8f4e76f8972781dcf79755e7cf2a32015eb093f5
galt
  Fri Apr 19 13:32:46 2019 -0700
tweaking summary/index.html static page output

diff --git src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
index 72ef033..6fa94bd 100644
--- src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
+++ src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
@@ -1,311 +1,312 @@
 /* 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. */
 #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 errExit(char *msg, char *field) 
 /* print http header + message and exit. msg can contain %s */
 {
 printf("Content-Type: text/html\n\n");
 puts("ERROR: ");
 if (!field)
     puts(msg);
 else
     printf(msg, field);
 exit(0);
 }
 
 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)
         errExit("Sorry, this file has access restrictions. Please <a href='/cgi-bin/hgLogin'>log in</a> first.", NULL);
     else
         errExit("Sorry, user %s does not have access to this file.", user->email);
 }
 
 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)
     errExit("%s is not a valid accession in the CDW.", acc);
 
 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)
     errExit("A file with suffix %s does not exist in the database", path);
     
 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(&central);
 
 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;
 }