0f349359a8bebbd67c7bd7bb732285dee71905fc
chmalee
  Tue May 7 08:43:51 2024 -0700
Start of requiring hub,genome,and file type with each file submission

diff --git src/hg/hgHubConnect/trackHubWizard.c src/hg/hgHubConnect/trackHubWizard.c
index ad39379..a3fe480 100644
--- src/hg/hgHubConnect/trackHubWizard.c
+++ src/hg/hgHubConnect/trackHubWizard.c
@@ -1,159 +1,173 @@
 /* trackHubWizard -- a user interface for creating a track hubs configuration files */
 
 /* Copyright (C) 2019 The Regents of the University of California
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "cart.h"
 #include "cheapcgi.h"
 #include "hdb.h"
 #include "hgConfig.h"
 #include "md5.h"
 #include "trashDir.h"
 #include "hgHubConnect.h"
 #include "jsHelper.h"
 #include "web.h"
 #include "wikiLink.h"
 #include "customTrack.h"
 #include "userdata.h"
 #include "jsonWrite.h"
+#include "cartJson.h"
 
-void doRemoveFile()
-/* Process the request to remove a file */
+void removeOneFile(char *userName, char *cgiFileName)
+/* Remove one single file for userName */
 {
-char *userName = getUserName();
-if (userName)
-    {
-    char *cgiFileName = cgiOptionalString("deleteFile");
 char *fileName = prefixUserFile(userName, cgiFileName);
 if (fileExists(fileName))
     {
     fprintf(stderr, "deleting file: '%s'\n", fileName);
     removeFileForUser(fileName, userName);
+    fflush(stderr);
+    }
+}
+
+void doRemoveFile(struct cartJson *cj, struct hash *paramHash)
+/* Process the request to remove a file */
+{
+char *userName = getUserName();
+if (userName)
+    {
+    struct jsonWrite *errors = jsonWriteNew();
+    // verify the argument is present:
+    (void)cartJsonRequiredParam(paramHash, "deleteFile", errors, "doRemoveFile");
+    struct jsonElement *deleteJson = hashFindVal(paramHash, "deleteFile");
+    struct slRef *ele, *deleteList = deleteJson->val.jeList;
+    for (ele = deleteList; ele != NULL; ele = ele->next)
+        {
+        struct jsonElement *jsonVal = ele->val;
+        removeOneFile(userName, jsonVal->val.jeString);
+        }
     fprintf(stdout, "Status: 204 No Content\n\n");
     fflush(stdout);
     exit(0);
     }
-    }
 fprintf(stdout, "Status: 404 Not Found\n\n");
 fflush(stdout);
 exit(0);
 }
 
+void doCreateHub(struct cartJson *cj, struct hash *paramHash)
+/* Make a new hub.txt with the parameters from the JSON request */
+{
+char *userName = getUserName();
+if (userName)
+    {
+    struct jsonWrite *errors = jsonWriteNew();
+    // verify the arguments:
+    (void)cartJsonRequiredParam(paramHash, "createHub", errors, "doCreateHub");
+    // params is an object with everything necessary to create a hub: name and assembly
+    struct hash *params = jsonObjectVal(hashFindVal(paramHash, "createHub"), "createHub");
+    char *db = hashFindVal(params, "db");
+    char *name = hashFindVal(params, "name");
+    fprintf(stderr, "creating hub '%s' for db '%s'\n", name, db);
+    fflush(stderr);
+    }
+fprintf(stderr, "Status: 204 No Content\n\n");
+fflush(stdout);
+exit(0);
+}
+
 static void outFilesForUser()
 /* List out the currently stored files for the user and their sizes */
 {
 char *userName = getUserName();
 struct jsonWrite *jw = jsonWriteNew(); // the JSON to return for the client javascript
 jsonWriteObjectStart(jw, NULL);
 if (userName)
     {
     // the url for this user:
     jsonWriteString(jw, "userUrl", webDataDir(userName));
     struct userHubs *hub, *hubList = listHubsForUser(userName);
     // unpack hub directories into a flat list of files
     jsonWriteListStart(jw, "fileList");
     for (hub = hubList; hub != NULL; hub = hub->next)
         {
         struct fileInfo *file;
         struct userFiles *uf = listFilesForUserHub(userName, hub->hubName);
         for (file = uf->fileList; file != NULL; file = file->next)
             {
             jsonWriteObjectStart(jw, NULL);
             jsonWriteString(jw, "name", file->name);
             jsonWriteNumber(jw, "size", file->size);
             jsonWriteString(jw, "hub", hub->hubName);
             jsonWriteString(jw, "genome", hub->genome);
             jsonWriteDateFromUnix(jw, "createTime", file->creationTime);
             jsonWriteObjectEnd(jw);
             }
         }
     jsonWriteListEnd(jw);
     }
 jsonWriteObjectEnd(jw);
 jsInlineF("var userFiles = %s;\n", dyStringCannibalize(&jw->dy));
 jsonWriteFree(&jw);
 }
 
