char * dsPrintContent(int token)
// returns the content of the current buffer as a string, but does not flush or free it
// NOTE: returned pointer is not cloned memory and will be changed by successive dsPrint calls
{
dsAssertToken(token);
return dyStringContents(dsStack);
}
void doSubmitToGreat(const char *path)
/* Send a URL to GREAT that it can use to retrieve the results. */
{
struct dyString *requestName = getRequestName();
struct dyString *requestURL = dyStringCreate("http://%s/%s", cgiServerNamePort(), path);
struct dyString *greatRequest;
greatRequest = dyStringCreate(
"<meta http-equiv='refresh' content='0;url=http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=%s&requestSpecies=%s&requestName=%s&requestSender=UCSC%20Table%20Browser'>",
dyStringContents(requestURL), database, dyStringContents(requestName));
hPrintf("<b>GREAT</b> is processing BED data from \"%s\"...please wait.\n", dyStringContents(requestName));
hWrites(dyStringContents(greatRequest));
freeDyString(&greatRequest);
freeDyString(&requestName);
freeDyString(&requestURL);
}
int dsPrintFlush(int token)
// Flushes the top buffer to the next lower one and empties top buffer.
// If there is no lower buffer then the content is printed to STDOUT (or registered out).
// Returns the length flushed.
{
dsAssertToken(token);
int len = dyStringLen(dsStack);
if (len != 0)
{
if (dsStack->next == NULL)
{
dsInitializeOut();
fprintf(dsOut,"%s",dyStringContents(dsStack));
fflush(dsOut);
}
else
dyStringAppend(dsStack->next,dyStringContents(dsStack));
dyStringClear(dsStack);
}
return len;
}
int dsPrintDirectly(int token,FILE *file)
// Prints the contents of the top buffer directly to a file.
// Will leave the filled buffer at top of stack
// Returns the length printed.
{
dsAssertToken(token);
int len = dyStringLen(dsStack);
if (len != 0)
fprintf(file,"%s",dyStringContents(dsStack));
fflush(file);
return len;
}
void doGreatTopLevel()
/* intermediate page for formats printed directly from top form */
{
struct dyString *name = getRequestName();
htmlOpen("Send BED data to GREAT as %s", dyStringContents(name));
freeDyString(&name);
verifyGreatAssemblies();
startGreatForm();
cgiMakeHiddenVar(hgtaDoTopSubmit, "get output");
printGreatSubmitButtons();
hPrintf("<div style='height:.9em;'></div>\n");
htmlClose();
}
boolean doTypeDefinition(char *type,boolean inTable,boolean showType)
// Write out description of the type if it is known
{
struct hash *typeHash = (struct hash *)cvTermTypeHash();
struct hash *ra = hashFindVal(typeHash,(char *)cvTermNormalized(type)); // Find by term
if (ra == NULL)
return FALSE;
char *label = hashFindVal(ra, CV_LABEL);
struct dyString *dyDefinition = dyStringNew(256);
if (inTable)
dyStringPrintf(dyDefinition,"<tr><td colspan=%d style='background:%s; color:%s;'> ",
TABLE_COLS_AVAILABLE(0),COLOR_LTGREEN,COLOR_DARKBLUE);
else
dyStringPrintf(dyDefinition,"<div style='max-width:900px;'>");
if (label != NULL)
{
dyStringPrintf(dyDefinition,"<B><em>%s</em></B>",label);
if (showType)
dyStringPrintf(dyDefinition," [%s]",type);
dyStringAppend(dyDefinition,": ");
}
else if (showType)
dyStringPrintf(dyDefinition,"<B>%s</B>: ",type);
char *val = getDescription(ra,NULL);
dyStringPrintf(dyDefinition,"%s",val);
freeMem(val);
if (inTable)
dyStringAppend(dyDefinition," </td></tr>");
else
dyStringPrintf(dyDefinition,"</div>");
printf("%s\n",dyStringContents(dyDefinition));
dyStringFree(&dyDefinition);
return TRUE;
}
static struct slRef *advancedSearchForTracks(struct sqlConnection *conn,struct group *groupList, char **descWords,int descWordCount, char *nameSearch, char *typeSearch, char *descSearch, char *groupSearch,
int numMetadataNonEmpty,int numMetadataSelects,char **mdbVar,char **mdbVal)
// Performs the advanced search and returns the found tracks.
