static struct slName *parsePath(char *path)
/* Convert : separated path into a name list. */
{
struct slName *list = NULL;
char *dupe = cloneString(path);
char *s, *e;
for (s = dupe; s != NULL && s[0] != 0; s = e)
{
e = strchr(s, ':');
if (e != NULL)
*e++ = 0;
slNameAddTail(&list, expandTilde(s));
}
freeMem(dupe);
return list;
}
static struct slRef *simpleSearchForTracksstruct(char *simpleEntry)
// Performs the simple search and returns the found tracks.
{
struct slRef *tracks = NULL;
// Prepare for trix search
if (!isEmpty(simpleEntry))
{
int trixWordCount = 0;
char *tmp = cloneString(simpleEntry);
char *val = nextWord(&tmp);
struct slName *el, *trixList = NULL;
while (val != NULL)
{
slNameAddTail(&trixList, val);
trixWordCount++;
val = nextWord(&tmp);
}
if (trixWordCount > 0)
{
// Unfortunately trixSearch can't handle the slName list
int i;
char **trixWords = needMem(sizeof(char *) * trixWordCount);
for (i = 0, el = trixList; el != NULL; i++, el = el->next)
trixWords[i] = strLower(el->name);
// Now open the trix file
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(database, trixFile, sizeof(trixFile));
struct trix *trix = trixOpen(trixFile);
struct trixSearchResult *tsList = trixSearch(trix, trixWordCount, trixWords, TRUE);
for ( ; tsList != NULL; tsList = tsList->next)
{
struct track *track = (struct track *) hashFindVal(trackHash, tsList->itemId);
if (track != NULL) // It is expected that this is NULL
{ // (e.g. when trix references trackDb tracks which have no tables)
refAdd(&tracks, track);
}
}
//trixClose(trix); // don't bother (this is a CGI that is about to end)
}
}
return tracks;
}
void txGeneAltProt(char *pepFile, char *isoformsFile, char *outFile)
/* txGeneAltProt - Figure out statistics on number of alternative proteins produced by alt-splicing.. */
{
struct hash *pepHash = faReadAllIntoHash(pepFile, dnaUpper);
struct hash *totalUniqHash = hashNew(18);
uglyf("Read %d from %s\n", pepHash->elCount, pepFile);
int lastClusterId = -1;
struct hash *uniqHash = NULL;
struct slName *clusterList = NULL;
FILE *f = mustOpen(outFile, "w");
struct lineFile *lf = lineFileOpen(isoformsFile, TRUE);
char *row[2];
while (lineFileRow(lf, row))
{
int clusterId = lineFileNeedNum(lf, row, 0);
char *tx = row[1];
if (clusterId != lastClusterId)
{
if (uniqHash != NULL)
{
outputCluster(lastClusterId, clusterList, f);
hashFree(&uniqHash);
slFreeList(&clusterList);
}
uniqHash = hashNew(0);
}
lastClusterId = clusterId;
struct dnaSeq *pep = hashFindVal(pepHash, tx);
if (pep != NULL)
{
if (!hashLookup(uniqHash, pep->dna))
{
hashAdd(uniqHash, pep->dna, NULL);
slNameAddTail(&clusterList, tx);
}
if (!hashLookup(totalUniqHash, pep->dna))
hashAdd(totalUniqHash, pep->dna, NULL);
}
}
outputCluster(lastClusterId, clusterList, f);
verbose(1, "%d total unique proteins\n", totalUniqHash->elCount);
carefulClose(&f);
}
struct patch *patchLoadAll(char *fileName)
/* Load in file with one patch per line in the format:
* original new1 new2 ... newN
* This suppresses patches where original and new are the same. */
{
struct patch *list = NULL, *patch;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
while (lineFileNextReal(lf, &line))
{
AllocVar(patch);
patch->source = cloneString(nextWord(&line));
char *dest;
while ((dest = nextWord(&line)) != NULL)
slNameAddTail(&patch->destList, cloneString(dest));
if (patch->destList != NULL)
slAddHead(&list, patch);
}
lineFileClose(&lf);