 void doTrackHubWizard()
 /* Offer an upload form so users can upload all their hub files */
 {
 jsIncludeFile("utils.js", NULL);
 jsIncludeFile("ajax.js", NULL);
 jsIncludeFile("lodash.3.10.0.compat.min.js", NULL);
 jsIncludeFile("cart.js", NULL);
 jsIncludeFile("tus.js", NULL);
 jsIncludeFile("hgMyData.js", NULL);
 webIncludeResourceFile("../style/bootstrap.min.css");
 webIncludeResourceFile("../style/gb.css");
 puts("<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css\">\n");
 puts("<link rel=\"stylesheet\" type=\"text/css\" "
     "href=\"https://cdn.datatables.net/1.10.12/css/jquery.dataTables.min.css\">\n");
 puts("<script type=\"text/javascript\" "
     "src=\"https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js\"></script>");
 puts("<div id='hubUpload' class='hubList'>\n");
 
 puts("<div class='row'>\n");
 puts("<div class='col-md-6'>\n");
 puts("<div class='row'>\n");
 puts("<div class='tabSection'>\n");
 puts("<h4>Create your own hub</h4>\n");
 puts("<p>After choosing files, click \"Create Hub\" to begin uploading the files to our server</p>\n");
 puts("<div class='buttonDiv' id='chooseAndSendFilesRow'>\n");
 puts("<button  id='btnForInput' class='button' for=\"chosenFiles\">Choose files</button>\n");
 puts("</div>\n"); // .buttonDiv
 puts("<div id='fileList' style=\"clear: right\"></div>\n");
 puts("</div>"); // .tabSection
 puts("</div>\n"); // row
 
 puts("<div class='row'>\n");
 puts("<div class='tabSection'>");
 puts("For information on making track hubs, see the following pages: \n "
     "<ul>\n"
     "<li><a href='../goldenPath/help/hubQuickStart.html' style='color:#121E9A' target=_blank>Quick Start Guide</a></li>\n"
     "<li><a href=\"../goldenPath/help/hgTrackHubHelp.html\" style='color:#121E9A' TARGET=_blank>Track Hub User's Guide</a></li>\n"
     "<li><a href=\"../goldenPath/help/hgTrackHubHelp#Hosting\" style='color:#121E9A' target=_blank>Where to Host Your Track Hub</a></li>\n"
     "<li><a href=\"../goldenPath/help/trackDb/trackDbHub.html\" style='color:#121E9A' target=_blank>Track Hub Settings Reference</a></li>\n"
     "<li><a href=\"../goldenPath/help/publicHubGuidelines.html\" style='color:#121E9A' target=_blank>Guidelines for Submitting a Public Hub</a></li>\n"
     "</ul>\n"
     "<BR>You may also <a href='../contacts.html' style='color:#121E9A'>contact us</a> if you have any "
     "issues or questions on hub development.");
 puts("</div>"); // .tabSection
 puts("</div>\n"); // col-md-6
 puts("</div>\n"); // row
 
 puts("<div id='chosenFilesSection' style=\"display: none\" class='col-md-6 tabSection'>");
 puts("<h4>Your uploaded hubs</h4>");
 webIncludeFile("inc/hgMyData.html");
 puts("</div>\n");
 puts("</div>\n"); // row
 puts("</div>\n"); // row
 
+// get the current files stored for this user
 outFilesForUser();
 jsInline("$(document).ready(function() {\nhubCreate.init();\n})");
 puts("</div>");
-// get the current files stored for this user
-}
-
-#define FILEVAR "userFile__filename"
-#define FILEVARBIN "userFile__binary"
-void doCreateHub(struct cart *cart)
-/* Called asynchronously when the user has submitted some files, return a json response of where 
- * the files live and the new quota */
-{
-// cheapcgi.c renames form variables as var__filename or var__binary for binary data, why?
-char *fileName = cartOptionalString(cart, FILEVAR);
-/*
-struct hashEl *hel, *helList = hashElListHash(cart->hash);
-for (hel = helList; hel != NULL; hel = hel->next)
-{
-fprintf(stderr, "hashEl name: '%s', value: '%s'\n", (char *)hel->name, (char *)hel->val);
-}
-*/
-fprintf(stderr, "fileName is: %s\n", fileName);
-fflush(stderr);
-char *pathToFile = "tempPath"; //prepBigData(cart, fileName, FILEVARBIN, FILEVAR);
-puts("Content-Type:text/javascript\n");
-printf("{\"status\": \"%s is uploaded to %s\"}\n", cgiOptionalString("userFile__filename"), pathToFile);
-fflush(stdout);
 }