#!/usr/bin/env python2.7

import sys, os, shutil, stat, argparse, datetime, hashlib

from ucscGb.gbData.ra.raFile import RaFile
from ucscGb.externalData.geo import submission
from ucscGb.externalData.geo import soft
from ucscGb.encode import encodeUtils
from ucscGb.encode.cv import CvFile
from ucscGb.encode.track import CompositeTrack, TrackFile


'''
mkGeoPkg - create a soft file and upload script for a given track, so that it
may be sumbitted to GEO.

To invoke the script, you must pass the composite and track name:
    mkGeoPkg hg19 wgEncodeSomeTrack
    
This is typically not enough however; most tracks are not completely covered
by their metadata, and it is necessary to supply additional information. The
most commonly needed information is:
    !Series_summary - this is taken from the track's html page description. 
        In most cases it can be copied, one paragraph per line.
    !Series_overall_design - this is taken from the Methods section on the
        track's page. As with summary, 1 paragraph per line.
    !Series_contributor - this is taken from the contributors list on the 
        track's page. It has a special format: "Last,First" where each person
        is listed on a separate line.
    !Sample_instrument_model - this is a bit more difficult, as it technically
        supposed to be a per-sample field. Occasionally this appears in the
        metaDb for newer tracks, if so, it's automatically added in. Otherwise
        it must be either specified on a whole-series basis, or added to the
        metadata. In many cases, we don't actually know all of them. This is
        okay. GEO will allow us to submit whatever information we do have, and
        they can take care of the rest. The instrumentModels dictionary below
        gives a list of the allowable entered values (the keys). The values
        map to the "human readable" version used by GEO.
        
You can supply all of the above information in an additional file and specify
it using the r (replace) option:
    mkGeoPkg -r somefile hg19 wgEncodeSomeTrack
    
The replace file must be organized with each of the above key value pairs as
in a soft file:
    !Series_summary = some summary stuff ...
    !Series_summary = another paragraph of summary ...
    !Series_overall_design = ...
    !Series_contributor = Researcher,Some
    !Series_contributor = Researcher,Another
    !Sample_instrument_model = Illumina_GA2
    
There is a template for this, named replaceTemplate in the directory.

You may need to only submit a part of the track, in this case you can specify
experiment ID numbers to include:

One problem you may run into while running the script is that the DataType is
not valid. This means that the huge dictionary called datatypes below isn't
filled in for that entry. If you can get ahold of the information, modify the
script and push the changes back out.

You may also get an error when trying to submit MicroArray data. This is to be
expected: MicroArray is currently not functional at all. We have no way as of
current to map our data to the format expected by GEO, so we've punted on this
issue for the time being.

Once you've successfully run the script, you'll have generated a soft file and
a script that will handle the uploading process. All of this will be put into
a directory named 'database_wgEncodeSomeTrack_year-month-day'. To begin the
upload, simply cd into the directoy and run upload.sh. This will start the
aspera copy program, copying files, a files list, and the soft file itself.

For each submission, you need to email GEO. Our current contact is:
    Steve Wilhite, wilhite@ncbi.nlm.nih.gov
    
You must specify which track you're submitting. GEO will only allow us 1TB of
space dedicated to ENCODE, so you must break down submissions larger than 1TB
and only submit as many submissions as they have room to process at any given
time. In a few days, GEO will get back to you with a list of accession numbers
which need to be put back into our metadata (see encodeAddGeoAccessions).
'''

cvDetails = {
    'cell':    [ 'organism', 'description', 'karyotype', 'lineage', 'sex' ],
    'antibody': [ 'antibodyDescription', 'targetDescription', 'vendorName', 'vendorId' ]
}

#if the term appears in the mdb and must overriding the value in the cv
cvOverride = [ 'sex' ]

