/* vgLoadGensat - Parse gensat XML file and turn it into VisiGene load files. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "options.h"
#include "portable.h"
#include "xp.h"
#include "xap.h"
#include "../lib/gs.h"


void usage()
/* Explain usage and exit. */
{
errAbort(
  "vgLoadGensat - Parse gensat XML file and turn it into VisiGene load files\n"
  "usage:\n"
  "   vgLoadGensat gensat.xml outDir\n"
  "options:\n"
  "   -xxx=XXX\n"
  );
}

static struct optionSpec options[] = {
   {NULL, 0},
};

char *levelAsNumber(char *level)
/* Return ascii version of floating point number between
 * 0 and 1, or NULL, depending on level string. */
{
if (sameString(level, "undetectable"))
    return "0";
else if (sameString(level, "weak"))
    return "0.5";
else if (sameString(level, "strong"))
    return "1.0";
else
    return NULL;
}

char *blankOutNotDone(char *s)
/* Return s, unless it's "not-done", in which
 * case return "". */
{
if (sameString(s, "not-done"))
    s = "";
return s;
}

void makeTabFile(char *gensatXml, char *tabFile, char *commentFile)
/* Parse XML file and turn it into tab-separated file. */
{
struct xap *xap = xapOpen(gensatXml, gsStartHandler, gsEndHandler);
struct gsGensatImage *image;
struct hash *tabFileHash = hashNew(0);
FILE *fComment = mustOpen(commentFile, "w");
FILE *f = mustOpen(tabFile, "w");
int i=0;
char *headDir = "Institutions/";
int headDirLen = strlen(headDir);
struct dyString *imageFileName = dyStringNew(0);

fprintf(f, "#");
fprintf(f, "submitId\t");
fprintf(f, "captionId\t");
fprintf(f, "gene\t");
fprintf(f, "locusLink\t");
fprintf(f, "genbank\t");
fprintf(f, "bac\t");
fprintf(f, "sex\t");
fprintf(f, "age\t");
fprintf(f, "sliceType\t");
fprintf(f, "bodyPart\t");
fprintf(f, "probeColor\t");
fprintf(f, "imageWidth\t");
fprintf(f, "imageHeight\t");
fprintf(f, "fileName\n");

while ((image = xapNext(xap, "GensatImage")) != NULL)
    {
    /* Fish fields we want out of image and info. */
    struct gsGensatImageImageInfo *info = image->gsGensatImageImageInfo;	/** Single instance required. **/
    struct gsGensatImageInfo *fileInfo = info->gsGensatImageImageInfoFullImg->gsGensatImageInfo;	/** Single instance required. **/
    struct gsGensatImageAnnotations *annotations;
    char *fileName = fileInfo->gsGensatImageInfoFilename->text;	/** Single instance required. **/
    int width = fileInfo->gsGensatImageInfoWidth->text;
    int height = fileInfo->gsGensatImageInfoHeight->text;
    int id = image->gsGensatImageId->text;	/** Single instance required. **/
    char *symbol = "";
    char *name = "";
    int locusLinkId = 0;
    char *acc = "";
    char *rawAge = NULL;
    double age = 0;
    char *sex = "";
    char *bac = "";
    int daysToBirth = 19;
    int daysToAdult = 61;
    int averageAdult = 100;
    char *bodyPart = "";
    char *comment = NULL;
    char *probeColor = NULL;
    struct gsGensatImageImageTechnique *gsGensatImageImageTechnique;	/** Single instance required. **/

    struct gsGensatImageSeqInfo *gsGensatImageSeqInfo;	/** Single instance required. **/
    char *sliceType = image->gsGensatImageSectionPlane->value;	/** Single instance required. **/
    char *level = image->gsGensatImageSectionLevel->text;	/** Single instance required. **/
    char *technique = image->gsGensatImageImageTechnique->value;	/** Single instance required. **/

