void getFileListAndReason(struct sqlConnection *conn)
/* Put up URL. */
{
edwMustGetUserFromEmail(conn, userEmail);
printf("Please enter in accessions (ENCFF identifiers) for files to deprecate:<BR>");
cgiMakeTextArea("fileList", fileList, 4, 60);
printf("<BR>");
printf("Please enter in reason for deprecating files:<BR>");
cgiMakeTextArea("reason", reason, 4, 60);
printf("<BR>");
printf("Allow me to deprecate files not uploaded by me: ");
cgiMakeCheckBox("allowBox", FALSE);
printf("<BR>");
cgiMakeButton("submit", "submit");
edwPrintLogOutButton();
}
void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\"> <BR>\n",
hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}
void doAdvFilterKeyPaste(struct sqlConnection *conn, struct column *colList,
struct column *col)
/* Handle upload keyword list button press in advanced filter form. */
{
char *varName = NULL;
char buf[1024];
cartRemovePrefix(cart, keyWordPastePrefix);
safef(buf, sizeof(buf), "Paste List : %s - %s", col->shortLabel, col->longLabel);
makeTitle(buf, NULL);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=POST>\n");
cartSaveSession(cart);
hPrintf("Paste in a list of items to match. ");
cgiMakeButton("submit", "submit");
hPrintf("<BR>\n");
varName = colVarName(col, keyWordPastedPrefix);
cgiMakeTextArea(varName, "", 10, 60);
hPrintf("</FORM>");
}
void doPasteIdentifiers(struct sqlConnection *conn)
/* Respond to paste identifiers button. */
{
struct sqlConnection *alternateConn = conn;
char *actualDb = database;
if (sameWord(curTable, WIKI_TRACK_TABLE))
{
alternateConn = wikiConnect();
actualDb = wikiDbName();
}
char *oldPasted = forCurTable() ?
cartUsualString(cart, hgtaPastedIdentifiers, "") : "";
struct hTableInfo *hti = maybeGetHti(actualDb, curTable, conn);
char *idField = getIdField(actualDb, curTrack, curTable, hti);
htmlOpen("Paste In Identifiers for %s", curTableLabel());
if (idField == NULL)
errAbort("Sorry, I can't tell which field of table %s to treat as the "
"identifier field.", curTable);
hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", getScriptName(),
cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
hPrintf("Please paste in the identifiers you want to include.\n");
if (sqlDatabaseExists("hgTemp"))
explainIdentifiers(actualDb, alternateConn, idField);
else
warn("No hgTemp database found for temporary tables.<br>Please src/product/README.mysql.setup for more information.");
hPrintf("<BR>\n");
cgiMakeTextArea(hgtaPastedIdentifiers, oldPasted, 10, 70);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoPastedIdentifiers, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearPasteIdentifierText, "clear");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
if (sameWord(curTable, WIKI_TRACK_TABLE))
wikiDisconnect(&alternateConn);
}
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 uploadPage()
/* Put up initial upload page. */
{
char *oldFileName = cartUsualString(cart, hggUploadFile "__filename", "");
cartWebStart(cart, database, "Upload Data to Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\">");
cartSaveSession(cart);
hPrintf("name of data set: ");
cartMakeTextVar(cart, hggDataSetName, "", 16);
hPrintf("<BR>");
hPrintf("description: ");
cartMakeTextVar(cart, hggDataSetDescription, "", 64);
hPrintf("<BR>\n");
hPrintf("file format: ");
cgiMakeDropList(hggFormatType, formatNames, ArraySize(formatNames),
cartUsualString(cart, hggFormatType, formatNames[0]));
hPrintf("<BR>\n");
hPrintf(" markers are: ");
cgiMakeDropList(hggMarkerType, markerNames, ArraySize(markerNames),
cartUsualString(cart, hggMarkerType, markerNames[0]));
hPrintf("<BR>\n");
hPrintf(" column labels: ");
cgiMakeDropList(hggColumnLabels, colLabelNames, ArraySize(colLabelNames),
cartUsualString(cart, hggColumnLabels, colLabelNames[0]));
hPrintf("<BR>\n");
hPrintf("display min value: ");
cartMakeTextVar(cart, hggMinVal, "", 5);
hPrintf(" max value: ");
cartMakeTextVar(cart, hggMaxVal, "", 5);
hPrintf("<BR>\n");
hPrintf("label values: ");
cartMakeTextVar(cart, hggLabelVals, "", 32);
hPrintf("<BR>\n");
hPrintf("draw connecting lines between markers separated by up to ");
cartMakeIntVar(cart, hggMaxGapToFill, 25000000, 8);
hPrintf(" bases.<BR>");
hPrintf("<BR>\n");
hPrintf("file name: <INPUT TYPE=FILE NAME=\"%s\" VALUE=\"%s\">", hggUploadFile,
oldFileName);
hPrintf("<BR>\n");
hPrintf(" or<BR>\n");
hPrintf("Paste URLs or data:<br>");
cgiMakeTextArea(hggUploadUrl, "", 7, 73);