slReverse(&list);
return list;
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n"
"<ul>\n"
"<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
"<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
"</ul>\n"
"<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if(metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
void checkMetaFiles(struct mdbObj *mdbObj, char *downDir, struct hash *allNames)
{
verbose(1, "----------------------------------------------\n");
verbose(1, "Checking that files specified in metaDb exist in download dir\n");
verbose(1, "----------------------------------------------\n");
for(; mdbObj != NULL; mdbObj=mdbObj->next)
{
struct mdbVar *mdbVar = hashFindVal(mdbObj->varHash, "objType");
if (mdbVar == NULL)
{
warn("objType not found in object %s", mdbObj->obj);
continue;
}
if (sameString(mdbVar->val, "composite")) // skip objType composite
continue;
mdbObj->deleteThis = FALSE;
mdbVar = hashFindVal(mdbObj->varHash, "composite");
if (mdbVar == NULL)
{
warn("composite not found in object %s", mdbObj->obj);
continue;
}
// char *composite = mdbVar->val;
mdbVar = hashFindVal(mdbObj->varHash, "fileName");
if (mdbVar == NULL)
{
mdbObj->deleteThis = TRUE;
warn("fileName not found in object %s", mdbObj->obj);
continue;
}
char *fileName = mdbVar->val;
char buffer[10 * 1024];
struct hash *bamNames = hashNew(8);
struct slName *list = slNameListFromString(fileName, ','), *el;
for(el=list; el; el=el->next)
{
if (hashLookup(allNames, el->name))
{
warn("duplicate fileName entry: %s", el->name);
}
else
{
hashAdd(allNames, el->name, NULL);
}
if (endsWith(el->name,".bam"))
{
hashAdd(bamNames, el->name, NULL);
}
if (endsWith(el->name,".bam.bai"))
{
el->name[strlen(el->name)-4] = 0;
struct hashEl *hel = hashLookup(bamNames, el->name);
el->name[strlen(el->name)] = '.';
if (hel == NULL)
{
warn(".bam.bai without corresponding .bam: %s", el->name);
}
else
{
hel->val = (void *)1;
}
}
}
// see if we have to add any .bam.bai to the list
for(el=list; el; el=el->next)
{
if (endsWith(el->name,".bam"))
{
struct hashEl *hel = hashLookup(bamNames, el->name);
if (hel->val == NULL)
{ // we have to add a .bam.bai to the list
char *bambai = addSuffix(el->name, ".bai");
warn(".bam.bai not found for corresponding .bam in meta.fileName: %s", el->name);
slNameAddTail(&list, bambai);
if (hashLookup(allNames, bambai))
{
warn("duplicate fileName entry: %s", bambai);
}
else
hashAdd(allNames, bambai, NULL);
}
}
}
// make sure the files are there
for(el=list; el; el=el->next)
{
if (!startsWith(mdbObj->obj, el->name))
{
warn("fileName %s does not start with object name %s", el->name, mdbObj->obj);
}
safef(buffer, sizeof buffer, "%s/%s", downDir, el->name);
verbose(2, "checking for fileExists %s\n", buffer);
if (!fileExists(buffer))
{
mdbObj->deleteThis = TRUE;
warn("metaDb file %s not found in download dir %s",buffer, downDir);
}
}
}
}
char *customPpNext(struct customPp *cpp)
/* Return next line. */
{
/* Check first for line to reuse. */
struct slName *reused = cpp->reusedLines;
if (reused)
{
/* We need to keep line actually reusing in memory until next
* call to customPpNext, so we move it to inReuse rather than
* immediately freeing it. */
freeMem(cpp->inReuse);
cpp->reusedLines = reused->next;
cpp->inReuse = reused;
return reused->name;
}
/* Get next line from file on top of stack. If at EOF
* go to next file in stack. If get a http:// or https:// or ftp:// line
