static void rTsWriteAsFlatTab(struct tagStanza *list, struct slName *fieldList,
FILE *f, char *idTag, boolean withParent,
int maxDepth, int depth)
/* Recursively write out list to file */
{
if (depth > maxDepth)
return;
struct tagStanza *stanza;
for (stanza = list; stanza != NULL; stanza = stanza->next)
{
char *idVal = NULL;
if (idTag != NULL)
{
idVal = slPairFindVal(stanza->tagList, idTag);
}
if (idTag == NULL || idVal != NULL)
{
struct hash *uniq = hashNew(0);
if (withParent && stanza->parent != NULL && idTag != NULL)
{
char *parentVal = slPairFindVal(stanza->parent->tagList, idTag);
if (parentVal != NULL)
{
hashAdd(uniq, "parent", parentVal);
}
}
struct tagStanza *family;
for (family = stanza; family != NULL; family = family->parent)
{
struct slPair *pair;
for (pair = family->tagList; pair != NULL; pair = pair->next)
{
if (!hashLookup(uniq, pair->name))
{
hashAdd(uniq, pair->name, pair->val);
}
}
}
struct slName *field;
for (field = fieldList; field != NULL; field = field->next)
{
if (field != fieldList)
fputc('\t', f);
char *val = naForNull(hashFindVal(uniq, field->name));
fputs(val, f);
}
fputc('\n', f);
hashFree(&uniq);
}
rTsWriteAsFlatTab(stanza->children, fieldList, f, idTag, withParent, maxDepth, depth+1);
}
}
static void rAddIndex(struct tagStorm *tagStorm, struct tagStanza *list,
struct hash *hash, char *tag, char *parentVal,
boolean unique)
/* Add stanza to hash index if it has a value for tag, or if val is passed in. */
{
struct tagStanza *stanza;
for (stanza = list; stanza != NULL; stanza = stanza->next)
{
char *val = slPairFindVal(stanza->tagList, tag);
if (val == NULL)
val = parentVal;
if (val != NULL)
{
if (unique)
{
struct tagStanza *oldStanza = hashFindVal(hash, val);
if (oldStanza != NULL)
errAbort("tag %s value %s not unique in %s", tag, val, tagStorm->fileName);
}
hashAdd(hash, val, stanza);
}
if (stanza->children != NULL)
rAddIndex(tagStorm, stanza->children, hash, tag, val, unique);
}
}
static char *mustFindVal(struct slPair *list, char *tag, struct lineFile *lf)
/* Look for tag in list and return value. If none complain and abort. */
{
char *val = slPairFindVal(list, tag);
if (val == NULL)
errAbort("missing required %s tag near line %d of %s", tag, lf->lineIx, lf->fileName);
return val;
}
static void rTsWriteAsFlatRa(struct tagStanza *list, FILE *f, char *idTag, boolean withParent,
int maxDepth, int depth)
/* Recursively write out list to file */
{
if (depth > maxDepth)
return;
struct tagStanza *stanza;
for (stanza = list; stanza != NULL; stanza = stanza->next)
{
char *idVal = NULL;
if (idTag != NULL)
idVal = slPairFindVal(stanza->tagList, idTag);
struct hash *uniq = hashNew(0);
if (idVal != NULL)
{
fprintf(f, "%s %s\n", idTag, idVal);
hashAdd(uniq, idTag, idVal);
}
if (withParent && stanza->parent != NULL && idTag != NULL)
{
char *parentVal = slPairFindVal(stanza->parent->tagList, idTag);
if (parentVal != NULL)
{
fprintf(f, "parent %s\n", parentVal);
hashAdd(uniq, "parent", parentVal);
}
}
struct tagStanza *family;
for (family = stanza; family != NULL; family = family->parent)
{
struct slPair *pair;
for (pair = family->tagList; pair != NULL; pair = pair->next)
{
if (!hashLookup(uniq, pair->name))
{
fprintf(f, "%s %s\n", pair->name, (char*)(pair->val));
hashAdd(uniq, pair->name, pair->val);
}
}
}
fputc('\n', f);
hashFree(&uniq);
rTsWriteAsFlatRa(stanza->children, f, idTag, withParent, maxDepth, depth+1);
}
}
char *mustFindInPairList(struct slPair *list, char *name, struct lineFile *lf)
/* Look through list for one with given name, and return associated value. Use
* lf for error reporting if not found. */
{
char *val = slPairFindVal(list, name);
if (val == NULL)
errAbort("Could not find required tag '%s' in stanza ending line %d of %s",
name, lf->lineIx, lf->fileName);
return val;
}
char *tagFindVal(struct tagStanza *stanza, char *name)
/* Return value of tag of given name within stanza or any of it's parents. */
{
struct tagStanza *ancestor;
for (ancestor = stanza; ancestor != NULL; ancestor = ancestor->parent)
{
char *val = slPairFindVal(ancestor->tagList, name);
if (val != NULL)
return val;
}
return NULL;
}
char *tagStanzaVal(struct tagStanza *stanza, char *tag)
/* Return value associated with tag in stanza or any of parent stanzas */
{
while (stanza != NULL)
{
char *val = slPairFindVal(stanza->tagList, tag);
if (val != NULL)
return val;
stanza = stanza->parent;
}
return NULL;
}
struct slPair *mdbSelectPairs(struct cart *cart, struct slPair *mdbVars)
// Returns the current mdb vars and vals in the table of drop down selects
{
// figure out how many metadata selects are visible.