{
int tracksFound = 0;
struct slRef *tracks = NULL;
if(!isEmpty(nameSearch) || typeSearch != NULL || descSearch != NULL || groupSearch != NULL || numMetadataNonEmpty)
{
// First do the metaDb searches, which can be done quickly for all tracks with db queries.
struct hash *matchingTracks = newHash(0);
struct slName *el, *metaTracks = NULL;
int i;
for(i = 0; i < numMetadataSelects; i++)
{
if(!isEmpty(mdbVal[i]))
{
#ifdef CV_SEARCH_SUPPORTS_FREETEXT
enum mdbCvSearchable searchBy = mdbCvSearchMethod(mdbVar[i]);
struct slName *tmp = NULL;
// If select is by free text then like
if (searchBy == cvsSearchByMultiSelect)
{
// TO BE IMPLEMENTED
// The mdbVal[1] will hve to be filled cartOptionalSlNameList(cart,???)
struct slName *choices = (struct slName *)mdbVal[i];
if (slCount(choices) == 1)
{
tmp = mdbObjSearch(conn, mdbVar[i], choices->name, "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
}
else if(choices != NULL)
{
// Then slNames will need to be assembled into a string in the form of 'a','b','c'
struct dyString *dyList = dyStringNew(256);
dyStringPrintf(dyList,"'%s'",choices->name);
struct slName *choice = choices->next;
for(;choice!=NULL;choice=choice->next)
dyStringPrintf(dyList,",'%s'",choice->name);
tmp = mdbObjSearch(conn, mdbVar[i], dyStringContents(dyList), "in", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
dyStringFree(&dyList);
}
}
else if (searchBy == cvsSearchBySingleSelect)
{
tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
}
else if (searchBy == cvsSearchByFreeText)
{
tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "like", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
}
else if (searchBy == cvsSearchByDateRange || searchBy == cvsSearchByIntegerRange)
{
// TO BE IMPLEMENTED
// Requires new mdbObjSearch API and more than one mdbVal[i]
}
if (tmp != NULL)
{
if(metaTracks == NULL)
metaTracks = tmp;
else
metaTracks = slNameIntersection(metaTracks, tmp);
}
#else///ifndif CV_SEARCH_SUPPORTS_FREETEXT
struct slName *tmp = mdbObjSearch(conn, mdbVar[i], mdbVal[i], "is", MDB_VAL_STD_TRUNCATION, TRUE, FALSE);
if(metaTracks == NULL)
metaTracks = tmp;
else
metaTracks = slNameIntersection(metaTracks, tmp);
#endif///ndef CV_SEARCH_SUPPORTS_FREETEXT
}
}
for (el = metaTracks; el != NULL; el = el->next)
hashAddInt(matchingTracks, el->name, 1);
struct group *group;
for (group = groupList; group != NULL; group = group->next)
{
if(groupSearch == NULL || sameString(group->name, groupSearch))
{
if (group->trackList != NULL)
{
struct trackRef *tr;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
#ifdef TRACK_SEARCH_ON_TYPE
char *trackType = cloneFirstWord(track->tdb->type); // will be spilled
#endif///def TRACK_SEARCH_ON_TYPE
if((isEmpty(nameSearch) || isNameMatch(track, nameSearch, "contains")) &&
#ifdef TRACK_SEARCH_ON_TYPE
(isEmpty(typeSearch) || (sameWord(typeSearch, trackType) && !tdbIsComposite(track->tdb))) &&
#endif///def TRACK_SEARCH_ON_TYPE
(isEmpty(descSearch) || isDescriptionMatch(track, descWords, descWordCount)) &&
(!numMetadataNonEmpty || hashLookup(matchingTracks, track->track) != NULL))
{
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)
{
#ifdef TRACK_SEARCH_ON_TYPE
trackType = cloneFirstWord(subTrack->tdb->type); // will be spilled
#endif///def TRACK_SEARCH_ON_TYPE
if((isEmpty(nameSearch) || isNameMatch(subTrack, nameSearch, "contains")) &&
#ifdef TRACK_SEARCH_ON_TYPE
(isEmpty(typeSearch) || sameWord(typeSearch, trackType)) &&
#endif///def TRACK_SEARCH_ON_TYPE
(isEmpty(descSearch) || isDescriptionMatch(subTrack, descWords, descWordCount)) &&
(!numMetadataNonEmpty || hashLookup(matchingTracks, subTrack->track) != NULL))
{
// XXXX to parent hash. - use tdb->parent instead.
