4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c index c08a9d4..83dbb6c 100644 --- src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c +++ src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c @@ -1,329 +1,329 @@ /* cdwGetFile - given a file ID and a security token (skipped for public cirm site), send the file using Apache */ /* Copyright (C) 2016 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "hgConfig.h" #include "cheapcgi.h" #include "sqlSanity.h" #include "htmshell.h" #include "portable.h" #include "cart.h" #include "cdw.h" #include "hdb.h" #include "hui.h" #include "cdw.h" #include "cdwValid.h" #include "web.h" #include "cdwLib.h" #include "wikiLink.h" #include "filePath.h" /* Global vars */ struct cart *cart; // User variables saved from click to click struct hash *oldVars; // Previous cart, before current round of CGI vars folded in struct cdwUser *user; // Our logged in user if any void errExitExt(char *msg, char *field, char *status) /* print http header + message and exit. msg can contain %s */ { if (status) { printf("Status: %s\n", status); } else { // provide a generic error code when status not specified // this will signal an error to the caller. printf("Status: %s\n", "400 BAD REQUEST"); } printf("Content-Type: text/html\n\n"); puts("ERROR: "); if (!field) puts(msg); else printf(msg, field); exit(0); } void errExit(char *msg, char *field) /* print http header + message and exit. msg can contain %s */ { errExitExt(msg, field, NULL); } void mustHaveAccess(struct sqlConnection *conn, struct cdwFile *ef) /* exit with error message if user does not have access to file ef */ { boolean isPublic = cfgOptionBooleanDefault("cdw.siteIsPublic", FALSE); if (isPublic) return; if (cdwCheckAccess(conn, ef, user, cdwAccessRead)) return; else if (user==NULL) errExitExt("Sorry, this file has access restrictions. Please <a href='/cgi-bin/hgLogin'>log in</a> first.", NULL, "401 Unauthorized"); else errExitExt("Sorry, user %s does not have access to this file.", user->email, "403 Forbidden"); } struct patcher /* deal with patching replacement bits in html */ { struct patcher *next; char *match; // string to match int size; // string size int count; // match count char *(*cdwLocalFunction)(struct cart *cart, boolean makeAbsolute); // function to make }; static void printFileReplaceVar(char *filePath) /* dump a text file to stdout with the html header, replace <!--menuBar--> with the menubar */ { printf("Content-Type: text/html\n\n"); int c; FILE *file = fopen(filePath, "r"); if (file == 0) errExit("Cannot open file %s", filePath); struct patcher *patcherList = NULL, *p = NULL; AllocVar(p); p->match = cloneString("<!--headDependencies-->"); p->cdwLocalFunction = &cdwHeadTagDependencies; slAddHead(&patcherList, p); AllocVar(p); p->match = cloneString("<!--pageHeader-->"); p->cdwLocalFunction = &cdwPageHeader; slAddHead(&patcherList, p); AllocVar(p); p->match = cloneString("<!--menuBar-->"); p->cdwLocalFunction = &cdwLocalMenuBar; slAddHead(&patcherList, p); AllocVar(p); p->match = cloneString("<!--pageFooter-->"); p->cdwLocalFunction = &cdwPageFooter; slAddHead(&patcherList, p); for(p=patcherList; p; p=p->next) { p->size = strlen(p->match); } while ((c = getc(file)) != EOF) { putchar(c); for(p=patcherList; p; p=p->next) { if (c==p->match[p->count]) p->count++; else p->count = 0; if (p->count==p->size) { putchar('\n'); // make view source more readable puts((*p->cdwLocalFunction)(cart, TRUE)); } } } fclose(file); } void sendFile(char *format, char *filePath, char *suggestFileName) /* format is one of "fastq", "fasta", defined in cdw.as. if format is NULL, use file extension. */ /* send file to user via Apache, using X-Sendfile or stdout, as needed */ { if (format==NULL || sameWord(format, "unknown")) { char ext[FILEEXT_LEN]; splitPath(filePath, NULL, NULL, ext); if (strlen(ext)>1) { format = cloneString(ext); format++; // skip over . character } } // html files are not sent via X-Sendfile as we need to replace one special variable if (sameWord(format, "html")) { printFileReplaceVar(filePath); return; } // pdf, jpeg files are shown directly in the internet browser, not downloaded else if (sameWord(format, "jpg")) printf("Content-Type: image/jpeg\n"); else if (sameWord(format, "pdf")) printf("Content-Type: application/pdf\n"); else if (sameWord(format, "png")) printf("Content-Type: image/png\n"); else if (sameWord(format, "json")) printf("Content-Type: application/json\n"); else if (sameWord(format, "text")) printf("Content-Type: text/plain\n"); else { printf("Content-Disposition: attachment; filename=%s\n", suggestFileName); printf("Content-Type: application/octet-stream\n"); } /* send pseudo-HTTP header to tell Apache to transfer filePath ( will honor byte range ) */ printf("Content-Length: %lld\n", (long long)fileSize(filePath)); printf("X-Sendfile: %s\n\n", filePath); } void sendFileByAcc(struct sqlConnection *conn, char* acc, boolean useSubmitFname, char *addExt) /* send file identified by acc (=cdwValidFile.licensePlate), suggests a canonical filename of the format * <licensePlate>.