2f0d3fa3d2bcbf3e23e834ca68565c470f73939d
chmalee
  Mon Oct 21 12:32:08 2024 -0700
Back end for auto-generating a hub with every user upload done

diff --git src/hg/hgHubConnect/trackHubWizard.c src/hg/hgHubConnect/trackHubWizard.c
index ed4d0f3..635b358 100644
--- src/hg/hgHubConnect/trackHubWizard.c
+++ src/hg/hgHubConnect/trackHubWizard.c
@@ -1,214 +1,203 @@
 /* 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"
 #include "trackHub.h"
 
 void removeOneFile(char *userName, char *cgiFileName)
 /* Remove one single file for userName */
 {
 char *fileName = prefixUserFile(userName, cgiEncodeFull(cgiFileName));
 if (fileExists(fileName))
     {
     fprintf(stderr, "deleting file: '%s'\n", fileName);
     removeFileForUser(fileName, userName);
     fflush(stderr);
     }
 else
     {
     fprintf(stderr, "file '%s' does not exist\n", fileName);
     fflush(stderr);
     }
 }
 
 void removeHubDir(char *userName, char *cgiFileName)
-/* Remove one single file for userName */
+/* Remove one single hub for userName */
 {
-char *fileName = prefixUserFile(userName, cgiEncodeFull(cgiFileName));
-if (fileExists(fileName))
+char *hubDir = prefixUserFile(userName, cgiEncodeFull(cgiFileName));
+if (isDirectory(hubDir))
     {
-    fprintf(stderr, "deleting file: '%s'\n", fileName);
-    removeHubForUser(fileName, userName);
+    fprintf(stderr, "deleting directory: '%s'\n", hubDir);
+    removeHubForUser(hubDir, 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
-    char *fname = ((struct jsonElement *)(deleteJson->val.jeList->val))->val.jeString;
-    boolean isHub = sameString("hub", ((struct jsonElement *)(deleteJson->val.jeList->next->val))->val.jeString);
+    // our array of objects, each object represents a track file
+    struct jsonElement *deleteJson = hashFindVal(paramHash, "fileList");
+    struct slRef *f, *fileList = deleteJson->val.jeList;
     jsonWriteListStart(cj->jw, "deletedList");
-    if (isHub)
-        removeHubDir(userName, fname);
-    else
-        removeOneFile(userName, fname);
-    jsonWriteString(cj->jw, NULL, fname);
+    for (f = fileList; f != NULL; f = f->next)
+        {
+        struct jsonElement *fileObj = (struct jsonElement *)f->val;
+        char *fileName = jsonStringField(fileObj, "fileName");
+        //char *fileType = jsonStringField(fileObj, "fileType");
+        //struct slName *hubList  = slNameListFromComma(jsonStringField(fileObj, "hubNameList"));
+        removeOneFile(userName, fileName);
+        jsonWriteString(cj->jw, NULL, fileName);
+        }
     jsonWriteListEnd(cj->jw);
+    /*
+    //for now don't worry about this:
+    //if (isHub)
+    //    removeHubDir(userName, fname);
+    */
     }
 }
 
 void doMoveFile(struct cartJson *cj, struct hash *paramHash)
 /* Move a file to a new hub */
 {
 }
 
-static void writeHubText(char *path, char *userName, char *encodedHubName, 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",
-    encodedHubName, 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");
     char *encodedName = cgiEncodeFull(name);
     fprintf(stderr, "creating hub '%s' for db '%s'\n", encodedName, db);
     fflush(stderr);
     // check if this hub already exists, must have a directory and hub.txt already:
     char *path = prefixUserFile(userName, encodedName);
     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, encodedName, 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);
         cgiDecodeFull(file->fileName, file->fileName, strlen(file->fileName));
         jsonWriteString(jw, "fileName", file->fileName);
         jsonWriteNumber(jw, "fileSize", file->fileSize);
         jsonWriteString(jw, "fileType", file->fileType);
-        jsonWriteString(jw, "hub", "");
+        jsonWriteString(jw, "hub", file->hubNameList);
         jsonWriteString(jw, "genome", file->db);
         jsonWriteString(jw, "lastModified", file->lastModified);
         jsonWriteString(jw, "uploadTime", 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);
         cgiDecodeFull(hub->hubName, hub->hubName, strlen(hub->hubName));
         jsonWriteString(jw, "hubName", hub->hubName);
         jsonWriteString(jw, "genome", hub->genome);
+        jsonWriteNumber(jw, "lastModified", getHubLatestTime(hub));
         jsonWriteObjectEnd(jw);
         }
     jsonWriteListEnd(jw);
+    */
     }
 jsonWriteObjectEnd(jw);
+jsInlineF("var isLoggedIn = %s\n", getUserName() ? "true" : "false");
 jsInlineF("var userFiles = %s;\n", dyStringCannibalize(&jw->dy));
 jsonWriteFree(&jw);
 }
 
 void doTrackHubWizard(char *database)
 /* 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");
 webIncludeResourceFile("hgMyData.css");
 
 // get the current files stored for this user
 outFilesForUser();
-jsInlineF("\nvar cartDb=\"%s %s\";\n", hGenome(database), trackHubSkipHubName(database));
+jsInlineF("\nvar cartDb=\"%s %s\";\n", trackHubSkipHubName(hGenome(database)), database);
 jsInline("$(document).ready(function() {\nhubCreate.init();\n})");
 puts("</div>");
 }