static struct trackDb *tdbFilterBy(struct trackDb **pTdbList, char *name, char *description,
char *group)
// returns tdbs that match supplied criterion, leaving unmatched in list passed in
{
// Set the word lists up once
struct slName *nameList = NULL;
if (name)
nameList = slNameListOfUniqueWords(cloneString(name),TRUE); // TRUE means respect quotes
struct slName *descList = NULL;
if (description)
descList = slNameListOfUniqueWords(cloneString(description),TRUE);
struct trackDb *tdbList = *pTdbList;
struct trackDb *tdbRejects = NULL;
struct trackDb *tdbMatched = NULL;
while (tdbList != NULL)
{
struct trackDb *tdb = slPopHead(&tdbList);
if (!tdbIsComposite(tdb))
slAddHead(&tdbRejects,tdb);
else if (group && differentString(tdb->grp,group))
slAddHead(&tdbRejects,tdb);
else if (name && !searchNameMatches(tdb, nameList))
slAddHead(&tdbRejects,tdb);
else if (description && !searchDescriptionMatches(tdb, descList))
slAddHead(&tdbRejects,tdb);
else
slAddHead(&tdbMatched,tdb);
}
*pTdbList = tdbRejects;
//warn("matched %d tracks",slCount(tdbMatched));
return tdbMatched;
}
void tryToDeprecate(struct sqlConnection *conn)
/* CGI variables are set - if possible deprecate, otherwise put up error message. */
{
pushWarnHandler(localWarn);
fileList = cgiString("fileList");
reason = cloneString(trimSpaces(cgiString("reason")));
if (isEmpty(reason))
{
warn("Please enter a reason for deprecation.");
getFileListAndReason(conn);
}
else
{
/* Go through list of accessions and make sure they are all well formed and correspond to files that exist. */
boolean ok = TRUE;
struct slName *accList = slNameListOfUniqueWords(cloneString(fileList), FALSE);
struct slName *acc;
struct slInt *idList = NULL, *idEl;
for (acc = accList; acc != NULL; acc = acc->next)
{
char *licensePlate = acc->name;
if (!startsWith(edwLicensePlatePrefix, licensePlate))
{
ok = FALSE;
warn("%s is not an accession, doesn't start with %s", licensePlate, edwLicensePlatePrefix);
break;
}
char query[256];
sqlSafef(query, sizeof(query), "select fileId from edwValidFile where licensePlate='%s'", licensePlate);
int id = sqlQuickNum(conn, query);
if (id == 0)
{
ok = FALSE;
warn("%s - no such accession. ", licensePlate);
break;
}
/* check to see is it ok tor deprecate this file */
if (!okToDeprecateThisFile(conn, id, userEmail))
{
ok = FALSE;
warn("You can not deprecate %s which was originally uploaded by %s.\n",
licensePlate, edwFindOwnerNameFromFileId(conn, id));
warn("Please click the check box below to override this rule.");
break;
}
idEl = slIntNew(id);
slAddTail(&idList, idEl);
}
if (accList == NULL)
{
warn("Please enter some file accessions");
ok = FALSE;
}
/* If a problem then put up page to try again, otherwise do deprecation. */
if (!ok)
getFileListAndReason(conn);
else
{
deprecateFileList(conn, idList, reason);
printf("Deprecated %d files<BR>\n", slCount(idList));
cgiMakeButton("submit", "Deprecate More Files");
printf(" ");
edwPrintLogOutButton();
}
}
}
static struct slRef *advancedSearchForTracks(struct sqlConnection *conn,struct group *groupList,
char *nameSearch, char *typeSearch, char *descSearch,
char *groupSearch, struct slPair *mdbPairs)
// Performs the advanced search and returns the found tracks.
{
int tracksFound = 0;
struct slRef *tracks = NULL;
int numMetadataNonEmpty = 0;
struct slPair *pair = mdbPairs;
for (; pair!= NULL;pair=pair->next)
{
if (!isEmpty((char *)(pair->val)))
numMetadataNonEmpty++;
}
if (!isEmpty(groupSearch) && sameString(groupSearch,ANYLABEL))
groupSearch = NULL;
if (!isEmpty(typeSearch) && sameString(typeSearch,ANYLABEL))
typeSearch = NULL;
if (isEmpty(nameSearch) && isEmpty(typeSearch) && isEmpty(descSearch)
&& isEmpty(groupSearch) && numMetadataNonEmpty == 0)
return NULL;
// First do the metaDb searches, which can be done quickly for all tracks with db queries.
struct hash *matchingTracks = NULL;
if (numMetadataNonEmpty)
{
struct mdbObj *mdbObj, *mdbObjs = mdbObjRepeatedSearch(conn,mdbPairs,TRUE,FALSE);
if (mdbObjs)
{
for (mdbObj = mdbObjs; mdbObj != NULL; mdbObj = mdbObj->next)
{
if (matchingTracks == NULL)
matchingTracks = newHash(0);
hashAddInt(matchingTracks, mdbObj->obj, 1);
}
mdbObjsFree(&mdbObjs);
}
if (matchingTracks == NULL)
return NULL;
}
// Set the word lists up once
struct slName *nameList = NULL;
if (!isEmpty(nameSearch))
nameList = slNameListOfUniqueWords(cloneString(nameSearch),TRUE); // TRUE means respect quotes
struct slName *descList = NULL;
if (!isEmpty(descSearch))
descList = slNameListOfUniqueWords(cloneString(descSearch),TRUE);
struct group *group;
for (group = groupList; group != NULL; group = group->next)
{
if (isEmpty(groupSearch) || sameString(group->name, groupSearch))
{
if (group->trackList == NULL)
continue;
struct trackRef *tr;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
char *trackType = cloneFirstWord(track->tdb->type); // will be spilled
if ((matchingTracks == NULL || hashLookup(matchingTracks, track->track) != NULL)
&& ( isEmpty(typeSearch)
|| (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb)))
&& (isEmpty(nameSearch) || searchNameMatches(track->tdb, nameList))
&& (isEmpty(descSearch) || searchDescriptionMatches(track->tdb, descList)))
{
if (track != NULL)
{
tracksFound++;
refAdd(&tracks, track);
}
else
warn("found group track is NULL.");
}
if (track->subtracks != NULL)
{
struct track *subTrack;
for (subTrack = track->subtracks; subTrack != NULL; subTrack = subTrack->next)
{
trackType = cloneFirstWord(subTrack->tdb->type); // will be spilled
if ( (matchingTracks == NULL
|| hashLookup(matchingTracks, subTrack->track) != NULL)
&& (isEmpty(typeSearch) || sameWord(typeSearch, trackType))
&& (isEmpty(nameSearch) || searchNameMatches(subTrack->tdb, nameList))
&& (isEmpty(descSearch) // subtracks inherit description
|| searchDescriptionMatches(subTrack->tdb, descList)
|| (tdbIsCompositeChild(subTrack->tdb) && subTrack->parent
&& searchDescriptionMatches(subTrack->parent->tdb, descList))))
{
if (track != NULL)
{
tracksFound++;
refAdd(&tracks, subTrack);
}
else
warn("found subtrack is NULL.");
}
}
}
}
}
}
return tracks;
}
