static boolean mdbSelectsAddFoundComposites(struct slPair **pMdbSelects,struct trackDb *tdbsFound)
// Adds a composite mdbSelect (if found in tdbsFound) to the head of the pairs list.
// If tdbsFound is NULL, then add dummy composite search criteria
{
// create comma separated list of composites
struct dyString *dyComposites = dyStringNew(256);
struct trackDb *tdb = tdbsFound;
for (;tdb != NULL; tdb = tdb->next)
{
if (tdbIsComposite(tdb))
dyStringPrintf(dyComposites,"%s,",tdb->track);
else if (tdbIsCompositeChild(tdb))
{
struct trackDb *composite = tdbGetComposite(tdb);
dyStringPrintf(dyComposites,"%s,",composite->track);
}
}
if (dyStringLen(dyComposites) > 0)
{
char *composites = dyStringCannibalize(&dyComposites);
composites[strlen(composites) - 1] = '\0'; // drop the last ','
slPairAdd(pMdbSelects,MDB_VAR_COMPOSITE,composites);
// Composite should not already be in the list, because it is only indirectly sortable
return TRUE;
}
//warn("No composites found");
dyStringFree(&dyComposites);
return FALSE;
}
struct slPair *fileFormatSearchWhiteList()
// Gets the whitelist of approved file formats that is allowed for search
{
char *crudeTypes[] =
{
"bam", // "bam.bai" is now alway selected with bam,
"tagAlign",
"bed.gz",
"bigBed",
"broadPeak",
"narrowPeak",
"fastq",
"bigWig",
"wig" // TODO: Add "other" category. TODO: make into multi-select
};
char *nicerTypes[] =
{
"Alignment binary (bam) - binary SAM", // "Alignment binary index (bai) - binary SAM index",
"Alignment tags (tagAlign)",
"bed - browser extensible data",
"bigBed - self index, often remote bed format",
"Peaks Broad (broadPeak) - ENCODE large region peak format",
"Peaks Narrow (narrowPeak) - ENCODE small region peak format",
"Raw Sequence (fastq) - High throughput sequence format",
"Signal (bigWig) - self index, often remote wiggle format",
"Signal (wig) - wiggle format"
};
struct slPair *fileTypes = NULL;
int ix = 0, count = sizeof(crudeTypes)/sizeof(char *);
for (ix=0;ix<count;ix++)
slPairAdd(&fileTypes, crudeTypes[ix],cloneString(nicerTypes[ix]));
return fileTypes;
}
struct slPair *raNextStanzaLinesAndUntouched(struct lineFile *lf)
// Return list of lines starting from current position, up through last line of next stanza.
// May return a few blank/comment lines at end with no real stanza.
// Will join continuation lines, allocating memory as needed.
// returns pairs with name=joined line and if joined,
// val will contain raw lines '\'s and linefeeds, else val will be NULL.
{
struct slPair *pairs = NULL;
boolean stanzaStarted = FALSE;
char *line, *raw;
int lineLen,rawLen;
while (lineFileNextFull(lf, &line, &lineLen, &raw, &rawLen)) // Joins continuation lines
{
char *clippedText = skipLeadingSpaces(line);
if (stanzaStarted && clippedText[0] == 0)
{
lineFileReuse(lf);
break;
}
if (!stanzaStarted && clippedText[0] != 0 && clippedText[0] != '#')
stanzaStarted = TRUE; // Comments don't start stanzas and may be followed by blanks
slPairAdd(&pairs, line,(raw != NULL?cloneString(raw):NULL));
}
slReverse(&pairs);
return pairs;
}
struct slPair *wildHashMakeList(struct hash *hash)
/* Makes a sub hash containing a list of hash elements whose names contain wildcards ('*', '?').
