void convertFixedStepSection(struct lineFile *lf, struct hash *vars, struct bgOut *out)
/* Read through section and output. */
{
char *chrom = requiredVar(vars, "chrom", lf);
int start = sqlUnsigned(requiredVar(vars, "start", lf)) - 1;
char *spanString = optionalVar(vars, "span", "1");
int span = sqlUnsigned(spanString);
int step = sqlUnsigned(optionalVar(vars, "step", spanString));
char *line;
while (lineFileNextReal(lf, &line))
{
line = skipLeadingSpaces(line);
if (isalpha(line[0]))
{
lineFileReuse(lf);
break;
}
eraseTrailingSpaces(line);
double val = sqlDouble(line);
bgOutWrite(out, chrom, start, start+span, val);
start += step;
}
}
static void parseMeta(struct gff3File *g3f, char *line)
/* parse a meta line of a gff3 file */
{
eraseTrailingSpaces(line);
if (sameString("###", line))
; // ignore
else if (sameString("##FASTA", line))
parseFasta(g3f);
else if (startsWithWord("##sequence-region", line))
parseSequenceRegion(g3f, line);
else if (startsWithWord("##feature-ontology", line))
parseFeatureOntology(g3f, line);
else if (startsWithWord("##attribute-ontology", line))
parseAttributeOntology(g3f, line);
else if (startsWithWord("##source-ontology", line))
parseSourceOntology(g3f, line);
else if (startsWithWord("##species", line))
parseSpecies(g3f, line);
else if (startsWithWord("##genome-build", line))
parseGenomeBuild(g3f, line);
else
gff3FileErr(g3f, "invalid meta line: %s", line);
}
void hgTrackDb(char *org, char *database, char *trackDbName, char *sqlFile, char *hgRoot,
boolean strict)
/* hgTrackDb - Create trackDb table from text files. */
{
struct trackDb *td;
char tab[PATH_LEN];
safef(tab, sizeof(tab), "%s.tab", trackDbName);
struct trackDb *tdbList = buildTrackDb(org, database, hgRoot, strict);
tdbList = flatten(tdbList);
slSort(&tdbList, trackDbCmp);
verbose(1, "Loaded %d track descriptions total\n", slCount(tdbList));
/* Write to tab-separated file; hold off on html, since it must be encoded */
{
verbose(2, "Starting write of tabs to %s\n", tab);
FILE *f = mustOpen(tab, "w");
for (td = tdbList; td != NULL; td = td->next)
{
hVarSubstTrackDb(td, database);
char *hold = td->html;
td->html = "";
subChar(td->type, '\t', ' '); /* Tabs confuse things. */
subChar(td->shortLabel, '\t', ' '); /* Tabs confuse things. */
subChar(td->longLabel, '\t', ' '); /* Tabs confuse things. */
trackDbTabOut(td, f);
td->html = hold;
}
carefulClose(&f);
verbose(2, "Wrote tab representation to %s\n", tab);
}
/* Update database */
{
char *create, *end;
char query[256];
struct sqlConnection *conn = sqlConnect(database);
/* Load in table definition. */
readInGulp(sqlFile, &create, NULL);
create = trimSpaces(create);
create = substituteTrackName(create, trackDbName);
end = create + strlen(create)-1;
if (*end == ';') *end = 0;
sqlRemakeTable(conn, trackDbName, create);
/* Load in regular fields. */
sqlSafef(query, sizeof(query), "load data local infile '%s' into table %s", tab, trackDbName);
verbose(2, "sending mysql \"%s\"\n", query);
sqlUpdate(conn, query);
verbose(2, "done tab file load");
/* Load in html and settings fields. */
for (td = tdbList; td != NULL; td = td->next)
{
if (isEmpty(td->html))
{
if (strict && !trackDbLocalSetting(td, "parent") && !trackDbLocalSetting(td, "superTrack") &&
!sameString(td->track,"cytoBandIdeo"))
{
fprintf(stderr, "Warning: html missing for %s %s %s '%s'\n",org, database, td->track, td->shortLabel);
}
}
else
{
updateBigTextField(conn, trackDbName, "tableName", td->track, "html", td->html);
}
if (td->settingsHash != NULL)
{
char *settings = settingsFromHash(td->settingsHash);
updateBigTextField(conn, trackDbName, "tableName", td->track,
"settings", settings);
if (showSettings)
{
verbose(1, "%s: type='%s';", td->track, td->type);
if (isNotEmpty(settings))
{
char *oneLine = replaceChars(settings, "\n", "; ");
eraseTrailingSpaces(oneLine);
verbose(1, " %s", oneLine);
freeMem(oneLine);
}
verbose(1, "\n");
}
freeMem(settings);
}
}
sqlDisconnect(&conn);
verbose(1, "Loaded database %s\n", database);
}
}
static struct htmlTag *htmlTagScan(char *html, char *dupe)
/* Scan HTML for tags and return a list of them.
