDisconnectCentral(&conn);
 }
 
 static void addIntro()
 {
 printf("Enter URL to remote hub.<BR>\n");
 }
 
 void makeClearButton(char *field)
 /* UI button that clears a text field */
 {
 char javascript[1024];
 safef(javascript, sizeof javascript,
         "document.mainForm.%s.value = '';", field);
 cgiMakeOnClickButton(javascript, "&nbsp;Clear&nbsp;");
 }
 
 void addPrivateHubForm(struct hubConnectStatus *hub, char *err)
 /* display UI for adding private hubs by URL or pasting data */
 {
 getDbAndGenome(cart, &database, &organism, oldVars);
 boolean gotClade = FALSE;
 boolean isUpdateForm = FALSE;
 if (hub)
     {
     isUpdateForm = TRUE;
     }
 else
     /* add form needs clade for assembly menu */
     gotClade = hGotClade();
 
 /* main form */
 printf("<FORM ACTION=\"%s\" METHOD=\"%s\" "
     " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n",
     "../cgi-bin/hgHubConnect", cartUsualString(cart, "formMethod", "POST"));
 cartSaveSession(cart);
 cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
 
 /* intro text */
 puts("<P>");
 puts("Add your own private data hub for the browser.");
 addIntro();
 puts("<P>");
 
 /* row for error message */
 if (err)
-    printf("<P><B>&nbsp;&nbsp;&nbsp;&nbsp;<I><FONT COLOR='RED'>Error</I></FONT>&nbsp;%s</B><P>", err);
+    printf("<P><B>&nbsp;&nbsp;&nbsp;&nbsp;<span style='color:red; font-style:italic;'>Error</span>&nbsp;%s</B><P>", err);
 
 printf("Enter URL:");
 
 hTextVar(hgHubDataText, "", 60);
 cgiMakeSubmitButton();
 
 puts("</FORM>");
 }
 
 void helpPrivateHub()
 {
 printf("Private hubs are constructed the same way as public hubs, but they "
    "aren't listed in hgcentral<BR>\n");
 }
 
 void doAddPrivateHub(struct cart *theCart, char *err)
 /* Write header and body of html page. */
 {
 cartWebStart(cart, database, "Add Private Hub");
 addPrivateHubForm(NULL, err);
 helpPrivateHub();
 cartWebEnd(cart);
 }
 
 void hubSaveInCart(struct cart *cart, struct hubConnectStatus *hub)
 {
 char hubName[1024];
 char *oldHubTrashName = cartOptionalString(cart, hubFileVar());
 static struct tempName tn;
 trashDirFile(&tn, "hub", "hub_", ".txt");
 char *hubTrashName = tn.forCgi;
 FILE *f = mustOpen(hubTrashName, "w");
 
 if (oldHubTrashName == NULL)
     {
     hub->id = -1;
     }
 else
     {
     struct lineFile *lf = lineFileOpen(oldHubTrashName, TRUE);
     int lineSize;
     char *line;
     int count = 1;
 
     while (lineFileNext(lf, &line, &lineSize))
 	{
 	count++;
 	fprintf(f, "%s\n", line);
 	}
     lineFileClose(&lf);
     unlink(oldHubTrashName);
     hub->id = -count;
     }
 hubWriteToFile(f, hub);
 carefulClose(&f);
 
 safef(hubName, sizeof(hubName), "%s%d", hgHubConnectHubVarPrefix, hub->id);
 cartSetString(cart, hubName, "1");
 
 cartSetString(cart, hubFileVar(), hubTrashName);
 }
 
 void checkForNewHub(struct cart *cart)
 {
 char *url = cartOptionalString(cart, hgHubDataText);
 
 if (url != NULL)
     {
     struct hubConnectStatus *hub = NULL;
     struct trackHub *tHub = NULL;
 
     struct errCatch *errCatch = errCatchNew();
     if (errCatchStart(errCatch))
 	tHub = trackHubOpen(url, "1");
     errCatchEnd(errCatch);
     if (errCatch->gotError)
 	{
 	warn(errCatch->message->string);
 	return;
 	}
     errCatchFree(&errCatch);
     AllocVar(hub);
 
     hub->hubUrl = cloneString(url);
     hub->errorMessage = "";
     hub->shortLabel = tHub->shortLabel;
     hub->longLabel = tHub->longLabel;
     hub->dbCount = 0;
     AllocArray(hub->dbArray, 1);
     hub->dbArray[0] = database;
 
     hubSaveInCart(cart, hub);
     }
 }
 
 void doMiddle(struct cart *theCart)
 /* Write header and body of html page. */
 {
 cart = theCart;
 setUdcCacheDir();
 if (cartVarExists(cart, hgHubDoAdd))
     doAddPrivateHub(cart, NULL);
 else
     {
     cartWebStart(cart, NULL, pageTitle);
     checkForNewHub(cart);
 
     printf(
        "<P>Track data hubs are collections of tracks from outside of UCSC that can be imported into "
        "the Genome Browser.  To import a public hub check the box in the list below. "
        "After import the hub will show up as a group of tracks with its own blue "
        "bar and label underneath the main browser graphic, and in the configure page. </P>\n"
        );
     makeGenomePrint();
 
     printf("<BR><P>");
     hgHubConnectPublic();
     printf("Contact <A HREF=\"mailto:genome@soe.ucsc.edu\"> genome@soe.ucsc.edu </A>to add a public hub.</P>\n");
     puts("<BR>");
     hgHubConnectPrivate();
     makeNewHubButton();
     puts("<BR>");
 
     printf("<FORM ACTION=\"%s\" METHOD=\"POST\" NAME=\"mainForm\">\n", destUrl);
     cartSaveSession(cart);
 
     cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on");
     cgiMakeButton("Submit", "Use Selected Hubs");
     puts("</FORM>");
 
     }
 cartWebEnd();
 }
 
 char *excludeVars[] = {"Submit", "submit", "hc_one_url", hgHubConnectCgiDestUrl, hgHubDoAdd, hgHubDataText, NULL};
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 oldVars = hashNew(10);
 cgiSpoof(&argc, argv);
 cartEmptyShell(doMiddle, hUserCookie(), excludeVars, oldVars);
 return 0;
 }