//hashAdd(parents, subTrack->track, track);
if (track != NULL)
{
tracksFound++;
refAdd(&tracks, subTrack);
}
else
warn("found subtrack is NULL.");
}
}
}
}
}
}
}
}
return tracks;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
if(prefix == NULL || database == NULL)
fail("Missing prefix or database parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
fail("gene autosuggest is not supported for this assembly");
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, description.name "
"from %s r, gbCdnaInfo, description where r.name2 = '%s' and gbCdnaInfo.acc = r.name "
"and gbCdnaInfo.description = description.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, description.name "
"from %s r, gbCdnaInfo, description where r.name2 LIKE '%s%%' and gbCdnaInfo.acc = r.name "
"and gbCdnaInfo.description = description.id order by r.name2, r.chrom, r.txStart", table, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", \"id\": \"%s:%d-%s\", \"internalId\": \"%s\"}", count == 1 ? "" : ",\n",
row[0], javaScriptLiteralEncode(row[5]), row[1], atoi(row[2])+1, row[3], javaScriptLiteralEncode(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}
void verifyGreatAssemblies()
{
// First read in the assembly name and description information into name lists
struct slName* supportedAssemblies = NULL;
struct lineFile *lf = lineFileOpen(greatData, TRUE);
int fieldCount = 1;
char* row[fieldCount];
int wordCount;
while ((wordCount = lineFileChopTab(lf, row)) != 0)
{
if (wordCount != fieldCount)
errAbort("The %s file is not properly formatted.\n", greatData);
slNameAddHead(&supportedAssemblies, row[0]);
}
lineFileClose(&lf);
boolean invalidAssembly = TRUE;
struct slName* currAssembly;
for (currAssembly = supportedAssemblies; currAssembly != NULL; currAssembly = currAssembly->next)
{
if (!hDbIsActive(currAssembly->name))
{
errAbort("Assembly %s in supported assembly file is not an active assembly.\n", currAssembly->name);
}
if (sameOk(database, currAssembly->name))
{
invalidAssembly = FALSE;
break;
}
}
if (invalidAssembly)
{
slReverse(&supportedAssemblies);
currAssembly = supportedAssemblies;
struct dyString* dy = dyStringNew(0);
addAssemblyToSupportedList(dy, currAssembly->name);
currAssembly = currAssembly->next;
while (currAssembly != NULL)
{
dyStringAppend(dy, ", ");
if (currAssembly->next == NULL)
dyStringAppend(dy, "and ");
addAssemblyToSupportedList(dy, currAssembly->name);
currAssembly = currAssembly->next;
}
hPrintf("<script type='text/javascript'>\n");
hPrintf("function logSpecies() {\n");
hPrintf("try {\n");
hPrintf("var r = new XMLHttpRequest();\n");
hPrintf("r.open('GET', 'http://great.stanford.edu/public/cgi-bin/logSpecies.php?species=%s');\n", database);
hPrintf("r.send(null);\n");
hPrintf("} catch (err) { }\n");
hPrintf("}\n");
hPrintf("window.onload = logSpecies;\n");
hPrintf("</script>\n");
errAbort("GREAT only supports the %s assemblies."
"\nPlease go back and ensure that one of those assemblies is chosen.",
dyStringContents(dy));
htmlClose();
dyStringFree(&dy);
}
slNameFreeList(&supportedAssemblies);
}
char *webTimeStampedLinkToResource(char *fileName, boolean wrapInHtml)
// If wrapInHtml
// returns versioned link embedded in style or script html (free after use).
// else
// returns full path of a versioned path to the requested resource file (js, or css).
// NOTE: png, jpg and gif should also be supported but are untested.
//
// In production sites we use a versioned softlink that includes the CGI version. This has the following benefits:
// a) flushes user's web browser cache when the user visits a GB site whose version has changed since their last visit;
// b) enforces the requirement that static files are the same version as the CGIs (something that often fails to happen in mirrors).
// (see notes in redmine #3170).
//
// In dev trees we use mtime to create a pseudo-version; this forces web browsers to reload css/js file when it changes,
// so we don't get odd behavior that can be caused by caching of mis-matched javascript and style files in dev trees.
//
// In either case, the actual file has to have been previously created by running make in the appropriate directory (kent/src/hg/js
// or kent/src/hg/htdocs/style).
{
char baseName[PATH_LEN];
char extension[FILEEXT_LEN];
splitPath(fileName, NULL, baseName, extension);
boolean js = sameString(".js",extension);
boolean style = !js && sameString(".css",extension);
boolean image = !js
&& !style
&& ( sameString(".png",extension)
|| sameString(".jpg",extension)
|| sameString(".gif",extension));
if (!js && !style) // && !image) NOTE: This code has not been tested on images but should work.
