f247b79b61ca172b3146284594b97c848db4c8bf braney Wed Sep 2 11:20:43 2026 -0700 hgSession, hgGenome: tighten handling of an uploaded file's name, refs #38172 Both CGIs print the name that arrives with an upload straight into the page. hgSession prints it in four of its load messages, so encode it once where it is read; the sibling URL message three lines above already did the same for the URL. hgGenome puts it in a quoted attribute, which wants attributeEncode. Raised in the v503 Preview II code review. diff --git src/hg/hgGenome/upload.c src/hg/hgGenome/upload.c index 879da8ec46a..c97c97f8bf9 100644 --- src/hg/hgGenome/upload.c +++ src/hg/hgGenome/upload.c @@ -1,248 +1,250 @@ /* Upload - put up upload pages and sub-pages. */ /* Copyright (C) 2011 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "ra.h" #include "portable.h" #include "cheapcgi.h" #include "localmem.h" #include "cart.h" #include "web.h" #include "chromInfo.h" #include "chromGraph.h" #include "chromGraphFactory.h" #include "errCatch.h" #include "hPrint.h" #include "customTrack.h" #include "hgGenome.h" #include "trashDir.h" +#include "htmshell.h" static char *markerNames[] = { cgfMarkerGuess, cgfMarkerGenomic, cgfMarkerSts, cgfMarkerSnp, // cgfMarkerAffy100, cgfMarkerAffy500, cgfMarkerAffy6, cgfMarkerAffy6SV, cgfMarkerHumanHap300, cgfMarkerHumanHap550, cgfMarkerHumanHap650, cgfMarkerHumanHap1M, cgfMarkerAgilentCgh244A, }; static char *formatNames[] = { cgfFormatGuess, cgfFormatTab, cgfFormatComma, cgfFormatSpace, }; static char *colLabelNames[] = { cgfColLabelGuess, cgfColLabelNumbered, cgfColLabelFirstRow, }; 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"); +/* oldFileName arrives with the upload and lands inside a quoted attribute. */ hPrintf("file name: <INPUT TYPE=FILE NAME=\"%s\" VALUE=\"%s\">", hggUploadFile, - oldFileName); + attributeEncode(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(); } static void addIfNonempty(struct hash *hash, char *cgiVar, char *trackVar) /* If cgiVar exists and is non-empty, add it to ra. */ { char *val = skipLeadingSpaces(cartUsualString(cart, cgiVar, "")); if (val[0] != 0) hashAdd(hash, trackVar, val); } void updateCustomTracks(struct customTrack *upList) /* Update custom tracks file with current upload data */ { struct customTrack *oldList = customTracksParseCart(database, cart, NULL, NULL); struct customTrack *outList = customTrackAddToList(oldList, upList, NULL, FALSE); customTracksSaveCart(database, cart, outList); hPrintf("These data are now available in the drop-down menus on the "); hPrintf("main page for graphing.<BR>"); } void trySubmitUpload(struct sqlConnection *conn, char *rawText) /* Called when they've submitted from uploads page */ { struct lineFile *lf = lineFileOnString("uploaded data", TRUE, rawText); struct customPp *cpp = customPpNew(lf); struct hash *settings = hashNew(8); addIfNonempty(settings, hggMinVal, "minVal"); addIfNonempty(settings, hggMaxVal, "maxVal"); addIfNonempty(settings, hggMaxGapToFill, "maxGapToFill"); addIfNonempty(settings, hggLabelVals, "linesAt"); struct customTrack *trackList = chromGraphParser(database, cpp, cartUsualString(cart, hggFormatType, formatNames[0]), cartUsualString(cart, hggMarkerType, cgfMarkerGenomic), cartUsualString(cart, hggColumnLabels, colLabelNames[0]), nullIfAllSpace(cartUsualString(cart, hggDataSetName, NULL)), nullIfAllSpace(cartUsualString(cart, hggDataSetDescription, NULL)), settings, TRUE); updateCustomTracks(trackList); } void submitUpload(struct sqlConnection *conn) /* Called when they've submitted from uploads page */ { char *urlText = cartUsualString(cart, hggUploadUrl, NULL); char *fileText = cartUsualString(cart, hggUploadFile, NULL); char *rawText = urlText; if (isNotEmpty(fileText)) rawText = fileText; int rawTextSize = strlen(rawText); struct errCatch *errCatch = errCatchNew(); cartWebStart(cart, database, "Data Upload Complete (%d bytes)", rawTextSize); hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\">"); cartSaveSession(cart); if (errCatchStart(errCatch)) trySubmitUpload(conn, rawText); errCatchFinish(&errCatch); cartRemove(cart, hggUploadFile); hPrintf("<CENTER>"); cgiMakeButton("submit", "OK"); hPrintf("</CENTER>"); hPrintf("</FORM>"); cartWebEnd(); }