* open file this references and push it onto stack. Meanwhile
* squirrel away 'browser' lines. */
struct lineFile *lf;
while ((lf = cpp->fileStack) != NULL)
{
char *line;
if (lineFileNext(lf, &line, NULL))
{
// if user pastes just a URL, create a track line automatically
// also allow a filename from a local directory if it has been allowed via udc.localDir in hg.conf
bool isLocalFile = cfgOption("udc.localDir")!=NULL && startsWith(cfgOption("udc.localDir"), line);
if (startsWith("http://", line) || startsWith("https://", line) || startsWith("ftp://", line) ||
isLocalFile)
{
if (customTrackIsBigData(line))
line = bigUrlToTrackLine(line);
else
{
lf = netLineFileOpen(line);
slAddHead(&cpp->fileStack, lf);
#ifdef PROGRESS_METER
off_t remoteSize = 0;
remoteSize = remoteFileSize(line);
cpp->remoteFileSize = remoteSize;
#endif
continue;
}
}
else if (!cpp->ignoreBrowserLines && startsWith("browser", line))
{
char afterPattern = line[7];
if (isspace(afterPattern) || afterPattern == 0)
{
slNameAddTail(&cpp->browserLines, line);
continue;
}
}
return line;
}
else
{
cpp->fileStack = lf->next;
lineFileClose(&lf);
}
}
return NULL;
}
struct rqlStatement *rqlStatementParse(struct lineFile *lf)
/* Parse an RQL statement out of text */
{
struct tokenizer *tkz = tokenizerOnLineFile(lf);
tkz->uncommentShell = TRUE;
tkz->uncommentC = TRUE;
tkz->leaveQuotes = TRUE;
struct rqlStatement *rql;
AllocVar(rql);
rql->command = cloneString(tokenizerMustHaveNext(tkz));
if (sameString(rql->command, "select"))
{
struct dyString *buf = dyStringNew(0);
struct slName *list = NULL;
char *tok = rqlParseFieldSpec(tkz, buf);
/* Look for count(*) as special case. */
boolean countOnly = FALSE;
if (sameString(tok, "count"))
{
char *paren = tokenizerNext(tkz);
if (paren[0] == '(')
{
while ((paren = tokenizerMustHaveNext(tkz)) != NULL)
{
if (paren[0] == ')')
break;
}
countOnly = TRUE;
freez(&rql->command);
rql->command = cloneString("count");
}
else
{
tokenizerReuse(tkz);
}
}
if (!countOnly)
{
list = slNameNew(tok);
for (;;)
{
/* Parse out comma-separated field list. */
char *comma = tokenizerNext(tkz);
if (comma == NULL || comma[0] != ',')
{
tokenizerReuse(tkz);
break;
}
slNameAddHead(&list, rqlParseFieldSpec(tkz, buf));
}
slReverse(&list);
rql->fieldList = list;
}
dyStringFree(&buf);
}
else if (sameString(rql->command, "count"))
{
/* No parameters to count. */
}
else
errAbort("Unknown RQL command '%s line %d of %s\n", rql->command, lf->lineIx, lf->fileName);
char *from = tokenizerNext(tkz);
if (from != NULL)
{
if (sameString(from, "from"))
{
for (;;)
{
struct dyString *buf = dyStringNew(0);
char *table = rqlParseFieldSpec(tkz, buf);
slNameAddTail(&rql->tableList, table);
char *comma = tokenizerNext(tkz);
if (comma == NULL)
break;
if (comma[0] != ',')
{
tokenizerReuse(tkz);
break;
}
dyStringFree(&buf);
}
}
else
{
errAbort("missing 'from' clause in %s\n", rql->command);
}
}
/* Parse where clause. */
char *where = tokenizerNext(tkz);
if (where != NULL)
{
if (!sameString(where, "where"))
{
tokenizerReuse(tkz);
}
else
{
rql->whereClause = rqlParseExpression(tkz);
rqlParseVarsUsed(rql->whereClause, &rql->whereVarList);
}
}
/* Parse limit clause. */
char *limit = tokenizerNext(tkz);
rql->limit = -1;
if (limit != NULL)
{
if (!sameString(limit, "limit"))
errAbort("Unknown clause '%s' line %d of %s", limit, lf->lineIx, lf->fileName);
char *count = tokenizerMustHaveNext(tkz);
if (!isdigit(count[0]))