errAbort("webTimeStampedLinkToResource: unknown resource type for %s.\n", fileName);
// Build and verify directory
char *dirName = "";
if (js)
dirName = cfgOptionDefault("browser.javaScriptDir", "js");
else if (style)
dirName = cfgOptionDefault("browser.styleDir","style");
else if (image)
dirName = cfgOptionDefault("browser.styleImagesDir","style/images");
struct dyString *fullDirName = NULL;
char *docRoot = hDocumentRoot();
if (docRoot != NULL)
fullDirName = dyStringCreate("%s/%s", docRoot, dirName);
else
// tolerate missing docRoot (i.e. when running from command line)
fullDirName = dyStringCreate("%s", dirName);
if (!fileExists(dyStringContents(fullDirName)))
errAbort("webTimeStampedLinkToResource: dir: %s doesn't exist.\n",
dyStringContents(fullDirName));
// build and verify real path to file
struct dyString *realFileName = dyStringCreate("%s/%s", dyStringContents(fullDirName), fileName);
if (!fileExists(dyStringContents(realFileName)))
errAbort("webTimeStampedLinkToResource: file: %s doesn't exist.\n",
dyStringContents(realFileName));
// build and verify link path including timestamp in the form of dir/baseName + timeStamp or CGI Version + ext
long mtime = fileModTime(dyStringContents(realFileName));
struct dyString *linkWithTimestamp;
char *scriptName = cgiScriptName();
if (scriptName == NULL)
scriptName = cloneString("");
boolean nonVersionedLinks = FALSE;
if (endsWith(scriptName, "qaPushQ"))
nonVersionedLinks = TRUE;
if (nonVersionedLinks)
linkWithTimestamp = dyStringCreate("%s/%s%s", dyStringContents(fullDirName), baseName, extension);
else if ((cfgOption("versionStamped") == NULL) && (hIsPreviewHost() || hIsPrivateHost()))
linkWithTimestamp = dyStringCreate("%s/%s-%ld%s", dyStringContents(fullDirName), baseName, mtime, extension);
else
linkWithTimestamp = dyStringCreate("%s/%s-v%s%s", dyStringContents(fullDirName), baseName, CGI_VERSION, extension);
if (!fileExists(dyStringContents(linkWithTimestamp)))
errAbort("Cannot find correct version of file '%s'; this is due to an installation error\n\nError details: %s does not exist",
fileName, dyStringContents(linkWithTimestamp));
// Free up all that extra memory
dyStringFree(&realFileName);
dyStringFree(&fullDirName);
char *linkFull = dyStringCannibalize(&linkWithTimestamp);
char *link = linkFull;
if (docRoot != NULL)
{
link = cloneString(linkFull + strlen(docRoot) + 1);
freeMem(linkFull);
}
if (wrapInHtml) // wrapped for christmas
{
struct dyString *wrapped = dyStringNew(0);
if (js)
dyStringPrintf(wrapped,"<script type='text/javascript' SRC='/%s'></script>\n", link);
else if (style)
dyStringPrintf(wrapped,"<LINK rel='STYLESHEET' href='/%s' TYPE='text/css' />\n", link);
else // Will be image, since these are the only three choices allowed
dyStringPrintf(wrapped,"<IMG src='/%s' />\n", link);
freeMem(link);
link = dyStringCannibalize(&wrapped);
}
return link;
}
void suggestGene(char *database, char *table, char *prefix)
/* Print out a Javascript list of objects describing genes that start with prefix. */
{
struct dyString *str = newDyString(10000);
dyStringPrintf(str, "[\n");
int exact = cgiOptionalInt("exact", 0);
boolean hasKnownCanonical = sameString(table, "knownCanonical");
initGenbankTableNames(database);
char query[2048];
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots
// using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query),
"select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x "
"where k.transcript = x.kgID and k.transcript = kg.name and x.geneSymbol = '%s' "
"order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query),
"select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d "
"where r.name2 = '%s' and g.acc = r.name and g.description = d.id "
"order by r.name2, r.chrom, r.txEnd - r.txStart desc",
table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query),
"select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x "
"where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' "
"order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d "
"where r.name2 LIKE '%s%%' and g.acc = r.name and g.description = d.id "
"order by r.name2, r.chrom, r.txStart",
table, gbCdnaInfoTable, descriptionTable, prefix);
}
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
int count = 0;
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
hFreeConn(&conn);
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
struct dyString *output = newDyString(10000);
setUdcCacheDir();
cgiSpoof(&argc, argv);
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
char *database = cgiString("db");
char *cmd = cgiString("cmd");
char *jsonp = cgiOptionalString("jsonp");
if (!hDbExists(database))
errAbort("Invalid database '%s'", database);
if (!strcmp(cmd, "defaultPos"))
{
dyStringPrintf(output, "{\"pos\": \"%s\"}", hDefaultPos(database));
}
else if (!strcmp(cmd, "metaDb"))
{
// Return list of values for given metaDb var
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=metaDb&var=cell
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
struct slPair *pair;
dyStringPrintf(output, "[\n");
for (pair = pairs; pair != NULL; pair = pair->next)
{
if (pair != pairs)
dyStringPrintf(output, ",\n");
dyStringPrintf(output, "['%s','%s']", javaScriptLiteralEncode(mdbPairLabel(pair)),
javaScriptLiteralEncode(mdbPairVal(pair)));
}
dyStringPrintf(output, "\n]\n");
}
else
errAbort("Assembly does not support metaDb");
}
// TODO: move to lib since hgTracks and hgApi share
#define METADATA_VALUE_PREFIX "hgt_mdbVal"
else if (startsWith(METADATA_VALUE_PREFIX, cmd))
{
// Returns metaDb value control: drop down or free text, with or without help link.