#talk to Venkat lol
cvPretend = { 'antibody Input': 'control' }

#if its not in cvDetails, which things should we check by default
cvDefaults = [ 'description' ]

mdbWhitelist = [
    'age',
    'bioRep',
    'control',
    'controlId',
    'fragSize',
    'labExpId',
    'labVersion',
    'mapAlgorithm',
    'obtainedBy',
    'phase',
    'readType',
    'region',
    'replicate',
    'restrictionEnzyme',
    'run',
    'softwareVersion',
    'spikeInPool',
    'strain'
]
    
def isRawFile(file):
    return (file.extension == 'fastq' or file.extension == 'csfasta' or file.extension == 'csqual')
    
def isSupplimentaryFile(file):
    return (not isRawFile(file)) and file.extension != 'fasta' and file.extension != 'bam' and file.extension != 'bai'
    
def sampleTitle(stanza, expVars, warn=False):
    concat = stanza[expVars[0]].replace('-m', '')
    for expVar in expVars[1:len(expVars)]:
        if expVar in stanza and stanza[expVar] != 'None':
            concat += '_' + stanza[expVar]
        elif warn:
            print 'warning: %s is None or not in %s' % (expVar, stanza.name)
    return concat
    
def linkName(file, track):
    return '%s_%s' % (track.database, file.name)
    
def createMappings(metadb):
    expIds = dict()
    geoMapping = dict()
    expVars = None
    series = None
    datatype = None
    
    for stanza in metadb.itervalues():
        
        if 'objType' in stanza and stanza['objType'] == 'composite':
            series = stanza
            expVars = stanza['expVars'].split(',')
            continue

        if 'expId' not in stanza:
            print stanza.name + ': no expId'
            continue

        if 'objStatus' in stanza:
            print stanza.name + ': skipping because ' + stanza['objStatus']
            continue
            
        if 'geoSampleAccession' not in stanza:
            # if this hasn't been submitted to GEO yet, we'll add it to the submission list
            if stanza['expId'] not in expIds:
                expIds[stanza['expId']] = list()
                
            expIds[stanza['expId']].append(stanza)
        
        else:
            # otherwise we keep track of the geo number for partially submitted samples
            if stanza['expId'] not in geoMapping:
                geoMapping[stanza['expId']] = stanza['geoSampleAccession']
            elif geoMapping[stanza['expId']] != 'Inconsistent' and geoMapping[stanza['expId']] != stanza['geoSampleAccession']:
                geoMapping[stanza['expId']] = 'Inconsistent'
                print stanza.name + ': inconsistent geo mapping'
        
        if datatype == None and 'dataType' in stanza:
            datatype = stanza['dataType']
        elif datatype != None and 'dataType' in stanza and datatype != stanza['dataType']:
            raise KeyError(stanza.name + ': inconsistent data type') 

    try:
        dt = datatype
        datatype = encodeUtils.dataTypes[dt]
        datatype.name = dt
    except KeyError:
        raise KeyError(datatype)
    
    return expIds, expVars, geoMapping, series, datatype
    
    
def createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit, argseries):
    
    if 'geoSeriesAccession' in series:
        print 'Existing series ' + series['composite'] + ' using geoSeriesAccession ' + series['geoSeriesAccession']
        return
        
    print 'Writing series ' + series['composite']
    
    seriesStanza = soft.SeriesStanza()
    seriesStanza['^SERIES'] = series['composite']
    seriesStanza['!Series_title'] = compositeTrack.trackDb[compositeTrack.name]['longLabel'] #STILL INCORRECT
    
    if '!Series_summary' in replace:
        seriesStanza['!Series_summary'] = replace['!Series_summary']
    else:
        print 'warning: no series summary found. Please include in replace file.'
        seriesStanza['!Series_summary'] = '[REPLACE]'
        if audit:
            print seriesStanza.name + ': no summary'
        
    if '!Series_overall_design' in replace:
        seriesStanza['!Series_overall_design'] = replace['!Series_overall_design']
    else:
        print 'no series overall design found. Please include in replace file.'
        seriesStanza['!Series_overall_design'] = '[REPLACE]'
        if audit:
            print seriesStanza.name + ': no overall design'
            
    seriesStanza['!Series_web_link'] = [ compositeTrack.url, 'http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html' ]
    
    if '!Series_contributor' in replace:
        seriesStanza['!Series_contributor'] = replace['!Series_contributor']
    else:
        seriesStanza['!Series_contributor'] = '[REPLACE]'
        if audit:
            print seriesStanza.name + ': no contributor'
        
    seriesStanza['!Series_gp_id'] = encodeUtils.gpIds[compositeTrack.organism + ' ' + datatype.source]
    
