02af9dedd3443875fc2b3eee09c48a5e6f85b1c3 chmalee Wed Nov 6 15:27:22 2024 -0800 Start of work on optional subdir and hubName metadata for hubtools uploads diff --git src/hg/hgHubConnect/hooks/post-finish.c src/hg/hgHubConnect/hooks/post-finish.c index 1335cd5..9988612 100644 --- src/hg/hgHubConnect/hooks/post-finish.c +++ src/hg/hgHubConnect/hooks/post-finish.c @@ -1,186 +1,196 @@ /* post-finish - tus daemon post-finish hook program. Reads * a JSON encoded request to finsh an upload from a tus * client and moves a downloaded file to a specific user * directory. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "wikiLink.h" #include "customTrack.h" #include "userdata.h" #include "jsonQuery.h" #include "jsHelper.h" #include "errCatch.h" #include "obscure.h" #include "hooklib.h" #include "jksql.h" #include "hdb.h" #include "hubSpace.h" #include "md5.h" #include "cheapcgi.h" void usage() /* Explain usage and exit. */ { errAbort( "post-finish - tus daemon post-finish hook program\n" "usage:\n" " post-finish < input\n" ); } /* Command line validation table. */ static struct optionSpec options[] = { {NULL, 0}, }; int postFinish() /* post-finish hook for tus daemon. Read JSON encoded hook request from * stdin and write a JSON encoded hook to stdout. Writing to stderr * will be redirected to the tusd log and not seen by the user, so for * errors that the user needs to see, they need to be in the JSON response */ { // TODO: create response object and do all error catching through that char *reqId = getenv("TUS_ID"); // always return an exit status to the daemon and print to stdout, as // stdout gets sent by the daemon back to the client int exitStatus = 0; struct jsonElement *response = makeDefaultResponse(); if (!(reqId)) { rejectUpload(response, "not a TUS request"); exitStatus = 1; } else { struct errCatch *errCatch = errCatchNew(0); if (errCatchStart(errCatch)) { // the variables for the row entry for this file, some can be NULL char *userName = NULL; char *fileName = NULL; long long fileSize = 0; char *fileType = NULL; char *db = NULL; char *location = NULL; char *reqLm = NULL; time_t lastModified = 0; + char *subdir = NULL; // special optional argument from hubtools commands + char *reqHubName = NULL; // special optional argument from hubtools commands struct lineFile *lf = lineFileStdin(FALSE); char *request = lineFileReadAll(lf); struct jsonElement *req = jsonParse(request); fprintf(stderr, "Hook request:\n"); jsonPrintToFile(req, NULL, stderr, 0); char *reqCookie= jsonQueryString(req, "", "Event.HTTPRequest.Header.Cookie[0]", NULL); if (reqCookie) { setenv("HTTP_COOKIE", reqCookie, 0); } fprintf(stderr, "reqCookie='%s'\n", reqCookie); userName = (loginSystemEnabled() || wikiLinkEnabled()) ? wikiLinkUserName() : NULL; fprintf(stderr, "userName='%s'\n'", userName); if (!userName) { errAbort("not logged in"); } else { // NOTE: All Upload.MetaData values are strings fileName = cgiEncodeFull(jsonQueryString(req, "", "Event.Upload.MetaData.fileName", NULL)); fileSize = jsonQueryInt(req, "", "Event.Upload.Size", 0, NULL); fileType = jsonQueryString(req, "", "Event.Upload.MetaData.fileType", NULL); db = jsonQueryString(req, "", "Event.Upload.MetaData.genome", NULL); reqLm = jsonQueryString(req, "", "Event.Upload.MetaData.lastModified", NULL); lastModified = sqlLongLong(reqLm) / 1000; // yes Javascript dates are in millis + subdir = jsonQueryString(req, "", "Event.Upload.MetaData.subdir", NULL); + reqHubName = jsonQueryString(req, "", "Event.Upload.MetaData.hubName", NULL); char *tusFile = jsonQueryString(req, "", "Event.Upload.Storage.Path", NULL); if (fileName == NULL) { errAbort("No Event.Upload.fileName setting"); } else if (tusFile == NULL) { errAbort("No Event.Path setting"); } else { char *tusInfo = catTwoStrings(tusFile, ".info"); char *dataDir = getDataDir(userName); - char *newFile = catTwoStrings(dataDir, fileName); - fprintf(stderr, "moving %s to %s\n", tusFile, newFile); + struct dyString *newFile = dyStringNew(0); + // if subdir provided we are throwing the files in there + if (subdir) + dataDir = catTwoStrings(dataDir, subdir); + dyStringPrintf(newFile, "%s%s", dataDir, fileName); + + fprintf(stderr, "moving %s to %s\n", tusFile, dyStringContents(newFile)); // TODO: check if file exists or not and let user choose to overwrite // and re-call this hook, for now just exit if the file exists - if (fileExists(newFile)) + if (fileExists(dyStringContents(newFile))) { - errAbort("file '%s' exists already, not overwriting", newFile); + errAbort("file '%s' exists already, not overwriting", dyStringContents(newFile)); } else { // set our mysql table location: - location = newFile; + location = dyStringContents(newFile); // the directory may not exist yet int oldUmask = 00; if (!isDirectory(dataDir)) { fprintf(stderr, "making directory '%s'\n", dataDir); // the directory needs to be 777, so ignore umask for now oldUmask = umask(0); makeDirsOnPath(dataDir); // restore umask umask(oldUmask); } - copyFile(tusFile, newFile); + copyFile(tusFile, dyStringContents(newFile)); // the files definitely should not be executable! - chmod(newFile, 0666); + chmod(dyStringContents(newFile), 0666); mustRemove(tusFile); mustRemove(tusInfo); + dyStringCannibalize(&newFile); } } } // we've passed all the checks so we can write a new or updated row // to the mysql table and return to the client that we were successful if (exitStatus == 0) { // create a hub for this upload, which can be edited later - char *hubName = createNewTempHubForUpload(reqId, userName, db, fileName, fileType); + char *hubName = createNewTempHubForUpload(reqId, userName, db, fileName, fileType, reqHubName); fprintf(stderr, "added hub.txt and hubSpace row for hub for file: '%s'\n", fileName); fflush(stderr); struct hubSpace *row = NULL; AllocVar(row); row->userName = userName; row->fileName = fileName; row->fileSize = fileSize; row->fileType = fileType; row->creationTime = NULL; // automatically handled by mysql row->lastModified = sqlUnixTimeToDate(&lastModified, TRUE); row->hubNameList = hubName; row->db = db; row->location = location; row->md5sum = md5HexForFile(row->location); addHubSpaceRowForFile(row); hubSpaceFree(&row); fprintf(stderr, "added hubSpace row for file '%s'\n", fileName); fflush(stderr); } } if (errCatch->gotError) { rejectUpload(response, errCatch->message->string); exitStatus = 1; } errCatchEnd(errCatch); } // always print a response no matter what jsonPrintToFile(response, NULL, stdout, 0); return exitStatus; } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 1) usage(); return postFinish(); }