// e.g. http://genome.ucsc.edu/hgApi?db=hg18&cmd=hgt_mdbVal3&var=cell
// TODO: Move guts to lib, so that hgTracks::searchTracks.c and hgApi.c can share
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
if (metaDbExists)
{
char *var = cgiOptionalString("var");
if (!var)
errAbort("Missing var parameter");
int ix = atoi(cmd+strlen(METADATA_VALUE_PREFIX)); // 1 based index
if (ix == 0) //
errAbort("Unsupported 'cmd' parameter");
enum cvSearchable searchBy = cvSearchMethod(var);
char name[128];
safef(name,sizeof name,"%s%i",METADATA_VALUE_PREFIX,ix);
if (searchBy == cvSearchBySingleSelect || searchBy == cvSearchByMultiSelect)
{
boolean fileSearch = (cgiOptionalInt("fileSearch",0) == 1);
struct slPair *pairs = mdbValLabelSearch(conn, var, MDB_VAL_STD_TRUNCATION, FALSE,
!fileSearch, fileSearch);
if (slCount(pairs) > 0)
{
char *dropDownHtml =
cgiMakeSelectDropList((searchBy == cvSearchByMultiSelect),
name, pairs, NULL, ANYLABEL, "mdbVal",
"style='min-width: 200px; font-size: .9em;' "
"onchange='findTracksMdbValChanged(this);'");
if (dropDownHtml)
{
dyStringAppend(output,dropDownHtml);
freeMem(dropDownHtml);
}
slPairFreeList(&pairs);
}
}
else if (searchBy == cvSearchByFreeText)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal freeText' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByWildList)
{
dyStringPrintf(output,"<input type='text' name='%s' value='' class='mdbVal wildList' "
"title='enter comma separated list of values' "
"onchange='findTracksMdbValChanged(this);' style='max-width:310px; "
"width:310px; font-size:.9em;'>", name);
}
else if (searchBy == cvSearchByDateRange || searchBy == cvSearchByIntegerRange)
{
// TO BE IMPLEMENTED
}
else
errAbort("Metadata variable not searchable");
dyStringPrintf(output,"<span id='helpLink%i'> </span>",ix);
}
else
errAbort("Assembly does not support metaDb");
}
else if (!strcmp(cmd, "tableMetadata"))
{ // returns an html table with metadata for a given track
char *trackName = cgiOptionalString("track");
boolean showLonglabel = (NULL != cgiOptionalString("showLonglabel"));
boolean showShortLabel = (NULL != cgiOptionalString("showShortLabel"));
if (trackName != NULL)
{
// hTrackDbForTrackAndAncestors avoids overhead of getting whole track list!
struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName);
if (tdb != NULL)
{
char * html = metadataAsHtmlTable(database,tdb,showLonglabel,showShortLabel);
if (html)
{
dyStringAppend(output,html);
freeMem(html);
}
else
dyStringPrintf(output,"No metadata found for track %s.",trackName);
}
else
dyStringPrintf(output,"Track %s not found",trackName);
}
else
dyStringAppend(output,"No track variable found");
}
else if (sameString(cmd, "codonToPos") || sameString(cmd, "exonToPos"))
{
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp;
char *name = cgiString("name");
char *table = cgiString("table");
int num = cgiInt("num");
struct sqlConnection *conn = hAllocConn(database);
sqlSafef(query, sizeof(query), "select name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from %s where name = '%s'", table, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row);
boolean found;
int start, end;
if (sameString(cmd, "codonToPos"))
found = codonToPos(gp, num, &start, &end);
else
found = exonToPos(gp, num, &start, &end);
if (found)
dyStringPrintf(output, "{\"pos\": \"%s:%d-%d\"}", gp->chrom, start + 1, end);
else
dyStringPrintf(output, "{\"error\": \"%d is an invalid %s for this gene\"}", num, sameString(cmd, "codonToPos") ? "codon" : "exon");
}
else
dyStringPrintf(output, "{\"error\": \"Couldn't find item: %s\"}", name);
sqlFreeResult(&sr);
hFreeConn(&conn);
}
else
{
warn("unknown cmd: %s",cmd);
errAbort("Unsupported 'cmd' parameter");
}
apiOut(dyStringContents(output), jsonp);
cgiExitTime("hgApi", enteredMainTime);
return 0;
}
static struct pubsExtra *pubsMakeExtra(struct track* tg, char *articleTable,
struct sqlConnection* conn, struct linkedFeatures* lf)
/* bad solution: a function that is called before the extra field is
* accessed and that fills it from a sql query. Will need to redo this like gencode,
* drawing from atom, variome and bedLoadN or bedDetails */
{
char query[LARGEBUF];
struct sqlResult *sr = NULL;
char **row = NULL;