    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneSymbol != NULL)
	symbol = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneSymbol->text;	
    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneName != NULL)
	name = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneName->text;	
    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneId != NULL)
	locusLinkId = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneId->text;	
    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoBacAddress != NULL)
        bac = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoBacAddress->text;
    if (image->gsGensatImageSeqInfo->gsGensatSequenceInfo->gsGensatSequenceInfoAccession != NULL)
	acc = image->gsGensatImageSeqInfo->gsGensatSequenceInfo->gsGensatSequenceInfoAccession->text;	
    if (image->gsGensatImageAge != NULL)
        rawAge = image->gsGensatImageAge->value;
    if (image->gsGensatImageSex != NULL)
        sex = image->gsGensatImageSex->value;
    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneSymbol != NULL)
	symbol = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoGeneSymbol->text;	
    if (image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoBacComment != NULL)
	comment = image->gsGensatImageGeneInfo->gsGensatGeneInfo->gsGensatGeneInfoBacComment->text;	

    /* Fix sex field. */
    tolowers(sex);
    if (sameString(sex, "unknown"))
        sex = "";

    /* Figure out age field. */
    if (sameString(rawAge, "adult"))
        age = averageAdult;
    else 
	{
	if (!isdigit(rawAge[1]))
	    errAbort("Don't understand age %s", rawAge);
	if (rawAge[0] == 'p')
	    age = daysToBirth + atof(rawAge+1);
	else if (rawAge[0] == 'e')
	    age = atof(rawAge+1);
	else
	    errAbort("Don't understand age %s", rawAge);
	}

    /* Process fileName to get rid of leading directory, and to reflect
     * conversion to jpeg, and to fix a couple of little glitches in
     * input data, and with Image Magick convert utility in tile mode. */
    if (!startsWith(headDir, fileName))
        errAbort("Expecting %s to begin with %s", fileName, headDir);
    fileName += headDirLen;
    chopSuffix(fileName);
    dyStringClear(imageFileName);
    dyStringAppend(imageFileName, fileName);
    dyStringAppend(imageFileName, ".jpg");
    fileName = imageFileName->string;
    subChar(fileName, '(', '_');
    stripChar(fileName, ')');
    stripString(fileName, ".full"); /* Image magick can't handle two suffixes */

    /* Figure out body part.  It'll be whole, head, or brain depending how old it is.
     * However sometimes the level field has something meaningful to say.  (Usually
     * it's just a number. */
    if (age < 12)
        bodyPart = "whole";
    else if (age < 16)
        bodyPart = "head";
    else
        bodyPart = "brain";
    if (strlen(level) > 1 && !isdigit(level[0]) && !sameString("other", level))
        bodyPart = level;

    /* Figure out probe color by looking at technique. */
    if (sameString(technique, "bac-brightfield"))
        probeColor = "dark red";
    else if (sameString(technique, "bac-confocal"))
        probeColor = "green";
    else if (sameString(technique, "ish-darkfield"))
        probeColor = "white";
    else
        errAbort("Unrecognized technique %s", technique);
        

    /* Print out fields */
    fprintf(f, "%d\t", id);
    if (comment != NULL)
        fprintf(f, "%d\t", id);
    else
        fprintf(f, "\t");
    fprintf(f, "%s\t", symbol);
    fprintf(f, "%d\t", locusLinkId);
    fprintf(f, "%s\t", acc);
    fprintf(f, "%s\t", bac);
    fprintf(f, "%s\t", sex);
    if (rawAge != NULL)
	fprintf(f, "%f\t", age);
    else
        fprintf(f, "\t");
    fprintf(f, "%s\t", sliceType);
    fprintf(f, "%s\t", bodyPart);
    fprintf(f, "%s\t", probeColor);
    fprintf(f, "%d\t", width);
    fprintf(f, "%d\t", height);
    fprintf(f, "%s\n", fileName);