The sub hash will be put into WILD_CARD_HASH_BIN for use by wildHashLookup(). */
{
struct slPair *wildList = NULL;
struct hashEl* hel = NULL;
struct hashCookie cookie = hashFirst(hash);
while ((hel = hashNext(&cookie)) != NULL)
{
if (strchr(hel->name,'*') != NULL || strchr(hel->name,'?') != NULL)
slPairAdd(&wildList, hel->name, hel);
}
if (wildList == NULL) // Note: adding an "empty" pair will
slPairAdd(&wildList, WILD_CARD_HASH_EMPTY, NULL); // prevent rebuilding this list
else if (slCount(wildList) > 1)
slSort(&wildList,wildExpressionCmp); // sort on length, so the most restrictive
// wildcard match goes first?
hashAdd(hash, WILD_CARD_HASH_BIN, wildList);
return wildList;
}
struct slPair *slPairTwoColumnFile(char *fileName)
/* Read in a two column file into an slPair list */
{
char *row[2];
struct slPair *list = NULL;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
while (lineFileRow(lf, row))
slPairAdd(&list, row[0], cloneString(row[1]));
lineFileClose(&lf);
slReverse(&list);
return list;
}
struct slPair *raNextStanzAsPairs(struct lineFile *lf)
// Return ra stanza as an slPair list instead of a hash. Handy to preserve the
// order. Will ignore '#' comments and joins continued lines (ending in '\').
{
struct slPair *list = NULL;
char *key, *val;
if (!raSkipLeadingEmptyLines(lf, NULL))
return NULL;
while (raNextTagVal(lf, &key, &val, NULL))
{
slPairAdd(&list, key, cloneString(val)); // key gets cloned by slPairAdd
}
slReverse(&list);
return list;
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web plabel */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Try and get some simple D3 things running inside of Genome Browser web framework.");
printf("<script src=\"//cdnjs.cloudflare.com/ajax/libs/d3/3.4.4/d3.min.js\"></script>");
printf("<script src=\"/js/d3pie.min.js\"></script>");
struct slPair *data= slPairNew("A","100");
slPairAdd(&data, "B", "10");
slPairAdd(&data, "C", "1");
slReverse(&data);
printf("<div id=\"pieChart1\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Subtitle");
printf("</div>\n");
slPairAdd(&data, "D", "10");
printf("<div id=\"pieChart2\">\n");
drawPrettyPieGraph(data, "pieChart1", "A new title", "cool subtitle!");
printf("</div>\n");
slPairAdd(&data, "W", "15");
printf("<div id=\"pieChart3\">\n");
drawPrettyPieGraph(data, "pieChart1", "Title", "Testing out what a much longer subtitle will look like... How many characters can I put here?");
printf("</div>\n");
slPairAdd(&data, "Z", "30");
printf("<div id=\"pieChart4\">\n");
drawPrettyPieGraph(data, "pieChart1", "How do much largers titles look?", "Subtitle");
printf("</div>\n");
printf("<style>\npieChart1{\n align:center;} </style>");
#ifdef SOON
drawPieGraph(data);
drawPieGraph(data);
slPairAdd(&data, "E", "15");
drawPieGraph(data);
slPairAdd(&data, "F", "25");
drawPieGraph(data);
slPairAdd(&data, "G", "50");
drawPieGraph(data);
#endif /* SOON */
cartWebEnd();
}
struct slPair *tagListIncludingParents(struct tagStanza *stanza)
/* Return a list of all tags including ones defined in parents. */
{
struct hash *uniq = hashNew(0);
struct slPair *list = NULL;
struct tagStanza *ts;
for (ts = stanza; ts != NULL; ts = ts->parent)
{
struct slPair *pair;
for (pair = ts->tagList; pair != NULL; pair = pair->next)
{
if (!hashLookup(uniq, pair->name))
{
slPairAdd(&list, pair->name, pair->val);
hashAdd(uniq, pair->name, pair);
}
}
}
hashFree(&uniq);
slReverse(&list);
return list;
}
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;
}