    # could use !Series_variable_* and !Series_repeats_*
    
    if not argseries:
        seriesStanza['!Series_sample_id'] = list()
        
        for idNum in expIds.iterkeys():
            if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent':
                seriesStanza['!Series_sample_id'].append(geoMapping[idNum])
            else:
                seriesStanza['!Series_sample_id'].append(sampleTitle(expIds[idNum][0], expVars))
        
    softfile[series['composite']] = seriesStanza
    
def createHighThroughputSoftFile(compositeTrack, cv, expIds, expVars, geoMapping, series, datatype, replace, audit, tarpath, argseries):
    
    print 'Creating HighThroughput soft file'

    softfile = soft.HighThroughputSoftFile()
    fileList = list()
    
    createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit, argseries)
    
    if argseries:
        return softfile, fileList
    
    for idNum in expIds.iterkeys():
        
        expId = expIds[idNum]
        firstStanza = expId[0]
        print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
        sample = soft.HighThroughputSampleStanza()

        sample['^SAMPLE'] = sampleTitle(firstStanza, expVars, 1)
        sample['!Sample_type'] = 'SRA'
        sample['!Sample_title'] = sample['^SAMPLE']
        
        if 'geoSeriesAccession' in series:
            sample['!Sample_series_id'] = series['geoSeriesAccession']
            
        count = 1
        
        #figure out if the instrument model is consistent across the entire sample
        instrumentModel = None
        for stanza in expId:    
            if 'seqPlatform' in stanza:
                if instrumentModel == None:
                    instrumentModel = submission.instrumentModels[stanza['seqPlatform']]
                else:
                    if instrumentModel != submission.instrumentModels[stanza['seqPlatform']]:
                        instrumentModel = None
                        if audit:
                            print 'expId' + str(expId) + ': inconsistent instrument model'
                        break
        
        for stanza in expId:
        
            for fname in stanza['fileName'].split(','):
              
                file = compositeTrack.files[fname]
                filelist = list()
                
                if file.extension == 'fasta':
                    print 'WARNING: fastas detected!!!'
                
                if isRawFile(file):
                
                    if file.name.endswith('.tgz') or file.name.endswith('.tar.gz'):
                    
                        if tarpath == None:
                            raise IOError('this track contains tarred fastqs. Please specify a path through the -z option')
                        dirname = tarpath + file.name.split('.')[0] + '/'
                        if os.path.exists(dirname):
                            print dirname + ' already exists, so not unzipping'
                        else:
                            os.mkdir(dirname)
                            os.system('tar -xf %s -C %s' % (file.path + file.name, dirname))
                        
                            for root, dirnames, filenames in os.walk(dirname):
                                for filename in filenames:
                                    if filename.endswith('.fastq') or filename.endswith('.txt'):
                                        os.system('gzip %s' % (root + '/' + filename))
                        
                        for root, dirnames, filenames in os.walk(dirname):
                            for filename in filenames:
                                print root + '/' + filename
                                filelist.append(TrackFile(root + '/' + filename))

                    else:
                        filelist.append(file)
                        
                    for f in filelist:
                        