struct pubsExtra *extra = NULL;
if (sameWord(tg->table, "pubsBlat"))
// legacy table format where bed-like table does not includ title but has to pull it out from 2nd table
sqlSafef(query, sizeof(query), "SELECT firstAuthor, year, title FROM %s WHERE articleId = '%s'",
articleTable, lf->name);
else
// new table format
sqlSafef(query, sizeof(query), "SELECT firstAuthor, year, title, impact, classes FROM %s "
"WHERE chrom = '%s' and chromStart = '%d' and name='%s'", tg->table, chromName, lf->start, lf->name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
char *firstAuthor = row[0];
char *year = row[1];
char *title = row[2];
char *impact = NULL;
char *classes = NULL;
extra = needMem(sizeof(struct pubsExtra));
extra->label = pubsFeatureLabel(firstAuthor, year);
if (isEmpty(title))
extra->mouseOver = extra->label;
else
extra->mouseOver = cloneString(title);
extra->color = NULL;
extra->shade = -1;
if (!sameWord(tg->table, "pubsBlat"))
{
impact = row[3];
classes = row[4];
if (!isEmpty(impact))
{
char *colorBy = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsColorBy");
if ((colorBy==NULL) || strcmp(colorBy,"topic")==0)
{
char *classCopy = classes;
char *mainClass = cloneNextWordByDelimiter(&classes, ',');
classes = classCopy;
if (mainClass!=NULL)
{
struct rgbColor *col = (struct rgbColor*) hashFindVal(pubsClassColors, mainClass);
extra->color = col;
// add class to mouseover text
struct dyString *mo = dyStringNew(0);
dyStringAppend(mo, extra->mouseOver);
dyStringAppend(mo, " (categories: ");
dyStringAppend(mo, classes);
dyStringAppend(mo, ")");
freeMem(extra->mouseOver);
extra->mouseOver = dyStringContents(mo);
}
}
else
{
if (sameString(colorBy,"impact"))
{
int impInt = atoi(impact);
if (impInt<=1)
extra->color = &impact1Color;
else if (impInt<=3)
extra->color = &impact2Color;
else if (impInt<=10)
extra->color = &impact3Color;
else
extra->color = &impact4Color;
// add impact to mouseover text
struct dyString *mo = dyStringNew(0);
dyStringAppend(mo, extra->mouseOver);
dyStringAppend(mo, " (impact ");
dyStringAppend(mo, impact);
dyStringAppend(mo, ")");
freeMem(extra->mouseOver);
extra->mouseOver = dyStringContents(mo);
}
if (sameString(colorBy,"year"))
{
int relYear = (atoi(year)-1990);
extra->shade = min(relYear/3, 10);
//extra->color = shadesOfGray[yearShade];
}
}
}
}
}
sqlFreeResult(&sr);
return extra;
}
boolean lineFileNextFull(struct lineFile *lf, char **retFull, int *retFullSize,
char **retRaw, int *retRawSize)
// Fetch next line from file joining up any that are continued by ending '\'
// If requested, and was joined, the unjoined raw lines are also returned
// NOTE: comment lines can't be continued! ("# comment \ \n more comment" is 2 lines.)
{
// May have requested reusing the last full line.
if (lf->fullLineReuse)
{
lf->fullLineReuse = FALSE;
assert(lf->fullLine != NULL);
*retFull = dyStringContents(lf->fullLine);
if (retFullSize)
*retFullSize = dyStringLen(lf->fullLine);
if (retRaw != NULL)
{
assert(lf->rawLines != NULL);
*retRaw = dyStringContents(lf->rawLines);
if (retRawSize)
*retRawSize = dyStringLen(lf->rawLines);
}
return TRUE;
}
// Empty pointers
*retFull = NULL;
if (retRaw != NULL)
*retRaw = NULL;
// Prepare lf buffers
if (lf->fullLine == NULL)
{
lf->fullLine = dyStringNew(1024);
lf->rawLines = dyStringNew(1024); // Better to always create it than test every time
}
else
{
dyStringClear(lf->fullLine);
dyStringClear(lf->rawLines);
}
char *line;
while (lineFileNext(lf, &line, NULL))
{
char *start = skipLeadingSpaces(line);
// Will the next line continue this one?
char *end = start;
if (*start == '#') // Comment lines can't be continued!
end = start + strlen(start);
else
{
while (*end != '\0') // walking forward for efficiency (avoid strlens())
{
for (;*end != '\0' && *end != '\\'; end++) ; // Tight loop to find '\'
if (*end == '\0')
break;
// This could be a continuation
char *slash = end;
if (*(++end) == '\\') // escaped
continue;
end = skipLeadingSpaces(end);
if (*end == '\0') // Just whitespace after '\', so true continuation mark
{
if (retRaw != NULL) // Only if actually requested.
{
dyStringAppendN(lf->rawLines,line,(end - line));
dyStringAppendC(lf->rawLines,'\n'); // New lines delimit raw lines.
