7b7bb68187bb42ead29a9a3b26a950205820c9ae
chmalee
  Wed Nov 20 15:54:48 2024 -0800
Make up to 25 rows show by default, make the table scroll down if it's more than 600 pixels, make the table collapse when there are less than 600 pixels height needed.

Remove the 'Action' title, remove the delete button from each row, make the checkboxes select files, on checkbox select populate an info section about how many files have been selected and give the option to view or delete them

Start of reworking the delete button to delete a list of files. The backend still needs to be smarter about creating the locations of files

Put some place holder text where the selected file information would appear so the page doesn't jump around

Start of work on back end for removing files. Changed the json returned for listing the files to list the full path to the file to make the requests to delete a file easier. Still need to decide on encoding vs decoding of the parent dirs during uploads

diff --git src/hg/lib/userdata.c src/hg/lib/userdata.c
index fdb9445..041d684 100644
--- src/hg/lib/userdata.c
+++ src/hg/lib/userdata.c
@@ -1,427 +1,456 @@
 /* userdata.c - code for managing data stored on a per user basis */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 
 #include "common.h"
 #include "hash.h"
 #include "portable.h"
 #include "trashDir.h"
 #include "md5.h"
 #include "hgConfig.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "customFactory.h"
 #include "wikiLink.h"
 #include "userdata.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hubSpace.h"
 
 char *getUserName()
 /* Query the right system for the users name */
 {
 return (loginSystemEnabled() || wikiLinkEnabled()) ? wikiLinkUserName() : NULL;
 }
 
 char *emailForUserName(char *userName)
 /* Fetch the email for this user from gbMembers hgcentral table */
 {
 struct sqlConnection *sc = hConnectCentral();
 struct dyString *query = sqlDyStringCreate("select email from gbMembers where userName = '%s'", userName);
 char *email = sqlQuickString(sc, dyStringCannibalize(&query));
 hDisconnectCentral(&sc);
 // this should be freeMem'd:
 return email;
 }
 
 char *getDataDir(char *userName)
 /* Return the full path to the user specific data directory, can be configured via hg.conf
  * on hgwdev, this is /data/apache/userdata/userStore/hash/userName/
  * on the RR, this is /userdata/userStore/hash/userName/ */
 {
 char *userDataBaseDir = cfgOption("userDataDir");
 if (!userDataBaseDir  || isEmpty(userDataBaseDir))
     errAbort("trying to save user file but no userDataDir defined in hg.conf");
 if (userDataBaseDir[0] != '/')
     errAbort("config setting userDataDir must be an absolute path (starting with '/')");
 
 char *encUserName = cgiEncode(userName);
 char *userPrefix = md5HexForString(encUserName);
 userPrefix[2] = '\0';
 
 struct dyString *newDataDir = dyStringNew(0);
 dyStringPrintf(newDataDir, "%s/%s/%s/", 
     userDataBaseDir, userPrefix, encUserName);
 
 fprintf(stderr, "userDataDir = '%s'\n", newDataDir->string);
 return dyStringCannibalize(&newDataDir);
 }
 
+char *stripDataDir(char *fname, char *userName)
+/* Strips the getDataDir(userName) off of fname */
+{
+char *dataDir = getDataDir(userName);
+int prefixSize = strlen(dataDir);
+if (startsWith(dataDir, fname))
+    {
+    char *ret = fname + prefixSize;
+    return ret;
+    }
+return NULL;
+}
+
 char *getHubDataDir(char *userName, char *hub)
 {
 char *dataDir = getDataDir(userName);
 return catTwoStrings(dataDir, hub);
 }
 
 char *webDataDir(char *userName)
 /* Return a web accesible path to the userDataDir, this is different from the full path tusd uses */
 {
 char *retUrl = NULL;
 if (userName)
     {
     char *encUserName = cgiEncode(userName);
     char *userPrefix = md5HexForString(encUserName);
     userPrefix[2] = '\0';
     struct dyString *userDirDy = dyStringNew(0);
     dyStringPrintf(userDirDy, "%s/%s/%s/", HUB_SPACE_URL, userPrefix, encUserName);
     retUrl = dyStringCannibalize(&userDirDy);
     }
 return retUrl;
 }
 