errAbort("Expecting number after limit, got %s line %d of %s",
count, lf->lineIx, lf->fileName);
rql->limit = atoi(count);
}
/* Check that are at end of statement. */
char *extra = tokenizerNext(tkz);
if (extra != NULL)
errAbort("Extra stuff starting with '%s' past end of statement line %d of %s",
extra, lf->lineIx, lf->fileName);
return rql;
}
static void addIfExists(struct hash *hash, struct slName **pList, char *name)
/* Add name to tail of list if it exists in hash. */
{
if (hashLookup(hash, name))
slNameAddTail(pList, name);
}
static struct slName *getProbeList(struct sqlConnection *conn, int id)
/* Get list of probes with hyperlinks to probe info page. */
{
struct slName *returnList = NULL;
char query[256];
char *sidUrl = cartSidUrlString(cart);
struct dyString *dy = dyStringNew(0);
struct slInt *probeList = NULL, *probe;
int submissionSource = 0;
/* Make up a list of all probes in this image. */
safef(query, sizeof(query),
"select probe from imageProbe where image=%d", id);
probeList = sqlQuickNumList(conn, query);
safef(query, sizeof(query),
"select submissionSet.submissionSource from image, submissionSet"
" where image.submissionSet = submissionSet.id and image.id=%d", id);
submissionSource = sqlQuickNum(conn, query);
for (probe = probeList; probe != NULL; probe = probe->next)
{
char *type;
/* Create hyperlink to probe page around gene name. */
dyStringClear(dy);
dyStringPrintf(dy, "<A HREF=\"%s?%s&%s=%d&%s=%d\" target=_parent>",
hgVisiGeneCgiName(), sidUrl, hgpDoProbe, probe->val, hgpSs, submissionSource);
safef(query, sizeof(query),
"select probeType.name from probeType,probe where probe.id = %d "
"and probe.probeType = probeType.id",
probe->val);
type = sqlQuickString(conn, query);
dyStringPrintf(dy, "%s", naForEmpty(type));
if (sameWord(type, "antibody"))
{
char *abName;
safef(query, sizeof(query),
"select antibody.name from probe,antibody "
"where probe.id = %d and probe.antibody = antibody.id"
, probe->val);
abName = sqlQuickString(conn, query);
if (abName != NULL)
{
dyStringPrintf(dy, " %s", abName);
freeMem(abName);
}
}
else if (sameWord(type, "RNA"))
{
safef(query, sizeof(query),
"select length(seq) from probe where id=%d", probe->val);
if (sqlQuickNum(conn, query) > 0)
dyStringPrintf(dy, " sequenced");
else
{
safef(query, sizeof(query),
"select length(fPrimer) from probe where id=%d", probe->val);
if (sqlQuickNum(conn, query) > 0)
dyStringPrintf(dy, " from primers");
}
}
else if (sameWord(type, "BAC"))
{
char *name;
safef(query, sizeof(query),
"select bac.name from probe,bac "
"where probe.id = %d and probe.bac = bac.id"
, probe->val);
name = sqlQuickString(conn, query);
if (name != NULL)
{
dyStringPrintf(dy, " %s", name);
freeMem(name);
}
}
dyStringPrintf(dy, "</A>");
freez(&type);
/* Add to return list. */
slNameAddTail(&returnList, dy->string);
}
slFreeList(&probeList);
slReverse(&returnList);
return returnList;
}
static struct slName *geneProbeList(struct sqlConnection *conn, int id)
/* Get list of gene names with hyperlinks to probe info page. */
{
struct slName *returnList = NULL;
char query[256], **row;
struct sqlResult *sr;
struct dyString *dy = dyStringNew(0);
struct probeAndColor *pcList = NULL, *pc;
int probeCount = 0;
/* Make up a list of all probes in this image. */
safef(query, sizeof(query),
"select probe,probeColor from imageProbe where image=%d", id);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
AllocVar(pc);
pc->probe = sqlUnsigned(row[0]);