}
end = slash; // Don't need to zero, because of appending by length
break;
}
}
}
// Stitch together full lines
if (dyStringLen(lf->fullLine) == 0)
dyStringAppendN(lf->fullLine,line,(end - line)); // includes first line's whitespace
else if (start < end) // don't include continued line's leading spaces
dyStringAppendN(lf->fullLine,start,(end - start));
if (*end == '\\')
continue;
// Got a full line now!
*retFull = dyStringContents(lf->fullLine);
if (retFullSize)
*retFullSize = dyStringLen(lf->fullLine);
if (retRaw != NULL && dyStringLen(lf->rawLines) > 0) // Only if actually requested & continued
{
// This is the final line which doesn't have a continuation char
dyStringAppendN(lf->rawLines,line,(end - line));
*retRaw = dyStringContents(lf->rawLines);
if (retRawSize)
*retRawSize = dyStringLen(lf->rawLines);
}
return TRUE;
}
return FALSE;
}
int main(int argc, char *argv[])
{
long enteredMainTime = clock1000();
cgiSpoof(&argc, argv);
char *prefix = cgiOptionalString("prefix");
char *database = cgiOptionalString("db");
initGenbankTableNames(database);
int exact = cgiOptionalInt("exact", 0);
struct sqlConnection *conn;
char query[2048];
char **row;
struct sqlResult *sr;
int count = 0;
boolean hasKnownCanonical;
struct dyString *str = newDyString(10000);
char *table;
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
popAbortHandler();
hasKnownCanonical = sameString(table, "knownCanonical");
puts("Content-Type:text/plain");
puts("\n");
dyStringPrintf(str, "[\n");
if(exact)
{
// NOTE that exact is no longer used by the UI as of v271, but there are still some robots using it so we still support it.
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol = '%s' order by x.geneSymbol, k.chrom, kg.txEnd - kg.txStart desc", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 = '%s' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txEnd - r.txStart desc", table, gbCdnaInfoTable, descriptionTable, prefix);
}
else
{
// We use a LIKE query b/c it uses the geneSymbol index (substr queries do not use indices in mysql).
// Also note that we take advantage of the fact that searches are case-insensitive in mysql.
// Unfortunately, knownCanonical sometimes has multiple entries for a given gene (e.g. 2 TTn's in mm9 knownCanonical;
// 3 POU5F1's in hg19); we return all of them (#5962).
if(hasKnownCanonical)
sqlSafef(query, sizeof(query), "select x.geneSymbol, k.chrom, kg.txStart, kg.txEnd, x.kgID, x.description "
"from knownCanonical k, knownGene kg, kgXref x where k.transcript = x.kgID and k.transcript = kg.name "
"and x.geneSymbol LIKE '%s%%' order by x.geneSymbol, k.chrom, kg.txStart", prefix);
else
sqlSafef(query, sizeof(query), "select r.name2, r.chrom, r.txStart, r.txEnd, r.name, d.name "
"from %s r, %s g, %s d where r.name2 LIKE '%s%%' and g.acc = r.name "
"and g.description = d.id order by r.name2, r.chrom, r.txStart", table, gbCdnaInfoTable, descriptionTable, prefix);
}
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
// ignore funny chroms (e.g. _hap chroms. See redmine #4257.
if(!strchr(row[1], '_'))
{
// We have some very long descriptions, e.g. 4277 chars for hg38 CLOCK, so truncate:
const int maxDesc = 120;
char *description = row[5];
if (strlen(description) > maxDesc + 4)
strcpy(description + maxDesc, "...");
count++;
dyStringPrintf(str, "%s{\"value\": \"%s (%s)\", "
"\"id\": \"%s:%d-%s\", "
"\"geneSymbol\": \"%s\", "
"\"internalId\": \"%s\"}",
count == 1 ? "" : ",\n", row[0], jsonStringEscape(description),
row[1], atoi(row[2])+1, row[3],
jsonStringEscape(row[0]),
jsonStringEscape(row[4]));
}
}
dyStringPrintf(str, "\n]\n");
puts(dyStringContents(str));
cgiExitTime("hgSuggest", enteredMainTime);
return 0;
}
void galleryDisplay(struct galleryEntry *galList)
/* Print a table containing the gallery data from galList */
{
struct galleryEntry *thisSession = galList;
/* Hide the orderable columns and disable ordering on the visible columns
* https://datatables.net/reference/option/columnDefs for more info.