                        sample['!Sample_raw_file_' + str(count)] = linkName(f, compositeTrack)
                        if f.extension == 'txt':
                            sample['!Sample_raw_file_type_' + str(count)] = 'fastq'
                        elif f.extension == 'csfasta':
                            sample['!Sample_raw_file_type_' + str(count)] = 'SOLiD_native_csfasta'
                        elif f.extension == 'csqual':
                            sample['!Sample_raw_file_type_' + str(count)] = 'SOLiD_native_qual'
                        else:
                            sample['!Sample_raw_file_type_' + str(count)] = f.extension
                        
                        sample['!Sample_raw_file_checksum_' + str(count)] = f.md5sum

                        if instrumentModel == None and 'seqPlatform' in stanza:
                            sample['!Sample_raw_file_instrument_model_' + str(count)] = submission.instrumentModels[stanza['seqPlatform']]
                            
                        fileList.append(f)    
                        count = count + 1
            
        count = 1
            
        for stanza in expId:
        
            for fname in stanza['fileName'].split(','):
                file = compositeTrack.files[fname]
        
                if isSupplimentaryFile(file):
                    sample['!Sample_supplementary_file_' + str(count)] = linkName(file, compositeTrack)
                    
                    if file.md5sum != None:
                        sample['!Sample_supplementary_file_checksum_' + str(count)] = file.md5sum
                    
                    sample['!Sample_supplementary_file_build_' + str(count)] = compositeTrack.database
                    
                    if instrumentModel == None and 'seqPlatform' in stanza:
                        sample['!Sample_supplementary_file_instrument_model_' + str(count)] = submission.instrumentModels[stanza['seqPlatform']]
                    
                    fileList.append(file)
                    count = count + 1
            
        sample['!Sample_source_name'] = firstStanza['cell']
        sample['!Sample_organism'] = compositeTrack.organism
        
        sample['!Sample_characteristics'] = list()
        allVars = expVars + mdbWhitelist
        
        for var in allVars:
            if var in firstStanza:
                foobar = var
                sample['!Sample_characteristics'].append(var + ': ' + firstStanza[var])
                for pretend in cvPretend.iterkeys():
                    if var + ' ' + firstStanza[var] == pretend:
                        foobar = cvPretend[pretend]
                if foobar in cvDetails:
                    for cvVar in cvDetails[foobar]:
                        if cvVar in cvOverride and cvVar in firstStanza:
                            sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + firstStanza[cvVar])
                        elif cvVar in cv[firstStanza[var]]:
                            sample['!Sample_characteristics'].append(var + ' ' + cvVar + ': ' + cv[firstStanza[var]][cvVar])
                else:
                    for cvVar in cvDefaults:
                        if firstStanza[var] in cv and cvVar in cv[firstStanza[var]]:
                            sample['!Sample_characteristics'].append(var + ' ' +  cvVar + ': ' + cv[firstStanza[var]][cvVar])
                
        sample['!Sample_biomaterial_provider'] = cv[firstStanza['cell']]['vendorName']
        
        if 'treatment' in firstStanza:
            sample['!Sample_treatment_protocol'] = firstStanza['treatment']
        
        if 'protocol' in cv[firstStanza['cell']]:
            for protocol in cv[firstStanza['cell']]['protocol'].split(' '):
                    key, val = protocol.split(':')
                    if key == 'ENCODE' or key == cv[firstStanza['lab']]['labPi']:
                        sample['!Sample_growth_protocol'] = val
        
        if datatype.molecule == 'RNA':
            if firstStanza['rnaExtract'] in submission.rnaExtractMapping:
                sample['!Sample_molecule'] = submission.rnaExtractMapping[firstStanza['rnaExtract']]
            elif firstStanza['localization'] in submission.localizationMapping:
                sample['!Sample_molecule'] = submission.localizationMapping[firstStanza['localization']]
                
        else:
            sample['!Sample_molecule'] = datatype.molecule
            
        if '!Sample_instrument_model' in replace and replace['!Sample_instrument_model'][0] == 'Unknown':
            sample['!Sample_extract_protocol'] = 'Instrument model unknown. ("%s" specified by default). For more information, see %s' % (submission.instrumentModels[replace['!Sample_instrument_model'][0]], compositeTrack.url)
        else:
            sample['!Sample_extract_protocol'] = compositeTrack.url
        sample['!Sample_library_strategy'] = datatype.strategy
        sample['!Sample_library_source'] = datatype.source
        sample['!Sample_library_selection'] = datatype.selection
        