pc->probeColor = sqlUnsigned(row[1]);
slAddHead(&pcList, pc);
++probeCount;
}
slReverse(&pcList);
for (pc = pcList; pc != NULL; pc = pc->next)
{
int geneId;
char *geneName;
int probe = pc->probe;
char *geneUrl = NULL;
/* Get gene ID and name. */
safef(query, sizeof(query),
"select gene from probe where id = %d", probe);
geneId = sqlQuickNum(conn, query);
geneName = vgGeneNameFromId(conn, geneId);
/* Get url for known genes page if any. */
geneUrl = getKnownGeneUrl(conn, geneId);
/* Print gene name, surrounded by hyperlink to known genes
* page if possible. */
dyStringClear(dy);
if (geneUrl != NULL)
dyStringPrintf(dy, "<A HREF=\"%s\" target=_parent>",
geneUrl);
dyStringPrintf(dy, "%s", geneName);
if (geneUrl != NULL)
dyStringAppend(dy, "</A>");
freez(&geneName);
/* Add color if there's more than one probe for this image. */
if (probeCount > 1)
{
char *color;
safef(query, sizeof(query),
"select probeColor.name from probeColor "
"where probeColor.id = %d"
, pc->probeColor);
color = sqlQuickString(conn, query);
if (color != NULL)
dyStringPrintf(dy, " (%s)", color);
freez(&color);
}
/* Add to return list. */
slNameAddTail(&returnList, dy->string);
}
slFreeList(&pcList);
slReverse(&returnList);
return returnList;
}
void writeLaneArray(FILE *f, struct tagStanza *stanza, char *csvList)
/* Write out an array of file objects base on file names in csvList */
{
struct slName *list = csvParse(csvList), *file;
/* Figure out number of files per lanes. We'll take the lane number for the
* file names if available, but if not we'll assume list is sorted and will
* put the appropriate number of files in each lane. */
int laneCounter = 1;
int filesPerLane = 1;
int curFileInLane = 0;
char *pairedEnds = tagMustFindVal(stanza, "assay.seq.paired_ends");
if (!sameString(pairedEnds, "no"))
filesPerLane = 2;
/* First pass, make a list of lanes */
struct laneFiles *laneList = NULL, *lane;
for (file = list; file != NULL; file = file->next)
{
/* Figure out laneIx, from file name if possible, otherwise by counting */
char *fileName = file->name;
int laneIx = laneFromFileName(fileName);
if (laneIx == 0)
laneIx = laneCounter;
/* Update laneCounter */
if (++curFileInLane >= filesPerLane)
{
++laneCounter;
curFileInLane = 0;
}
/* Find lane in laneList, make new lane if it's not there. */
lane = laneFilesFind(laneList, laneIx);
if (lane == NULL)
{
AllocVar(lane);
lane->laneIx = laneIx;
slAddHead(&laneList, lane);
}
slNameAddTail(&lane->fileList, fileName);
}
slReverse(&laneList);
slSort(&laneList, laneFilesCmp);
/* Now make a lane array and go through lane list */
boolean firstOut = TRUE;
fputc('[', f);
for (lane = laneList; lane != NULL; lane = lane->next)
{
/* Write comma between lane objects */
if (firstOut)
firstOut = FALSE;
else
fputc(',', f);
/* Write lane object starting with lane index*/
fputc('{', f);
fprintf(f, "\"%s\": %d", "number", lane->laneIx);
/* Rest of lane fields are based on files we contain */
for (file = lane->fileList; file != NULL; file = file->next)
{
/* Calculate type */
char *fileName = file->name;
char *type = NULL;
if (sameString(pairedEnds, "no"))
{
type = "r1";
}
else if (sameString(pairedEnds, "yes"))
{
int end = endFromFileName(fileName);
if (end == 1)
type = "r1";
else
type = "r2";
}
else
errAbort("Unrecognized paired_ends %s", pairedEnds);
fprintf(f, ",\"%s\":", type);
writeJsonVal(f, fileName, FALSE);
}
fputc('}', f);
}
fputc(']', f);
slFreeList(&list);
}
