a4c8987ac13d72f85a7c3adde3f867456a85516f
chmalee
  Thu Sep 26 15:52:46 2024 -0700
Save newly created hubs to file table, return hubs when loading the page

diff --git src/hg/hgHubConnect/trackHubWizard.c src/hg/hgHubConnect/trackHubWizard.c
index f7ea546..60d961a 100644
--- src/hg/hgHubConnect/trackHubWizard.c
+++ src/hg/hgHubConnect/trackHubWizard.c
@@ -1,177 +1,190 @@
 /* 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"
 #include "hubSpace.h"
 #include "hubConnect.h"
 
 void removeOneFile(char *userName, char *cgiFileName)
 /* Remove one single file for userName */
 {
-char *fileName = prefixUserFile(userName, cgiFileName);
+char *fileName = prefixUserFile(userName, cgiEncodeFull(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 jsonElement *deleteJson = hashFindVal(paramHash, "fileNameList");
     //struct jsonWrite *errors = jsonWriteNew();
     // TODO: Check request is well-formed
     struct slRef *ele, *deleteList = deleteJson->val.jeList;
     jsonWriteListStart(cj->jw, "deletedList");
     for (ele = deleteList; ele != NULL; ele = ele->next)
         {
         struct jsonElement *jsonVal = ele->val;
         removeOneFile(userName, jsonVal->val.jeString);
         jsonWriteString(cj->jw, NULL, jsonVal->val.jeString);
         }
     jsonWriteListEnd(cj->jw);
     }
 }
 
 void doMoveFile(struct cartJson *cj, struct hash *paramHash)
 /* Move a file to a new hub */
 {
 }
 
 static void writeHubText(char *path, char *userName, char *hubName, char *db)
 /* Create a hub.txt file, optionally creating the directory holding it */
 {
 int oldUmask = 00;
 oldUmask = umask(0);
 makeDirsOnPath(path);
 // restore umask
 umask(oldUmask);
 // now make the hub.txt with some basic information
 char *hubFile = catTwoStrings(path, "/hub.txt");
 FILE *f = mustOpen(hubFile, "w");
 //fprintf(stderr, "would write \"hub %s\nemail %s\nshortLabel %s\nlongLabel %s\nuseOneFile on\n\ngenome %s\n\n\" to %s", hubName, emailForUserName(userName), hubName, hubName, db, hubFile);
 fprintf(f, "hub %s\n"
     "email %s\n"
     "shortLabel %s\n"
     "longLabel %s\n"
     "useOneFile on\n\n"
     "genome %s\n\n",
     hubName, emailForUserName(userName), hubName, hubName, db);
 carefulClose(&f);
 }
 
 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");
     // paramHash is an object with everything necessary to create a hub: name and assembly
     char *db = jsonStringVal(hashFindVal(paramHash, "db"), "db");
     char *name = jsonStringVal(hashFindVal(paramHash, "name"), "name");
     fprintf(stderr, "creating hub '%s' for db '%s'\n", name, db);
     fflush(stderr);
     // check if this hub already exists, must have a directory and hub.txt already:
     char *path = prefixUserFile(userName, name);
     if (isDirectory(path))
         {
         // can't make a hub that already exists!
         fprintf(stdout, "Status: 400 Bad Request\n\n");
         fprintf(stdout, "Hub already exists, select hub from dropdown or try a different name");
         fflush(stdout);
         exit(1);
         }
     else
         {
         // good we can make a new directory and stuff a hub.txt in it
         // the directory needs to be 777, so ignore umask for now
         writeHubText(path, userName, name, db);
         // TODO: add a row to the hubspace table for the hub.txt
+        //addHubTxtToTable(userName, path, name, db);
         // return json to fill out the table
         jsonWriteString(cj->jw, "hubName", name);
         jsonWriteString(cj->jw, "db", db);
+        time_t now = time(NULL);
+        jsonWriteString(cj->jw, "creationTime", sqlUnixTimeToDate(&now, FALSE));
         }
     }
 }
 
 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));
     jsonWriteListStart(jw, "fileList");
     struct hubSpace *file, *fileList = listFilesForUser(userName);
     for (file = fileList; file != NULL; file = file->next)
         {
         jsonWriteObjectStart(jw, NULL);
         jsonWriteString(jw, "fileName", file->fileName);
         jsonWriteNumber(jw, "fileSize", file->fileSize);
         jsonWriteString(jw, "fileType", file->fileType);
-        jsonWriteString(jw, "hub", "temp");
+        jsonWriteString(jw, "hub", "");
         jsonWriteString(jw, "genome", file->db);
         jsonWriteString(jw, "createTime", file->creationTime);
         jsonWriteObjectEnd(jw);
         }
     jsonWriteListEnd(jw);
+    jsonWriteListStart(jw, "hubList");
+    struct userHubs *hub, *hubList = listHubsForUser(userName);
+    for (hub = hubList; hub != NULL; hub = hub->next)
+        {
+        jsonWriteObjectStart(jw, NULL);
+        jsonWriteString(jw, "hubName", hub->hubName);
+        jsonWriteString(jw, "genome", hub->genome);
+        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);
 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/2.1.3/css/dataTables.dataTables.min.css\">\n");
 puts("<script type=\"text/javascript\" "
     "src=\"https://cdn.datatables.net/2.1.3/js/dataTables.min.js\"></script>");
 puts("<link rel=\"stylesheet\" type=\"text/css\" "
     "href=\"https://cdn.datatables.net/buttons/3.1.1/css/buttons.dataTables.min.css\">\n");
 puts("<script type=\"text/javascript\" "
     "src=\"https://cdn.datatables.net/buttons/3.1.1/js/dataTables.buttons.min.js\"></script>");
 
 // the skeleton HTML:
 webIncludeFile("inc/hgMyData.html");
 
 // get the current files stored for this user
 outFilesForUser();
 jsInline("$(document).ready(function() {\nhubCreate.init();\n})");
 puts("</div>");
 }