* Then set up the ordering drop-down menu */
printf ("<script type=\"text/javascript\">");
printf("$(document).ready(function () {\n"
" $('#sessionTable').DataTable({\"columnDefs\": [{\"visible\":false, \"targets\":[2,3]},\n"
" {\"orderable\":false, \"targets\":[0,1]}\n"
" ],\n"
" \"dom\":\"lftip\",\n"
" \"stateSave\":true,\n"
" \"stateSaveCallback\": %s,\n"
" \"stateLoadCallback\": %s,\n"
" });\n"
/* Recover previous sorting choice from the cart settings, if available */
" var startOrder = $('#sessionTable').DataTable().order();\n"
" if (startOrder[0][0] == 3) {\n"
" if (startOrder[0][1] == \"asc\") {\n"
" $('#sortMethod').val(\"useAsc\");\n"
" } else {\n"
" $('#sortMethod').val(\"useDesc\");\n"
" }\n"
" } else {\n"
" if (startOrder[0][0] == 2) {\n"
" if (startOrder[0][1] == \"asc\") {\n"
" $('#sortMethod').val(\"dateAsc\");\n"
" } else {\n"
" $('#sortMethod').val(\"dateDesc\");\n"
" }\n"
" } else {\n"
" $('#sessionTable').DataTable().order([3,'desc']).draw();\n"
" $('#sortMethod').val(\"useDesc\");\n"
" }\n"
" }\n"
"});\n",
jsDataTableStateSave(hgPublicSessionsPrefix), jsDataTableStateLoad(hgPublicSessionsPrefix, cart));
printf ("function changeSort() {\n"
" var newSort = document.getElementById('sortMethod').value;\n"
" var theTable = $('#sessionTable').DataTable();\n"
" if (newSort == \"useDesc\") {theTable.order([3,'desc']).draw(); }\n"
" if (newSort == \"useAsc\") {theTable.order([3,'asc']).draw(); }\n"
" if (newSort == \"dateDesc\") {theTable.order([2,'desc']).draw(); }\n"
" if (newSort == \"dateAsc\") {theTable.order([2,'asc']).draw(); }\n"
"}\n");
printf("</script>\n");
printf ("<p>\n");
printf ("<b>Sort by:</b> <select id=\"sortMethod\" onchange=\"changeSort()\">\n");
printf ("\t\t<option value=\"useDesc\">Popularity (descending)</option>\n");
printf ("\t\t<option value=\"useAsc\">Popularity (ascending)</option>\n");
printf ("\t\t<option value=\"dateDesc\">Creation (newest first)</option>\n");
printf ("\t\t<option value=\"dateAsc\">Creation (oldest first)</option>\n");
printf ("</select></p>\n");
printf ("<table id=\"sessionTable\" class=\"sessionTable stripe hover row-border compact\" width=\"100%%\">\n"
" <thead>"
" <tr>"
" <th>Screenshot</th>\n"
" <th>Session Properties</th>\n"
" <th>Creation Date</th>\n"
" <th>Use Count</th>\n"
" </tr>\n"
" </thead>\n");
printf ("<tbody>\n");
while (thisSession != NULL)
{
char *settingString = NULL;
printf ("\t<tr>\n");
if (isNotEmpty(thisSession->imgUri))
{
printf ("\t\t<td><a href=\"../cgi-bin/hgTracks?%s\">",
dyStringContents(thisSession->sessionUrl));
printf ("<img src=\"%s\" class=\"sessionThumbnail\"></a></td>\n", thisSession->imgUri);
}
else
{
printf ("\t\t<td><center><nobr>Screenshot not available</nobr><br>\n");
printf ("\t\t<a href=\"../cgi-bin/hgTracks?%s\">Click Here</a> to view</center></td>\n",
dyStringContents(thisSession->sessionUrl));
}
struct hash *settingsHash = raFromString(thisSession->settings);
settingString = (char*) hashFindVal(settingsHash, "description");
if (settingString == NULL)
settingString = "";
else
{
settingString = replaceChars(settingString, "\\\\", "\\__ESC__");
settingString = replaceChars(settingString, "\\r", "\r");
settingString = replaceChars(settingString, "\\n", "\n");
settingString = replaceChars(settingString, "\\__ESC__", "\\");
}
printf ("\t\t<td><b>Description:</b> %s<br>\n", settingString);
printf ("\t\t<b>Author:</b> %s<br>\n", thisSession->userName);
printf ("\t\t<b>Session Name:</b> %s<br>\n", thisSession->sessionName);
printf ("\t\t<b>Genome Assembly:</b> %s<br>\n", thisSession->db);
printf ("\t\t<b>Creation Date:</b> %s<br>\n", thisSession->firstUse);
printf ("\t\t<b>Views:</b> %ld\n", thisSession->useCount);
printf ("\t\t</td>\n");
struct tm creationDate;
strptime(thisSession->firstUse, "%Y-%m-%d", &creationDate);
/* Hidden columns */
printf ("\t\t<td>%ld</td>\n", mktime(&creationDate));
printf ("\t\t<td>%ld</td>\n", thisSession->useCount);
printf ("\t</tr>\n");
thisSession = thisSession->next;
}
printf ("</tbody>\n");
printf ("</table>\n");
}