<originalExtension> * Example URL: http://hgwdev.soe.ucsc.edu/cgi-bin/cdwGetFile?acc=SCH000FSW * * if useSubmitFname is TRUE, suggest the submission filename, not a canonical name. * if addExt is not NULL, will not retrieve the file identified by accession but rather its index file, * with the given extension (.tbi or .bai) */ { struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc); if (vf==NULL) errExitExt("%s is not a valid accession in the CDW.", acc, "404 Not Found"); struct cdwFile *ef = cdwFileFromId(conn, vf->fileId); char* filePath = cdwPathForFileId(conn, vf->fileId); if (addExt != NULL) { if (! (sameWord(addExt, ".bai") || sameWord(addExt, ".tbi"))) errAbort("ERROR: The addExt argument to cdwGetFile can only be .bai or .tbi. No other values are allowed."); if ((endsWith(filePath, ".vcf") || endsWith(filePath, ".VCF")) && sameWord(addExt, ".tbi")) // the .tbi files of .vcf files are actually named .vcf.gz.tbi filePath = catTwoStrings(filePath, ".gz.tbi"); else filePath = catTwoStrings(filePath, addExt); } else { addExt = ""; // make sure reference to addExt does not fail below // for .vcf files, we send the .vcf.gz version if (endsWith(filePath, ".vcf") || endsWith(filePath, ".VCF")) filePath = catTwoStrings(filePath, ".gz"); } mustHaveAccess(conn, ef); char suggestName[8000]; if (useSubmitFname) safef(suggestName, sizeof(suggestName), "%s%s", basename(ef->submitFileName), addExt); else { char *formatExt = fileExtFromFormat(vf->format); if (vf->format && sameWord(vf->format, "unknown") && ef && ef->submitFileName && endsWith(ef->submitFileName, ".tar.gz")) formatExt = cloneString(".tar.gz"); safef(suggestName, sizeof(suggestName), "%s%s%s", vf->licensePlate, formatExt, addExt); freez(&formatExt); } sendFile(vf->format, filePath, suggestName); } void sendFileByPath(struct sqlConnection *conn, char *path) /* send file identified by a submission pathname (cdwFile.submitFileName), * suggests the original filename. */ /* path can be a suffix that matches a filename, so the initial '/hive' or * '/data' can be omitted. * * Example URL for testing: * http://hgwdev.soe.ucsc.edu/cgi-bin/cdwGetFile/hive/groups/cirm/pilot/labs/quake/130625_M00361_0080_000000000-A43D1/Sample_1_L13_C31_IL3541-701-506/1_L13_C31_IL3541-701-506_TAAGGCGA-ACTGCATA_L001_R1_001.fastq.gz */ { int fileId = cdwFileIdFromPathSuffix(conn, path); if (fileId == 0) errExitExt("A file with suffix %s does not exist in the database", path, "404 Not Found"); char *localPath = cdwPathForFileId(conn, fileId); if (localPath == NULL) errExit("A local file with suffix %s was not found in the database. This is an internal error.", path); struct cdwFile *ef = cdwFileFromId(conn, fileId); if (ef == NULL) errExit("Could not find cdwFile for path %s", path); mustHaveAccess(conn, ef); sendFile(NULL, localPath, basename(ef->submitFileName)); } struct cdwUser *authUserViaToken(struct sqlConnection *conn) /* get the cgi variable "token" and return the cdw user for it */ { char *token = cgiOptionalString("token"); if (token==NULL) return NULL; // get the userId for this token struct sqlConnection *central = hConnectCentral(); char query[4096]; sqlSafef(query, sizeof(query), "SELECT userId FROM cdwDownloadToken WHERE token='%s'", token); int userId = sqlQuickNum(central, query); if (userId==0) return NULL; hDisconnectCentral(¢ral); return cdwUserFromId(conn, userId); } void dispatch(struct sqlConnection *conn) /* Dispatch page after to routine depending on cdwCommand variable */ { char *userName = wikiLinkUserName(); if (userName==NULL) // alternative to cookie is a token on the URL, for queries from wget user = authUserViaToken(conn); else user = cdwUserFromUserName(conn, userName); char *acc = cgiOptionalString("acc"); char *path = getenv("PATH_INFO"); // CGI gets trailing /x/y/z like path via this env. var. if (path==NULL) path = cgiOptionalString("path"); // when calling via cgi-spoof from command line boolean useSubmitFname = cgiOptionalInt("useSubmitFname", 0); char *addExt = cgiOptionalString("addExt"); if (acc != NULL) sendFileByAcc(conn, acc, useSubmitFname, addExt); else if (path != NULL) sendFileByPath(conn, path); else errExit("Need at least the HTTP GET parameter 'acc' with an accession ID " "or a file path with the HTTP parameter 'path' or the path directly after the CGI name, " "separated by '/', e.g. cdwGetFile/valData/ce10/ce10.2bit';", NULL); } void localWebWrap(struct cart *theCart) /* We got the http stuff handled, and a cart. */ { cart = theCart; struct sqlConnection *conn = sqlConnect(cdwDatabase); dispatch(conn); sqlDisconnect(&conn); } char *excludeVars[] = {"submit", NULL}; int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); oldVars = hashNew(0); cartEmptyShellNoContent(localWebWrap, hUserCookie(), excludeVars, oldVars); return 0; }