-char *prefixUserFile(char *userName, char *fname)
-/* Allocate a new string that contains the full per-user path to fname, NULL otherwise */
+char *prefixUserFile(char *userName, char *fname, char *parentDir)
+/* Allocate a new string that contains the full per-user path to fname, NULL otherwise.
+ * parentDir is optional and will go in between the per-user dir and the fname */
 {
 char *pathPrefix = getDataDir(userName);
 if (pathPrefix)
+    {
+    if (parentDir)
+        {
+        struct dyString *ret = dyStringCreate("%s%s%s%s", pathPrefix, parentDir, lastChar(parentDir) == '/' ? "" : "/", fname);
+        return dyStringCannibalize(&ret);
+        }
+    else
         return catTwoStrings(pathPrefix, fname);
+    }
 else
     return NULL;
 }
 
 void addHubSpaceRowForFile(struct hubSpace *row)
 /* We created a file for a user, now add an entry to the hubSpace table for it */
 {
 struct sqlConnection *conn = hConnectCentral();
 
 // now write out row to hubSpace table
 if (!sqlTableExistsOnMain(conn, "hubSpace"))
     {
     errAbort("No hubSpace MySQL table is present. Please send an email to genome-www@soe.ucsc.edu  describing the exact steps you took just before you got this error");
     }
 hubSpaceSaveToDb(conn, row, "hubSpace", 0);
 hDisconnectCentral(&conn);
 }
 
 static boolean checkHubSpaceRowExists(struct hubSpace *row)
 /* Return TRUE if row already exists */
 {
 struct sqlConnection *conn = hConnectCentral();
 struct dyString *queryCheck = sqlDyStringCreate("select count(*) from hubSpace where userName='%s' and fileName='%s' and parentDir='%s'", row->userName, row->fileName, row->parentDir);
 int ret = sqlQuickNum(conn, dyStringCannibalize(&queryCheck));
 hDisconnectCentral(&conn);
 return ret > 0;
 }
 
 static void makeParentDirRows(char *userName, time_t lastModified, char *db, char *parentDirStr)
 /* For each '/' separated component of parentDirStr, create a row in hubSpace. Return the 
  * final subdirectory component of parentDirStr */
 {
 int i, slashCount = countChars(parentDirStr, '/');
 char *components[256];
 struct dyString *currLocation = dyStringNew(0);
 int foundSlashes = chopByChar(cloneString(parentDirStr), '/', components, slashCount);
 if (foundSlashes > 256)
     errAbort("parentDir setting '%s' too long", parentDirStr);
 for (i = 0; i < foundSlashes; i++)
     {
     char *subdir = components[i];
     if (sameString(subdir, "."))
         continue;
     fprintf(stderr, "making row for parent dir: '%s'\n", subdir);
     if (!subdir)
         errAbort("error: empty subdirectory components for parentDir string '%s'", parentDirStr);
     struct hubSpace *row = NULL;
     AllocVar(row);
     row->userName = userName;
     row->fileName = subdir;
     row->fileSize = 0;
     row->fileType = subdir;
     row->creationTime = NULL;
     row->lastModified = sqlUnixTimeToDate(&lastModified, TRUE);
     row->db = db;
     row->location = cloneString(dyStringContents(currLocation));
     row->md5sum = "";
     row->parentDir = i > 0 ? components[i-1] : "";
     // only insert a row for this parentDir if it's unique to the table
     if (!checkHubSpaceRowExists(row))
         addHubSpaceRowForFile(row);
     dyStringAppendC(currLocation, '/');
     dyStringAppend(currLocation, components[i]);
     }
 }
 
 char *writeHubText(char *path, char *userName, char *hubName, char *db)
 /* Create a hub.txt file, optionally creating the directory holding it. For convenience, return
  * the file name of the created hub, which can be freed. */
 {
 int oldUmask = 00;
 oldUmask = umask(0);
 makeDirsOnPath(path);
 // restore umask
 umask(oldUmask);
 // now make the hub.txt with some basic information
 char *hubFile = NULL;
 struct dyString *hubFileDy = dyStringCreate("%s%shub.txt", path, endsWith(path, "/") ? "" : "/");
 hubFile = dyStringCannibalize(&hubFileDy);
 if (fileExists(hubFile))
     return hubFile;
 
 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);
 return hubFile;
 }
 
 char *hubNameFromParentDir(char *parentDir)
 /* Assume parentDir does not have leading '/' or '.', parse out the first dir component */
 {
 char *copy = cloneString(parentDir);
 char *firstSlash = strchr(copy, '/');
 if (!firstSlash)
     {
     return copy;
     }
 firstSlash = 0;
 return copy;
 }
 
