void fullCaption(struct sqlConnection *conn, int id)
/* Print information about image. */
{
char *publication, *copyright;
char *caption = NULL;
int imageFile = -1;
struct slInt *imageList;
int imageCount=0;
int oldId = 0;
struct captionElement *captionElements;
int forwardedId = vgForwardedImage(conn, id);
if (forwardedId)
{
oldId = id;
id = forwardedId;
}
caption = visiGeneCaption(conn, id);
imageFile = visiGeneImageFile(conn, id);
showSource(conn, oldId);
showSource(conn, id);
publication = visiGenePublication(conn,id);
if (publication != NULL)
{
char *pubUrl = visiGenePubUrl(conn,id);
printf("<B>Reference:</B> ");
if (pubUrl != NULL && pubUrl[0] != 0)
printf("<A HREF=\"%s\" target=_blank>%s</A>", pubUrl, publication);
else
{
printf("%s", naForEmpty(publication));
}
printf("<BR>\n");
}
printf("<B>Year:</B> %d ", visiGeneYear(conn,id));
printf("<B>Contributors:</B> %s<BR>\n",
naForNull(visiGeneContributors(conn,id)));
if (caption != NULL)
{
printf("<B>Notes:</B> %s<BR>\n", caption);
freez(&caption);
}
imageList = visiGeneImagesForFile(conn, imageFile);
imageCount = slCount(imageList);
captionElements = makePaneCaptionElements(conn, imageList);
printCaptionElements(conn, captionElements, imageList);
copyright = visiGeneCopyright(conn, id);
if (copyright != NULL)
printf("<B>Copyright:</B> %s<BR>\n", copyright);
showAcknowledgement(conn, oldId);
showAcknowledgement(conn, id);
printf("<BR>\n");
}
void cdwFakeManifestFromSubmit(char *submitIdString, char *outDir)
/* cdwFakeManifestFromSubmit - Create a fake submission based on a real one that is in the warehouse. */
{
struct sqlConnection *conn = cdwConnect();
char query[512];
sqlSafef(query, sizeof(query), "select * from cdwSubmit where id=%s", submitIdString);
struct cdwSubmit *submit = cdwSubmitLoadByQuery(conn, query);
if (submit == NULL)
errAbort("Can't find submission %s", submitIdString);
uglyf("%d files in query\n", submit->newFiles);
sqlSafef(query, sizeof(query), "select * from cdwFile where submitId=%s", submitIdString);
struct cdwFile *ef, *efList = cdwFileLoadByQuery(conn, query);
FILE *maniF = NULL, *valiF = NULL;
for (ef = efList; ef != NULL; ef = ef->next)
{
struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
if (vf != NULL)
{
/* First time through create out directory and open output files. */
if (maniF == NULL)
{
char *fakeVersion = "##validateManifest version 1.7";
makeDirsOnPath(outDir);
setCurrentDir(outDir);
maniF = mustOpen("manifest.txt", "w");
printSharedHeader(maniF);
fprintf(maniF, "\n");
fprintf(maniF, "%s\n", fakeVersion);
valiF = mustOpen("validated.txt", "w");
printSharedHeader(valiF);
fprintf(valiF, "\tmd5_sum\tsize\tmodified\tvalid_key\n");
fprintf(valiF, "%s\n", fakeVersion);
}
/* Figure out file names */
char cdwPath[PATH_LEN], rootName[FILENAME_LEN], ext[FILEEXT_LEN];
safef(cdwPath, sizeof(cdwPath), "%s%s", cdwRootDir, ef->cdwFileName);
splitPath(ef->cdwFileName, NULL, rootName, ext);
char localPath[PATH_LEN];
safef(localPath, sizeof(localPath), "%s%s", rootName, ext);
/* Create sym-linked file and write to manifest */
symlink(cdwPath, localPath);
fprint2(maniF, valiF, "%s", localPath);
/* Write other columns shared between manifest and validated */
fprint2(maniF, valiF, "\t%s", vf->format);
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->outputType));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->experiment));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->enrichedIn));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->ucscDb));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->replicate));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->part));
fprint2(maniF, valiF, "\t%s", naForEmpty(vf->pairedEnd));
fprintf(maniF, "\n");
/* Print out remaining fields in validated.txt */
fprintf(valiF, "\t%s\t%lld\t%lld\n", ef->md5, ef->size, ef->updateTime);
}
}
carefulClose(&maniF);
carefulClose(&valiF);
}
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;
}
