void webMain(struct liftOverChain *chain, char *dataFormat, boolean multiple)
/* set up page for entering data */
{
struct dbDb *dbList;
char *fromOrg = hArchiveOrganism(chain->fromDb), *toOrg = hArchiveOrganism(chain->toDb);
cgiParagraph(
"This tool converts genome coordinates and genome annotation files "
"between assemblies. "
"The input data can be pasted into the text box, or uploaded from a file. "
"If a pair of assemblies cannot be selected from the pull-down menus,"
" a direct lift between them is unavailable. "
"However, a sequential lift may be possible. "
"Example: lift from Mouse, May 2004, to Mouse, Feb. 2006, and then from Mouse, "
"Feb. 2006 to Mouse, July 2007 to achieve a lift from mm5 to mm9. "
"");
/* create HMTL form */
puts("<FORM ACTION=\"../cgi-bin/hgLiftOver\" METHOD=\"POST\" "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n");
cartSaveSession(cart);
/* create HTML table for layout purposes */
puts("\n<TABLE WIDTH=\"100%%\">\n");
/* top two rows -- genome and assembly menus */
cgiSimpleTableRowStart();
cgiTableField("Original Genome: ");
cgiTableField("Original Assembly: ");
cgiTableField("New Genome: ");
cgiTableField("New Assembly: ");
cgiTableRowEnd();
cgiSimpleTableRowStart();
/* genome */
cgiSimpleTableFieldStart();
dbList = hGetLiftOverFromDatabases();
printSomeGenomeListHtmlNamed(HGLFT_FROMORG_VAR, chain->fromDb, dbList, onChange);
cgiTableFieldEnd();
/* from assembly */
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->fromDb, dbList, HGLFT_FROMDB_VAR,
TRUE, onChange);
cgiTableFieldEnd();
/* to assembly */
cgiSimpleTableFieldStart();
dbDbFreeList(&dbList);
dbList = hGetLiftOverToDatabases(chain->fromDb);
printLiftOverGenomeList(HGLFT_TOORG_VAR, chain->toDb, dbList, onChange);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printAllAssemblyListHtmlParm(chain->toDb, dbList, HGLFT_TODB_VAR, TRUE, "");
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiParagraph(" ");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum ratio of bases that must remap:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINMATCH,chain->minMatch,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum chain size in target:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZET,chain->minSizeT,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Minimum hit size in query:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeIntVar(HGLFT_MINSIZEQ,chain->minSizeQ,4);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Allow multiple output regions:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_MULTIPLE,multiple);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("Min ratio of alignment blocks/exons that must map:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeDoubleVar(HGLFT_MINBLOCKS,chain->minBlocks,6);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiTableField("If thickStart/thickEnd is not mapped, use the closest mapped base:");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
cgiMakeCheckBox(HGLFT_FUDGETHICK,(chain->fudgeThick[0]=='Y') ? TRUE : FALSE);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file format menu */
cgiParagraph(
" For descriptions of the supported data formats, see the bottom of this page.");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiTableField("Data Format: ");
cgiSimpleTableFieldStart();
cgiMakeDropList(HGLFT_DATAFORMAT_VAR,
formatList, sizeof(formatList)/sizeof (char*) - 1, dataFormat);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* text box and two buttons (submit, reset) */
cgiParagraph(" Paste in data:\n");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeTextArea(HGLFT_USERDATA_VAR, cartCgiUsualString(cart, HGLFT_USERDATA_VAR, NULL), 10, 80);
cgiTableFieldEnd();
/* right element of table is a nested table
* with two buttons stacked on top of each other */
cgiSimpleTableFieldStart();
cgiSimpleTableStart();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeSubmitButton();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
cgiMakeClearButton("mainForm", HGLFT_USERDATA_VAR);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
cgiTableFieldEnd();
cgiTableRowEnd();
cgiTableEnd();
/* next row -- file upload controls */
cgiParagraph(" Or upload data from a file:");
cgiSimpleTableStart();
cgiSimpleTableRowStart();
printf("<TD><INPUT TYPE=FILE NAME=\"%s\"></TD>\n", HGLFT_DATAFILE_VAR);
puts("<TD><INPUT TYPE=SUBMIT NAME=SubmitFile VALUE=\"Submit File\"></TD>\n");
cgiTableRowEnd();
cgiTableEnd();
printf("<input type=\"hidden\" name=\"%s\" value=\"0\">\n",
HGLFT_REFRESHONLY_VAR);
puts("</FORM>\n");
cartSaveSession(cart);
puts("</FORM>");
freeMem(fromOrg);
freeMem(toOrg);
}
void doMiddle()
/* Write what goes between BODY and /BODY */
{
pushWarnHandler(localWarn);
if (!cgiServerHttpsIsOn())
usage();
struct sqlConnection *conn = edwConnectReadWrite();
printf("<FORM ACTION=\"edwWebRegisterScript\" METHOD=POST>\n");
printf("<B>Register Script with ENCODE Data Warehouse</B><BR>\n");
#ifdef SOON
uglyf("HTTP_AUTHENTICATION: '%s'<BR>\n", getenv("HTTP_AUTHENTICATION"));
uglyf("HTTP_AUTHORIZATION: '%s'<BR>\n", getenv("HTTP_AUTHORIZATION"));
dumpEnv(mainEnv);
#endif
if (userEmail == NULL)
{
printf("Please sign in:");
printf("<INPUT TYPE=BUTTON NAME=\"signIn\" VALUE=\"sign in\" id=\"signin\">");
}
else if (cgiVarExists("description"))
{
struct edwUser *user = edwUserFromEmail(conn, userEmail);
if (user == NULL)
edwWarnUnregisteredUser(userEmail);
else
{
char password[HEXED_32_SIZE];
edwRandomHexed32(password);
char babyName[HEXED_32_SIZE];
edwRandomBabble(babyName, sizeof(babyName));
edwRegisterScript(conn, user, babyName, password, cgiString("description"));
printf("Script now registered.<BR>\n");
printf("The script user name is %s.<BR>\n", babyName);
printf("The script password is %s.<BR>\n", password);
printf("Please save the script user name and password somewhere. ");
puts("Please pass these two and the URL");
puts(" of your validated manifest file (validated.txt) to our server to submit data.");
puts("Construct a URL of the form:<BR>");
printf("<PRE>https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit"
"?user=%s&password=%s&url=%s\n</PRE>",
babyName, password,
cgiEncode("http://your.host.edu/your_dir/validated.txt"));
puts("That is pass the CGI encoded variables user, password, and url to the ");
puts("web services CGI at");
puts("https://encodedcc.sdsc.edu/cgi-bin/edwScriptSubmit. ");
puts("You can use the http://encodedcc.sdsc.edu/cgi-bin/edwWebBrowse site to ");
puts("monitor your submission interactively. Please contact your wrangler if you ");
puts("have any questions.<BR>");
cgiMakeButton("submit", "Register another script");
}
printf(" ");
edwPrintLogOutButton();
}
else
{
struct edwUser *user = edwUserFromEmail(conn, userEmail);
edwPrintLogOutButton();
if (user == NULL)
edwWarnUnregisteredUser(userEmail);
else
{
printf("%s is authorized to register a new script<BR>\n", userEmail);
printf("<BR>Script description:\n");
cgiMakeTextVar("description", NULL, 80);
cgiMakeSubmitButton();
}
}
printf("</FORM>\n");
}
