void writeFastqTab(struct sqlConnection *conn, struct eapGraph *eg,
struct fullExperiment *expList, char *assembly, char *outFile)
/* Write out a table in simple html based on eeList*/
{
FILE *f = mustOpen(outFile, "w");
struct fullExperiment *exp;
for (exp = expList; exp != NULL; exp = exp->next)
{
long long pooledPeakId = pooledBroadPeaksForExp(exp);
if (pooledPeakId > 0)
{
struct slRef *ref, *refList = NULL;
eapGraphAncestorsOfFormat(eg, pooledPeakId, "fastq", -1, &refList);
for (ref = refList; ref != NULL; ref = ref->next)
{
struct eapInput *in = ref->val;
struct edwFile *file = edwFileFromId(conn, in->fileId);
fprintf(f, "%s\t%s\t%s\n", file->edwFileName, exp->name, exp->exp->biosample);
edwFileFree(&file);
}
slFreeList(&refList);
}
}
carefulClose(&f);
}
void edwCorrectFileTags(char *tabFileName)
/* edwCorrectFileTags - Use this to correct tags in the edwFile table and corresponding fields
* in the edwValidFile table without forcing a validateManifest rerun or a reupload.. */
{
struct sqlConnection *conn = edwConnectReadWrite();
char *requiredFields[] = {"accession",};
char *forbiddenFields[] = {"md5_sum", "size", "valid_key", "file_name"};
struct fieldedTable *table = fieldedTableFromTabFile(tabFileName, tabFileName,
requiredFields, ArraySize(requiredFields));
checkForbiddenFields(table, forbiddenFields, ArraySize(forbiddenFields));
int accessionIx = stringArrayIx("accession", table->fields, table->fieldCount);
struct fieldedRow *fr;
for (fr = table->rowList; fr != NULL; fr = fr->next)
{
char *acc = fr->row[accessionIx];
long long id = edwNeedFileIdForLicensePlate(conn, acc);
struct edwFile *ef = edwFileFromId(conn, id);
int i;
char *tags = ef->tags;
for (i=0; i<table->fieldCount; ++i)
{
if (i != accessionIx)
tags = cgiStringNewValForVar(tags, table->fields[i], fr->row[i]);
}
edwFileResetTags(conn, ef, tags);
edwFileFree(&ef);
}
}
struct edwFile *edwFileFromIdOrDie(struct sqlConnection *conn, long long fileId)
/* Return edwValidFile given fileId - aborts if not found. */
{
struct edwFile *ef = edwFileFromId(conn, fileId);
if (ef == NULL)
errAbort("Couldn't find file for id %lld\n", fileId);
return ef;
}
void changeFormat(struct sqlConnection *conn, struct edwValidFile *vf, char *format)
/* Set up vf to change format. */
{
struct edwFile *ef = edwFileFromId(conn, vf->fileId);
char *newTags = cgiStringNewValForVar(ef->tags, tagToChange, format);
edwFileResetTags(conn, ef, newTags);
edwFileFree(&ef);
}
struct edwFile *getFilesFromIds(struct sqlConnection *conn, uint ids[], int idCount)
/* Get a list of files specified in an array of ids. */
{
struct edwFile *list = NULL, *el;
int i;
for (i=0; i<idCount; ++i)
{
el = edwFileFromId(conn, ids[i]);
slAddHead(&list, el);
}
slReverse(&list);
return list;
}
static int handleOldFileTags(struct sqlConnection *conn, struct submitFileRow *sfrList,
boolean update)
/* Check metadata on files mentioned in manifest that by MD5 sum we already have in
* warehouse. We may want to update metadata on these. This returns the number
* of files with tags updated. */
{
struct submitFileRow *sfr;
int updateCount = 0;
for (sfr = sfrList; sfr != NULL; sfr = sfr->next)
{
struct edwFile *newFile = sfr->file;
struct edwFile *oldFile = edwFileFromId(conn, sfr->md5MatchFileId);
verbose(2, "looking at old file %s (%s)\n", oldFile->submitFileName, newFile->submitFileName);
struct cgiDictionary *newTags = cgiDictionaryFromEncodedString(newFile->tags);
struct cgiDictionary *oldTags = cgiDictionaryFromEncodedString(oldFile->tags);
boolean updateName = !sameString(oldFile->submitFileName, newFile->submitFileName);
boolean updateTags = !cgiDictionarySame(oldTags, newTags);
if (updateName)
{
if (!update)
errAbort("%s already uploaded with name %s. Please use the 'update' option if you "
"want to give it a new name.",
newFile->submitFileName, oldFile->submitFileName);
updateSubmitName(conn, oldFile->id, newFile->submitFileName);
}
if (updateTags)
{
if (!update)
{
char *name="", *oldVal="", *newVal="";
cgiDictionaryFirstDiff(oldTags, newTags, &name, &oldVal, &newVal);
errAbort("%s is duplicate of %s in warehouse, but %s column went from %s to %s.\n"
"Please use the 'update' option if you are meaning to update the information\n"
"associated with this file and try again if this is intentional.",
newFile->submitFileName, oldFile->edwFileName,
name, oldVal, newVal);
}
edwFileResetTags(conn, oldFile, newFile->tags, TRUE);
}
if (updateTags || updateName)
++updateCount;
cgiDictionaryFree(&oldTags);
cgiDictionaryFree(&newTags);
}
return updateCount;
}
