95e2c3a93202ee912624bb730724313faae7c886
chmalee
  Wed Dec 4 16:41:31 2024 -0800
Use the DataTables select API instead of implementing my own checkboxes

Working child/parent rows. Just need to add checkboxes to the children and indent them a smidge

Fix log in for api key in pre-finish hook. Make the pre-finish hook determine if we came from hubtools or not and don't create hub.txts if we did. Fix writing of parentRows. Make client not use .child() but instead show or hide based on a load time constraint, which is not quite working all the way yet

Make select/deselect work with child files. Remove some dead code

Make deletes work by moving any requested directories to the end of the delete list and then deleting the directories so rmdir doesn't fail

Fix new table rows not animating on add

Make newly updloaded files show up in table include their parent dir and hub.txt, and indent them appropriately

Hash filenames to file objects in the client so we don't add duplicate rows to the table when multiple files are uploaded at once. Update the selected file div after deleting files. Make clicks on hub.txt files load the hub. Turn the file clicked on to pack. Remove some old copy from the template page

Revert early experimental commit when trying to allow bigDataUrl uploads directly through hgCustom

Fix up some comments to be more correct

Remove old CGI experiment

diff --git src/hg/hgHubConnect/trackHubWizard.c src/hg/hgHubConnect/trackHubWizard.c
index d876d58..84a1842 100644
--- src/hg/hgHubConnect/trackHubWizard.c
+++ src/hg/hgHubConnect/trackHubWizard.c
@@ -49,155 +49,134 @@
     {
     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)
     {
     // our array of objects, each object represents a track file
     struct jsonElement *deleteJson = hashFindVal(paramHash, "fileList");
-    struct slRef *f, *fileList = deleteJson->val.jeList;
+    struct slRef *copy, *f, *fileList = deleteJson->val.jeList;
+    struct slRef *dirList = NULL;
     jsonWriteListStart(cj->jw, "deletedList");
-    for (f = fileList; f != NULL; f = f->next)
+    for (f = fileList; f != NULL; )
+        {
+        struct jsonElement *fileObj = (struct jsonElement *)f->val;
+        char *fileName = jsonStringField(fileObj, "fileName");
+        char *fileType = jsonStringField(fileObj, "fileType");
+        char *db = jsonStringField(fileObj, "genome");
+        char *fullPath = jsonStringField(fileObj, "fullPath");
+        copy = f->next;
+        if (sameString(fileType, "dir"))
+            {
+            f->next = NULL;
+            slAddHead(&dirList, f);
+            }
+        else
+            {
+            removeOneFile(userName, fileName, fullPath, db, fileType);
+            // write out the fullPath so the DataTable can remove the correct row:
+            jsonWriteString(cj->jw, NULL, fullPath);
+            }
+        f = copy;
+        }
+    // now attempt to delete any requested directories, but don't die if they still have contents
+    for (f = dirList; f != NULL; f = f->next)
         {
         struct jsonElement *fileObj = (struct jsonElement *)f->val;
         char *fileName = jsonStringField(fileObj, "fileName");
         char *fileType = jsonStringField(fileObj, "fileType");
         char *db = jsonStringField(fileObj, "genome");
-        //char *parentDir = jsonStringField(fileObj, "parentDir");
         char *fullPath = jsonStringField(fileObj, "fullPath");
         removeOneFile(userName, fileName, fullPath, db, fileType);
-        jsonWriteString(cj->jw, NULL, fileName);
+        // write out the fullPath so the DataTable can remove the correct row:
+        jsonWriteString(cj->jw, NULL, fullPath);
         }
     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 */
 {
 }
 
-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, NULL);
-    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, 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, "parentDir", file->parentDir);
         jsonWriteString(jw, "genome", file->db);
         jsonWriteString(jw, "lastModified", file->lastModified);
         jsonWriteString(jw, "uploadTime", file->creationTime);
         jsonWriteString(jw, "fullPath", stripDataDir(file->location, userName));
+        jsonWriteString(jw, "md5sum", file->md5sum);
         jsonWriteObjectEnd(jw);
         }
     jsonWriteListEnd(jw);
     }
 jsonWriteObjectEnd(jw);
 jsInlineF("var isLoggedIn = %s\n", getUserName() ? "true" : "false");
 jsInlineF("var userFiles = %s;\n", dyStringCannibalize(&jw->dy));
 jsInlineF("var hubNameDefault = \"%s\";\n", defaultHubNameForUser(getUserName()));
 // if the user is not logged, the 0 for the quota is ignored
 jsInlineF("var userQuota = %llu\n", getUserName() ? checkUserQuota(getUserName()) : 0);
 jsInlineF("var maxQuota = %llu\n", getUserName() ? getMaxUserQuota(getUserName()) : HUB_SPACE_DEFAULT_QUOTA);
 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);
-// this file must be included as a module for now as it needs to import:
-//puts("<script src=\"../js/hgMyData.js\" type=\"module\"></script>");
 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>");
+puts("<link rel=\"stylesheet\" type=\"text/css\" "
+    "href=\"https://cdn.datatables.net/select/2.1.0/css/select.dataTables.min.css\">\n");
+puts("<script type=\"text/javascript\" "
+    "src=\"https://cdn.datatables.net/select/2.1.0/js/dataTables.select.min.js\"></script>");
 puts("<link href=\"https://releases.transloadit.com/uppy/v4.5.0/uppy.min.css\" rel=\"stylesheet\">");
 puts("<script type=\"text/javascript\" src=\"https://releases.transloadit.com/uppy/v4.5.0/uppy.min.js\"></script>");
 jsIncludeFile("hgMyData.js", NULL);
 
 // 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", trackHubSkipHubName(hGenome(database)), database);
 jsInline("$(document).ready(function() {\nhubCreate.init();\n})");
 puts("</div>");
 }