void sendFileByAcc(struct sqlConnection *conn, char* acc)
/* 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 */
{
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);
mustHaveAccess(conn, ef);
// use the license plate as the basename of the downloaded file.
// Take the extension from the submitted filename, as cdwFile.format is not the same as the extension
// e.g. format=fasta -> fa.gz
char *submitExt = skipBeyondDelimit(basename(ef->submitFileName), '.');
char suggestName[8000];
safef(suggestName, sizeof(suggestName), "%s.%s", vf->licensePlate, submitExt);
apacheSendX(vf->format, filePath, suggestName);
}
void cdwGroupFile(char *groupName, char *where)
/* cdwGroupFile - Associate a file with a group.. */
{
/* Get group from database, error out if no good */
struct sqlConnection *conn = cdwConnectReadWrite();
struct cdwGroup *group = cdwNeedGroupFromName(conn, groupName);
/* Get list of all stanzas matching query */
struct tagStorm *tags = cdwTagStorm(conn);
struct dyString *rqlQuery = dyStringNew(0);
dyStringPrintf(rqlQuery, "select accession from cdwFileTags where accession");
if (where != NULL)
dyStringPrintf(rqlQuery, " and %s", where);
struct slRef *ref, *matchRefList = tagStanzasMatchingQuery(tags, rqlQuery->string);
/* Make one pass through mostly for early error reporting and building up
* hash of cdwValidFiles keyed by accession */
struct hash *validHash = hashNew(0);
for (ref = matchRefList; ref != NULL; ref = ref->next)
{
struct tagStanza *stanza = ref->val;
char *acc = tagFindVal(stanza, "accession");
if (acc != NULL)
{
struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
if (vf == NULL)
errAbort("%s not found in cdwValidFile", acc);
hashAdd(validHash, acc, vf);
}
}
/* Second pass through matching list we call routine that actually adds
* the group/file relationship. */
for (ref = matchRefList; ref != NULL; ref = ref->next)
{
struct tagStanza *stanza = ref->val;
char *acc = tagFindVal(stanza, "accession");
if (acc != NULL)
{
struct cdwValidFile *vf = hashFindVal(validHash, acc);
if (vf != NULL)
{
addGroupToValidFile(conn, vf, group);
}
}
}
if (clDry)
verbose(1, "Would have %s", (clRemove ? "removed" : "added"));
else
verbose(1, "%s", (clRemove ? "Removed" : "Added"));
verbose(1, " group %s to %d files\n", group->name, validHash->elCount);
}
void cdwChangeAccess(char *chmodString, char *rqlWhere)
/* cdwChangeAccess - Change access to files.. */
{
char cWhere, cDir, cAccess;
parseChmodString(chmodString, &cWhere, &cDir, &cAccess);
/* Get list of all stanzas matching query */
struct sqlConnection *conn = cdwConnectReadWrite();
struct tagStorm *tags = cdwTagStorm(conn);
struct dyString *rqlQuery = dyStringNew(0);
dyStringPrintf(rqlQuery, "select accession from cdwFileTags where accession and %s", rqlWhere);
struct slRef *ref, *matchRefList = tagStanzasMatchingQuery(tags, rqlQuery->string);
/* Make one pass through mostly for early error reporting and building up
* hash of cdwValidFiles keyed by accession */
struct hash *validHash = hashNew(0);
for (ref = matchRefList; ref != NULL; ref = ref->next)
{
struct tagStanza *stanza = ref->val;
char *acc = tagFindVal(stanza, "accession");
if (acc != NULL)
{
struct cdwValidFile *vf = cdwValidFileFromLicensePlate(conn, acc);
if (vf == NULL)
errAbort("%s not found in cdwValidFile", acc);
hashAdd(validHash, acc, vf);
}
}
/* Second pass through matching list we call routine that actually adds
* the group/file relationship. */
for (ref = matchRefList; ref != NULL; ref = ref->next)
{
struct tagStanza *stanza = ref->val;
char *acc = tagFindVal(stanza, "accession");
if (acc != NULL)
{
struct cdwValidFile *vf = hashFindVal(validHash, acc);
if (vf != NULL)
{
changeAccess(conn, vf->fileId, cWhere, cDir, cAccess);
}
}
}
}