        # if the instrumentModel is consistent, just use that
        # otherwise take the first seqPlatform value from metadata
        # if that still fails, check the replacement file
        # finally just make it say [REPLACE]
        if instrumentModel != None:
            sample['!Sample_instrument_model'] = instrumentModel
        else:
            for stanza in expId:    
                if 'seqPlatform' in stanza:
                    sample['!Sample_instrument_model'] = submission.instrumentModels[stanza['seqPlatform']]
                    break
            if '!Sample_instrument_model' not in sample:
                if '!Sample_instrument_model' in replace:
                    sample['!Sample_instrument_model'] = submission.instrumentModels[replace['!Sample_instrument_model'][0]]
            if '!Sample_instrument_model' not in sample:
                sample['!Sample_instrument_model'] = '[REPLACE]'
                if audit:
                    print stanza.name + ': no instrument'
                
        sample['!Sample_data_processing'] = compositeTrack.url

        if idNum in geoMapping and geoMapping[idNum] != 'Inconsistent':
            sample['!Sample_geo_accession'] = geoMapping[idNum]
        
        softfile[firstStanza['metaObject']] = sample
        
    return softfile, fileList
        
        
def createMicroArraySoftFile(compositeTrack, cv, expIds, expVars, geoMapping, series, datatype, replace, audit):
    
    #raise KeyError('microarray')
    
    print 'Creating MicroArray soft file'

    softfile = soft.MicroArraySoftFile()
    fileList = list()
    
    createSeries(softfile, compositeTrack, expIds, expVars, geoMapping, series, datatype, replace, audit)
    
    for idNum in expIds.iterkeys():
        
        expId = expIds[idNum]
        firstStanza = expId[0]
        print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
        sample = soft.MicroArraySampleStanza()
            
        sample['^SAMPLE'] = sampleTitle(firstStanza, expVars, 1)
        
        if 'geoSeriesAccession' in series:
            sample['!Sample_series_id'] = series['geoSeriesAccession']    
            
        #sample['!Sample_title'] = concat
        
        count = 1
            
        count = 1
            
        for stanza in expId:
        
            for fname in stanza['fileName'].split(','):
                file = compositeTrack.files[fname]
        
                if isSupplimentaryFile(file):
                    sample['!Sample_supplementary_file_' + str(count)] = linkName(file, compositeTrack)
                    
                    if file.md5sum != None:
                        sample['!Sample_supplementary_file_checksum_' + str(count)] = file.md5sum
                    
                    sample['!Sample_supplementary_file_build_' + str(count)] = compositeTrack.database
                
                    fileList.append(file)
                    count = count + 1

        # sample['!Sample_table'] = KeyOptional # CEL file
        # sample['!Sample_source_name_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_organism_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_characteristics_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_biomaterial_provider_ch'] = KeyZeroPlusNumbered
        # sample['!Sample_treatment_protocol_ch'] = KeyZeroPlusNumbered
        # sample['!Sample_growth_protocol_ch'] = KeyZeroPlusNumbered
        # sample['!Sample_molecule_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_extract_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_label_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_label_protocol_ch_1'] = '[REPLACE]' #KeyOnePlusNumbered
        # sample['!Sample_hyb_protocol'] = '[REPLACE]' #KeyOnePlus
        # sample['!Sample_scan_protocol'] = '[REPLACE]' #KeyOnePlus
        # sample['!Sample_data_processing'] = '[REPLACE]' #KeyOnePlus
        # sample['!Sample_description'] = '[REPLACE]' #KeyZeroPlus
        # sample['!Sample_platform_id'] = '[REPLACE]'
        # sample['!Sample_geo_accession'] = KeyOptional
        # sample['!Sample_anchor'] = KeyRequired SAGE ONLY
        # sample['!Sample_type'] = KeyRequired SAGE ONLY
        # sample['!Sample_tag_count'] = KeyRequired SAGE ONLY
        # sample['!Sample_tag_length'] = KeyRequired SAGE ONLY
        # sample['!Sample_table_begin'] = ''
        # sample['!Sample_table_end'] = ''
    