 void createNewTempHubForUpload(char *requestId, char *userName, char *db, char *trackFileName, char *trackType, char *parentDir)
 /* Creates a hub.txt for this upload with a random hub name. Returns the full path to the hub
  * for convenience.  */
 {
 char *hubFileName = NULL;
 char *path = NULL;
 struct dyString *hubPath = dyStringNew(0);
 char *hubName = hubNameFromParentDir(parentDir);
 dyStringPrintf(hubPath, "%s%s", getDataDir(userName), hubName);
 fprintf(stderr, "hubPath: %s\n", hubPath->string);
 path = hubFileName = writeHubText(dyStringCannibalize(&hubPath), userName, hubName, db);
 char *encodedTrack = cgiEncodeFull(trackFileName);
 struct dyString *trackFilePath = dyStringCreate("%s%s%s", parentDir != NULL ? parentDir : "", parentDir != NULL ? "/" : "", encodedTrack);
 FILE *f = mustOpen(hubFileName, "a");
 fprintf(f, "track %s\n"
     "bigDataUrl %s\n"
     "type %s\n"
     "shortLabel %s\n"
     "longLabel %s\n"
     "\n",
     encodedTrack, dyStringCannibalize(&trackFilePath),
     trackType, trackFileName, trackFileName);
 carefulClose(&f);
 
 // we should update the mysql table now with a record of the hub.txt
 struct hubSpace *row = NULL;
 AllocVar(row);
 row->userName = userName;
 row->fileName = "hub.txt";
 row->fileSize = fileSize(hubFileName);
 row->fileType = "hub";
 row->creationTime = NULL;
 time_t lastModTime = fileModTime(hubFileName);
 row->lastModified = sqlUnixTimeToDate(&lastModTime, TRUE);
 row->db = db;
 row->location = path;
 row->md5sum = md5HexForFile(hubFileName);
 fprintf(stderr, "making parent dir rows\n");
 fflush(stderr);
 makeParentDirRows(userName, lastModTime, db, parentDir);
 row->parentDir = hubName;
 struct dyString *parentsPath = dyStringCreate("%s%s", getDataDir(userName), parentDir);
 fprintf(stderr, "parentDir of hub.txt: '%s'\n", parentsPath->string);
 fflush(stderr);
 if (!checkHubSpaceRowExists(row))
     addHubSpaceRowForFile(row);
 }
 
-static void deleteHubSpaceRow(char *fname)
+static void deleteHubSpaceRow(char *fname, char *userName)
 /* Deletes a row from the hubspace table for a given fname */
 {
 struct sqlConnection *conn = hConnectCentral();
-struct dyString *deleteQuery = sqlDyStringCreate("delete from hubSpace where location='%s'", fname);
+struct dyString *deleteQuery = sqlDyStringCreate("delete from hubSpace where location='%s' and userName='%s'", fname, userName);
 sqlUpdate(conn, dyStringCannibalize(&deleteQuery));
 }
 
 void removeFileForUser(char *fname, char *userName)
 /* Remove a file for this user if it exists */
 {
 // The file to remove must be prefixed by the hg.conf userDataDir
 if (!startsWith(getDataDir(userName), fname))
     return;
 if (fileExists(fname))
     {
     // delete the actual file
     mustRemove(fname);
     // delete the table row
-    deleteHubSpaceRow(fname);
+    deleteHubSpaceRow(fname, userName);
     }
 }
 
 void removeHubForUser(char *path, char *userName)
 /* Remove a hub directory for this user (and all files in the directory), if it exists */
 {
 if (!startsWith(getDataDir(userName), path))
     return;
 if (isDirectory(path))
     {
     struct fileInfo *f, *flist = listDirX(path, NULL, TRUE);
     for (f = flist; f != NULL; f = f->next)
         mustRemove(f->name);
     // now we have deleted all the files in the dir we can safely rmdir
     mustRemove(path);
-    deleteHubSpaceRow(path);
+    deleteHubSpaceRow(path, userName);
     }
 }
 
 static time_t getFileListLatestTime(struct userFiles *userFiles)
 /* Return the greatest last access time of the files in userFiles->fileList */
 {
 if (!userFiles->fileList)
     errAbort("no files in userFiles->fileList");
 time_t modTime = 0;
 struct fileInfo *f;
 for (f = userFiles->fileList; f != NULL; f = f->next)
     {
     if (f->lastAccess > modTime)
         {
         modTime = f->lastAccess;
         }
     }
 return modTime;
 }
 
 time_t getHubLatestTime(struct userHubs *hub)
 /* Return the latest access time of the files in a hub */
 {
 // NOTE: every hub is guaranteed to have at least one file
 return getFileListLatestTime(hub->fileList);
 }
 