hPrintf("<BR>\n");
hPrintf("<BR>\n");
cgiMakeButton(hggSubmitUpload, "submit");
hPrintf("</FORM>\n");
hPrintf("<i>Note: If you are uploading more than one data set please give them ");
hPrintf("different names. Only the most recent data set of a given name is ");
hPrintf("kept. Otherwise data sets will be kept for at least 48 hours from ");
hPrintf("last use. After that time you may have to upload them again.</i>");
/* Put up section that describes file formats. */
webNewSection("Upload file formats");
hPrintf("%s",
"<P>The upload file is a table in some format. In all formats there is "
"a single line for each marker. "
"Each line starts with information on the marker, and ends with "
"the numerical values associated with that marker. The exact format "
"of the line depends on what is selected from the markers drop "
"down menu. If this is <i>chromosome base</i> then the line will "
"contain the tab or space-separated fields: chromosome, position, "
"and value(s). The first base in a chromosome is considered position 0. "
"An example <i>chromosome base</i> type line is:<PRE><TT>\n"
"chrX 100000 1.23\n"
"</TT></PRE>The lines for other marker types contain two fields: "
"marker and value(s). For dbSNP rsID's an example is:<PRE><TT>\n"
"rs10218492 0.384\n"
"</TT></PRE>"
"</P><P>"
"The file can contain multiple value fields. In this case a "
"separate graph will be available for each value column in the input "
"table. It's a "
"good idea to set the display min/max values above if you want the "
"graphs to share the same scale."
"</P>"
);
webNewSection("Using the upload page");
hPrintf(
"To upload a file in any of the supported formats, "
"locate the file on your computer using the controls next to <B>file name</B>, "
"or supply a <B>URL</B> to the data, "
"and then submit. The other controls on this form are optional, though "
"filling them out will sometimes enhance the display. In general "
"the controls that default to <i>best guess</i> can be left alone, "
"since the guess is almost always correct. The controls for display min and "
"max values and connecting lines can be set later via the configuration "
"page as well. Here is a description of each control."
"<UL>"
"<LI><B>name of data set:</B> Displayed in graph drop-down in Genome Graphs "
" and as trackname in Genome Browser. Only the first 16 characters are "
" visible in some contexts. For data sets with multiple graphs, this is the "
" first part of the name, shared with all members of the data set.</LI>"
"<LI><B>description:</B> A short sentence describing the data set. Displayed in "
"the Genome Graphs and Genome Browser configuration pages, and as the center "
"label in the Genome Browser.</LI>"
"<LI><B>file format:</B> Controls whether the upload file is a tab-separated, "
" comma-separated, or space separated table.</LI>"
"<LI><B>markers are:</B> Describes how to map the data to chromosomes. The choices "
" are either the first column of the file is an ID of some sort, or the first column "
" is a chromosome and the next a base. The IDs can be SNP rs numbers, STS marker names "
" or ID's from any of the supported genotyping platforms.</LI>"
"<LI><B>column labels:</B> Controls whether the first row of the upload file is "
" interpreted as labels rather than data. If the first row contains text in the "
" numerical fields, or if the mapping fields are empty, it is interpreted by "
" \"best guess\" as labels. This is generally correct, but you can override this "
" interpretation by explicitly setting the control. </LI>"
"<LI><B>display min value/max value:</B> Set the range of the data set that will "
" be plotted. If left blank, the range will be taken from the min/max values in the "
" data set itself. For all data sets to share the same scale usually you'll need "
" to set this.</LI>"
"<LI><B>label values:</B> A comma-separated list of numbers for the vertical axis. "
" If left blank the axis will be labeled at the 1/3 and 2/3 point. </LI>"
"<LI><B>draw connecting lines:</B> Lines connecting data points separated by "
" no more than this number of bases are drawn. </LI>"
"<LI><B>file name, or Paste URLs or data:</B> Specify the uploaded data --"
" enter either a file on your local computer; or a URL at which the data file can be"
" found; or simply paste-in the data. If entries are made in both fields, the file name will take"
" precedence. </LI>");
cartWebEnd();
}