        if 'geoSampleAccession' in firstStanza:
            sample['!Sample_geo_accession'] = firstStanza['geoSampleAccession'] 
    
        softfile[firstStanza['metaObject']] = sample
        
    return softfile, fileList
    
    
def createSpecialSoftFile(database, composite, organism, compositeUrl, mdb, cv, track, md5sums, expIds, expVars, geoMapping, series, datatype):
    softfile = SoftFile()
    fileList = list()
    
    createSeries(softfile, composite, compositeUrl, track, expIds, geoMapping, series)
    
    for idNum in expIds.iterkeys():
        
        expId = expIds[idNum]
        firstStanza = expId[0]
        print 'Writing sample ' + firstStanza['metaObject'] + ' (' + idNum + ')'
        sample = HighThroughputSampleStanza()
        
        hasbigwig = 0
        for stanza in expId:
        
            if getFileType(stanza['fileName']) == 'bigWig':
                hasbigwig = 1
                
        if hasbigwig == 0:
            continue
        
        sample['^SAMPLE'] = firstStanza['geoSampleAccession']
        
        if 'geoSeriesAccession' in series:
            sample['!Sample_series_id'] = series['geoSeriesAccession']
            
        sample['!Sample_geo_accession'] = firstStanza['geoSampleAccession']
        
        count = 1
            
        for stanza in expId:
        
            if getFileType(stanza['fileName']) == 'bigWig':
                sample['!Sample_supplementary_file_' + str(count)] = stanza['fileName']
                
                if 'checksum' in stanza:
                    sample['!Sample_supplementary_file_checksum_' + str(count)] = stanza['checksum']
                elif md5sums != None and stanza['fileName'] in md5sums:
                    sample['!Sample_supplementary_file_checksum_' + str(count)] = md5sums[stanza['fileName']]
                
                # sample['!Sample_supplementary_file_build_' + str(count)] = database
                
                fileList.append(stanza['fileName'])
                count = count + 1
                
        softfile[firstStanza['geoSampleAccession']] = sample
        
    return softfile, fileList
        
def main():

    parser = argparse.ArgumentParser(description = 'Prepares a submission to GEO. Creates a soft file and shell script with the correct call to aspera.')
    parser.add_argument('-t', '--trackPath', help='Overrides the default track path ~/kent/src/hg/makeDb/trackDb/')
    parser.add_argument('-r', '--replace', help='Give the name of a file that has contents to be used to replace unspecified tags in metadata (description, contributers, etc) and instrument model')
    parser.add_argument('-a', '--audit', action='store_true', default=False, help='Instead of building the files, will just give you a list of errors')
    parser.add_argument('-z', '--zip', help='Specifies a directory path to unzip tarred fastqs to, only applicable for tracks with tarred fastqs')
    parser.add_argument('-s', '--series', action='store_true', default=False, help='Only generates the series stanza, instead of generating the entire soft file')
    parser.add_argument('database', help='The database, typically hg19 or mm9')
    parser.add_argument('composite', help='The composite name, wgEncodeCshlLongRnaSeq for instance')
    parser.add_argument('expIds', nargs='*', help='Any number of expIds separated by spaces, you can also specify a range by using a hyphen, "140 150 160-170" for instance, or leave blank to specify the entire file')
    
    if len(sys.argv) == 1:
        parser.print_usage()
        return
    
    args = parser.parse_args(sys.argv[1:])
        
    compositeTrack = CompositeTrack(args.database, args.composite, args.trackPath)