+char *findParentDirs(char *parentDir, char *userName, char *fname)
+/* For a given file with parentDir, go up the tree and find the full path back to
+ * the rootmost parentDir */
+{
+return NULL;
+}
+
 struct userFiles *listFilesForUserHub(char *userName, char *hubName)
 /* Get all the files for a particular hub for a particular user */
 {
 struct userFiles *userListing;
 AllocVar(userListing);
 char *path = getHubDataDir(userName, hubName);
 struct fileInfo *fiList = listDirX(path,NULL,FALSE);
 userListing->userName = userName;
 userListing->fileList = fiList;
 return userListing;
 }
 
 struct userHubs *listHubsForUser(char *userName)
 /* Lists the directories for a particular user */
 {
 struct userHubs *userHubs = NULL;
 char *path = getDataDir(userName);
 struct fileInfo *fi, *fiList = listDirX(path,NULL,FALSE);
 for (fi = fiList; fi != NULL; fi = fi->next)
     {
     if (fi->isDir)
         {
         struct userHubs *hub;
         AllocVar(hub);
         hub->hubName = cloneString(fi->name);
         hub->userName = cloneString(userName);
         char hubPath[PATH_LEN];
         safef(hubPath, sizeof(hubPath), "%s%s", path, fi->name);
         struct userFiles *hubFileList = listFilesForUserHub(userName, hub->hubName);
         hub->lastModified = getFileListLatestTime(hubFileList);
         hub->fileList = hubFileList;
         slAddHead(&userHubs, hub);
         }
     }
 return userHubs;
 }
 
 struct hubSpace *listFilesForUser(char *userName)
 /* Return the files the user has uploaded */
 {
 struct sqlConnection *conn = hConnectCentral();
 struct dyString *query = sqlDyStringCreate("select userName, fileName, fileSize, fileType, creationTime, DATE_FORMAT(lastModified, '%%c/%%d/%%Y, %%l:%%i:%%s %%p') as lastModified, db, location, md5sum, parentDir from hubSpace where userName='%s' order by creationTime, fileName", userName);
 struct hubSpace *fileList = hubSpaceLoadByQuery(conn, dyStringCannibalize(&query));
 hDisconnectCentral(&conn);
 return fileList;
 }
 
 #define defaultHubName "defaultHub"
 char *defaultHubNameForUser(char *userName)
 /* Return a name to use as a default for a hub, starts with defaultHub, then defaultHub2, ... */
 {
 if (!userName)
     return defaultHubName;
 struct dyString *query = sqlDyStringCreate("select distinct(fileName) from hubSpace where parentDir='' and fileName like '%s%%' and userName='%s'", defaultHubName, userName);
 struct sqlConnection *conn = hConnectCentral();
 struct slName *hubNames = sqlQuickList(conn, dyStringCannibalize(&query));;
 hDisconnectCentral(&conn);
 if (hubNames == NULL)
     // user has no hubs created
     return defaultHubName;
 slSort(&hubNames,slNameCmpStringsWithEmbeddedNumbers);
 slReverse(&hubNames);
 // now the first element of the list has the most recent integer to use (or no integer)
 char *currHubName = cloneString(hubNames->name);
 int currHubStrLen = strlen(currHubName);
 int defaultLen = strlen(defaultHubName);
 if (currHubStrLen == defaultLen)
     // probably a common case
     return "defaultHub2";
 else
     {
     currHubName[defaultLen-1] = 0;
     currHubName += strlen(defaultHubName);
     int hubNum = sqlUnsigned(currHubName) + 1;
     struct dyString *hubName = dyStringCreate("%s%d", defaultHubName, hubNum);
     return dyStringCannibalize(&hubName);
     }
 }
 
 long long getMaxUserQuota(char *userName)
 /* Return how much space is allocated for this user or the default */
 {
 return HUB_SPACE_DEFAULT_QUOTA;
 }
 
 long long checkUserQuota(char *userName)
 /* Return the amount of space a user is currently using */
 {
 long long quota = 0;
 struct hubSpace *hubSpace, *hubSpaceList = listFilesForUser(userName);
 for (hubSpace = hubSpaceList; hubSpace != NULL; hubSpace = hubSpace->next)
     {
     quota += hubSpace->fileSize;
     }
 return quota;
 }
 
 char *storeUserFile(char *userName, char *newFileName, void *data, size_t dataSize)
 /* Give a fileName and a data stream, write the data to:
  * userDataDir/hashedUserName/userName/fileName
  * where userDataDir comes from hg.conf and
  * hashedUserName is based on the md5sum of the userName
  * to prevent proliferation of too many directories.
  *
  * After sucessfully saving the file, return a web accessible url
  * to the file. */
 {
 char *userDir = getDataDir(userName);
 makeDirsOnPath(userDir);
 char *pathToFile = catTwoStrings(userDir, newFileName);
 FILE *newFile = mustOpen(pathToFile, "wb");
 // the data will start with a line feed so get rid of that
 mustWrite(newFile, data, dataSize);
 // missing an EOF?
 carefulClose(&newFile);
 return pathToFile;
 }