    /* Print out expression info if any. */
    if ((annotations = image->gsGensatImageAnnotations) != NULL)
        {
	struct gsGensatAnnotation *ann ;
	for (ann = annotations->gsGensatAnnotation; ann != NULL; ann = ann->next)
	    {
	    char *level = ann->gsGensatAnnotationExpressionLevel->value;
	    char *pattern = ann->gsGensatAnnotationExpressionPattern->value;
	    char *region = "";
	    char *cellType = "";
	    char *cellSubtype = "";
	    if (ann->gsGensatAnnotationRegion != NULL)
	        region = ann->gsGensatAnnotationRegion->text;
	    if (ann->gsGensatAnnotationCellType != NULL)
	        cellType = ann->gsGensatAnnotationCellType->text;
	    if (ann->gsGensatAnnotationCellSubtype != NULL)
	        cellSubtype = ann->gsGensatAnnotationCellSubtype->text;
	    level = levelAsNumber(level);
	    cellType = blankOutNotDone(cellType);
	    cellSubtype = blankOutNotDone(cellSubtype);
	    pattern = blankOutNotDone(pattern);
	    if (level != NULL)
		fprintf(f, "\texpression\t%s\t%s\t%s\t%s\t%s\n", 
		    region, level, cellType, cellSubtype, pattern);
	    }
	}

    /* Print out comment if any. */
    if (comment != NULL)
        {
	subChar(comment, '\t', ' ');
	subChar(comment, '\n', ' ');
	fprintf(fComment, "%d\t%s\n", id, comment);
	}

    gsGensatImageFree(&image);
    }
xapFree(&xap);
carefulClose(&f);
carefulClose(&fComment);
}

void makeRaFile(char *fileName)
/* Make up ra file - that describes whole gensat set. */
{
FILE *f = mustOpen(fileName, "w");

fprintf(f, "submitSet gensat1\n");
fprintf(f, "fullDir ../visiGene/full/inSitu/Mouse/gensat\n");
fprintf(f, "thumbDir ../visiGene/200/inSitu/Mouse/gensat\n");
fprintf(f, "priority 2000\n");
fprintf(f, "submissionSource GENSAT\n");
fprintf(f, "acknowledgement Thanks to Michael Dicuccio at NCBI for helping "
	   "load these images into VisiGene.\n");
fprintf(f, "contributor Heintz N., Curran T., Hatten M., Magdaleno S., Jensen P., Gong S., Mehta S., Wang C., Concepcion A., Kowalic E., Losos K., Feng H., Thompson T., Ford B., Baker S., Doughty M., Dinzey J., Dyer A., Grevstad C., Hinkle A., Kizima L., Madden C., Pariser E., Zheng C., Kus L., Milosevic A., Didkovsky N., Nowak N., Joyner A., Lehman K., Cheung T., Asbury A., Eden C., Batten D.,\n");
fprintf(f, "publication A gene expression atlas of the central nervous system based on bacterial artificial chromosomes\n");
fprintf(f, "pubUrl http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14586460\n");
fprintf(f, "journal Nature\n");
fprintf(f, "journalUrl http://www.nature.com\n");
fprintf(f, "year 2003\n");
fprintf(f, "setUrl http://www.ncbi.nlm.nih.gov/projects/gensat/\n");
fprintf(f, "itemUrl http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gensat&term=%%s\n");
fprintf(f, "taxon 10090\n");


carefulClose(&f);
}


void vgLoadGensat(char *gensatXml, char *outDir)
/* vgLoadGensat - Parse gensat XML file and turn it into VisiGene load files. */
{
char tabFile[PATH_LEN], raFile[PATH_LEN], commentFile[PATH_LEN];

makeDir(outDir);
safef(tabFile, sizeof(tabFile), "%s/gensat.tab", outDir);
safef(raFile, sizeof(raFile), "%s/gensat.ra", outDir);
safef(commentFile, sizeof(commentFile), "%s/gensat.txt", outDir);
makeRaFile(raFile);
makeTabFile(gensatXml, tabFile, commentFile);
}

int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 3)
    usage();
vgLoadGensat(argv[1], argv[2]);
return 0;
}