    cvPath = compositeTrack.trackPath + 'cv/alpha/cv.ra'
    controlledVocab = CvFile(cvPath)
    
    if args.zip != None and not args.zip.endswith('/'):
        args.zip += '/'
    
    replace = dict()
    if args.replace != None:
        for line in open(args.replace):
            if line == '':
                continue
            key, val = map(str.strip, line.split('=', 1))
            if key not in replace:
                replace[key] = list()
            replace[key].append(val)
        
    tempids = list()
    ids = list()
    
    for id in args.expIds:
        if '-' in id:
            start, end = id.split('-', 1)
            tempids.extend(range(int(start), int(end) + 1))
        else:
            tempids.append(int(id))
    for id in tempids:
        if str(id) in compositeTrack.alphaMetaDb.experiments.keys():
            ids.append(int(id))

    expIds, expVars, geoMapping, series, datatype = createMappings(compositeTrack.alphaMetaDb)
  
    submission = dict()
    if len(ids) == 0:
        submission = expIds
    else:
        for expId in ids:
            if str(expId) in expIds.keys():
                submission[str(expId)] = expIds[str(expId)]
    expIdStr = ' '
    for id in args.expIds:
        expIdStr = expIdStr + id + ',' 
    expIdStr = expIdStr[:len(expIdStr) - 1]
    print 'Generating soft using expIds ' + ','.join(submission.keys())
    
    if datatype.type == 'HighThroughput':
        softfile, fileList = createHighThroughputSoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype, replace, args.audit, args.zip, args.series)
    elif datatype.type == 'MicroArray':
        softfile, fileList = createMicroArraySoftFile(compositeTrack, controlledVocab, submission, expVars, geoMapping, series, datatype, replace, args.audit, args.zip, args.series)
    else:
        raise KeyError('unsupported type ' + datatype.name)
    
    if not args.audit and not args.series:
        print 'Creating directory'
    
        d = datetime.datetime.today()
        datestring = '%4d-%02d-%02d' % (d.year, d.month, d.day)
        
        dirname = '%s_%s_%s/' % (compositeTrack.database, compositeTrack.name, datestring)
        linkdirname = '%s_%s/' % (compositeTrack.database, compositeTrack.name)
    
        os.mkdir(dirname)
        os.mkdir(dirname + linkdirname)
    
        print 'Writing file'
        
        outfileName = '%s%s_%s.soft' % (dirname + linkdirname, compositeTrack.database, compositeTrack.name)
        outfile = open(outfileName, 'w')
        outfile.write(str(softfile))
        fileslistname = '%sfiles.txt' % (dirname + linkdirname)
        fileslist = open(fileslistname, 'w')
        scriptname = '%supload.sh' % dirname
        outscript = open(scriptname, 'w')
        
        outscript.write('#!/bin/sh\n\n')
        outscript.write('/cluster/home/mmaddren/.aspera/connect/bin/ascp -i ~/encode_geo_key/encode_geo_key.ppk --symbolic-links=follow -QTdr -l300m %s asp-geo@upload.ncbi.nlm.nih.gov:ENCODE\n' % linkdirname)
        outscript.close()
    elif args.series:
        outfileName = '%s_%s.soft' % (compositeTrack.database, compositeTrack.name)
        outfile = open(outfileName, 'w')
        outfile.write(str(softfile))
        outfile.close()
        
    for file in fileList:
        if not os.path.exists(file.path):
            print IOError(file.path + ' does not exist')
        elif not args.audit:
            linkname = linkName(file, compositeTrack)
            linkpath = linkdirname + linkname
            os.symlink(file.fullname, dirname + linkpath)
        
            #outscript.write(linkpath + ' \\\n')
            fileslist.write(linkname + '\n')
    
    if not args.audit and not args.series:
        #outscript.write()
        
        fileslist.close()

        os.system('chmod +x ' + scriptname)
        
        print 'Finished!'
    
if __name__ == '__main__':
    main()