int numMetadataSelects = 0;
struct slPair *mdbSelectPairs = NULL;
if (mdbVars == NULL)
return 0;
// Get the current number of rows in the table of mdb selects
for (;;)
{
char buf[256];
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
char *str = cartOptionalString(cart, buf);
if (isEmpty(str))
break;
else
numMetadataSelects++;
}
// Requesting to add or delete any?
int delSearchSelect = cartUsualInt(cart, TRACK_SEARCH_DEL_ROW, 0); // 1-based row to delete
int addSearchSelect = cartUsualInt(cart, TRACK_SEARCH_ADD_ROW, 0); // 1-based row to insert after
if (delSearchSelect)
numMetadataSelects--;
if (addSearchSelect)
numMetadataSelects++;
if (numMetadataSelects)
{
int ix;
char buf[256];
for (ix = 0; ix < numMetadataSelects; ix++)
{
int offset; // used to handle additions/deletions
if (addSearchSelect > 0 && ix >= addSearchSelect)
offset = 0; // do nothing to offset (i.e. copy data from previous row)
else if (delSearchSelect > 0 && ix + 1 >= delSearchSelect)
offset = 2;
else
offset = 1;
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, ix + offset);
char *var = cartOptionalString(cart, buf);
char *val = NULL;
// We need to make sure var is valid in this assembly; if it isn't, reset it to "cell".
if (slPairFindVal(mdbVars,var) == NULL)
var = "cell";
else
{
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, ix + offset);
enum cvSearchable searchBy = cvSearchMethod(var);
if (searchBy == cvSearchByMultiSelect)
{
// Multi-selects as comma delimited list of values
struct slName *vals = cartOptionalSlNameList(cart,buf);
if (vals)
{
val = slNameListToString(vals,','); // A comma delimited list of values
slNameFreeList(&vals);
}
}
else if (searchBy == cvSearchBySingleSelect
|| searchBy == cvSearchByFreeText
|| searchBy == cvSearchByWildList)
val = cloneString(cartUsualString(cart, buf,ANYLABEL));
//else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
// {
// // TO BE IMPLEMENTED
// }
if (val != NULL && sameString(val, ANYLABEL))
val = NULL;
}
slPairAdd(&mdbSelectPairs,var,val); // val already cloned
}
if (delSearchSelect > 0)
{
safef(buf, sizeof(buf), "%s%d", METADATA_NAME_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
safef(buf, sizeof(buf), "%s%d", METADATA_VALUE_PREFIX, numMetadataSelects + 1);
cartRemove(cart, buf);
}
}
else
{
// create defaults
slPairAdd(&mdbSelectPairs,"cell", NULL);
slPairAdd(&mdbSelectPairs,"antibody",NULL);
}
slReverse(&mdbSelectPairs);
return mdbSelectPairs;
}
char *tagFindLocalVal(struct tagStanza *stanza, char *name)
/* Return value of tag of given name within stanza, or NULL * if tag does not exist.
* This does *not* look at parent tags. */
{
return slPairFindVal(stanza->tagList, name);
}