* Html is the text to scan, and dupe is a copy of it
* which this routine will insert 0's in in the course of
* parsing.*/
{
char *s = dupe, c, *e, *tagName;
struct htmlTag *tagList = NULL, *tag;
struct htmlAttribute *att;
int pos;
for (;;)
{
c = *s++;
if (c == 0)
break;
if (c == '<')
{
if (*s == '!') /* HTML comment. */
{
s += 1;
if (s[0] == '-' && s[1] == '-')
s = stringIn("-->", s);
else
s = strchr(s, '>');
if (s == NULL)
{
warn("End of file in comment");
break;
}
}
else
{
/* Grab first word into tagName. */
e = s;
for (;;)
{
c = *e;
if (c == '>' || c == 0 || isspace(c))
break;
e += 1;
}
if (c != 0)
*e++ = 0;
tagName = s;
s = e;
/* Allocate tag, fill in name, and stick it on list. */
AllocVar(tag);
tag->name = cloneString(tagName);
slAddHead(&tagList, tag);
pos = tagName - dupe - 1;
tag->start = html+pos;
/* If already got end tag (or EOF) stop processing tag. */
if (c == '>' || c == 0)
{
tag->end = html + (e - dupe);
continue;
}
/* Process name/value pairs until get end tag. */
for (;;)
{
char *name, *val;
boolean gotEnd = FALSE;
/* Check for end tag. */
s = skipLeadingSpaces(s);
if (s[0] == '>' || s[0] == 0)
{
tag->end = html + (s - dupe);
if (s[0] == '>')
tag->end += 1;
break;
}
/* Get name - everything up to equals. */
e = s;
for (;;)
{
c = *e;
if (c == '=')
break;
else if (c == '>')
break;
else if (c == 0)
break;
else if (isspace(c))
break;
e += 1;
}
if (c == 0)
{
warn("End of file in tag");
break;
}
name = s;
*e++ = 0;
eraseTrailingSpaces(name);
if (c == '>')
{
val = "";
gotEnd = TRUE;
tag->end = html + (e - dupe);
}
else if (isspace(c))
{
val = "";
}
else
{
val = e = skipLeadingSpaces(e);
if (e[0] == '"' || e[0] == '\'')
{
if (!parseQuotedStringNoEscapes(val, val, &e))
break;
}
else
{
for (;;)
{
c = *e;
if (c == '>')
{
gotEnd = TRUE;
*e++ = 0;
tag->end = html + (e - dupe);
break;
}
else if (isspace(c))
{
*e++ = 0;
break;
}
else if (c == 0)
break;
++e;
}
}
}
AllocVar(att);
att->name = cloneString(name);
att->val = cloneString(val);
slAddTail(&tag->attributes, att);
s = e;
if (gotEnd)
break;
}
}
}
}
slReverse(&tagList);
return tagList;
}
struct tagStorm *idfToStormTop(char *fileName)
/* Convert an idf.txt format file to a tagStorm with a single top-level stanza */
{
/* Create a tag storm with one as yet empty stanza */
struct tagStorm *storm = tagStormNew(fileName);
struct tagStanza *stanza = tagStanzaNew(storm, NULL);
/* Some stuff to help turn File_Data1, File_Data2, etc to a comma separated list */
char *additionalFilePrefix = "idf.Comment_AdditionalFile_Data";
struct dyString *additionalFileDy = dyStringNew(0);
/* There can be multiple secondary accession tags, so handle these too */
char *secondaryAccessionTag = "idf.Comment_SecondaryAccession";
struct dyString *secondaryAccessionDy = dyStringNew(0);
/* Parse lines from idf file into stanza */
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *line;
struct dyString *dyVal = dyStringNew(0);
while (lineFileNextReal(lf, &line))
{
/* Erase trailing tab... */
eraseTrailingSpaces(line);
/* Parse line into tab-separated array and make sure it's a reasonable size */
char *row[256];
int rowSize = chopTabs(line, row);
if (rowSize == ArraySize(row))
errAbort("Line %d of %s has too many fields", lf->lineIx, lf->fileName);
if (rowSize < 2)
continue;
/* Convert first element to tagName */
char tagName[256];
aeFieldToNormalField("idf.", trimSpaces(row[0]), tagName, sizeof(tagName));
/* Special case where we already are a comma separated list */
if (sameString(tagName, "idf.Publication_Author_List"))
{
tagStanzaAppend(storm, stanza, tagName, row[1]);
}
else if (startsWith(additionalFilePrefix, tagName))
{
csvEscapeAndAppend(additionalFileDy, row[1]);
}
else if (sameString(secondaryAccessionTag, tagName))
{
csvEscapeAndAppend(secondaryAccessionDy, row[1]);
}
else
{
/* Convert rest of elements to possibly comma separated values */
dyStringClear(dyVal);
int i;
for (i=1; i<rowSize; ++i)
csvEscapeAndAppend(dyVal, row[i]);
tagStanzaAppend(storm, stanza, tagName, dyVal->string);
}
}
if (additionalFileDy->stringSize != 0)
tagStanzaAppend(storm, stanza, additionalFilePrefix, additionalFileDy->string);
if (secondaryAccessionDy->stringSize != 0)
tagStanzaAppend(storm, stanza, secondaryAccessionTag, secondaryAccessionDy->string);
dyStringFree(&secondaryAccessionDy);
dyStringFree(&additionalFileDy);
dyStringFree(&dyVal);
lineFileClose(&lf);
return storm;
}
