#build list of available data
import string, os, sys, glob, shutil, re
import galaxy.util
from galaxy import datatypes, config

from galaxy.model import Dataset

states = Dataset.states

repository = "/usr/local/galaxy/data/rg/library"

def getSampleNames(sampleName):
    fileName = sampleName.file_name
    f = file(fileName, 'r')
    sampleData = f.readlines()
    f.close()
    header = string.strip(sampleData[0])
    i = 0
    samples = []

    x_re = re.compile(r'\t')
    headerItems = x_re.split(header)

    for (sample) in headerItems:
        sample = string.strip(sample, '"')
        i += 1
        samples.append((sample,str(i),False))

    return samples

def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
    """tricky. We wrote
    outlist = ['%s\t%s\t%s' % (mng,newfiles[i],newnames[i]) for i in range(length(newfiles))]
    to the end of the log
    containing tab separated filepaths and types which we now need to create in
    the history
    This code was written for the security branch
    """
    mng = '### makenewgalaxy'
    tmpString = '### tmp'
    killme = string.punctuation + string.whitespace
    trantab = string.maketrans(killme,'_'*len(killme))
    job_name = param_dict.get( 'title', 'makeAffyBatch' ).translate(trantab)
    dbkey = param_dict.get('dbkey','hg18')
    base_dataset = out_data.items()[0][1]
    history = base_dataset.history
    if history == None:
        print "unknown history!"
        return
    logpath = out_data['logmeta'].file_name
    loglist = file(logpath,'r').readlines()
    newfiles = [x for x in loglist if x.split('\t')[0] == mng]
    # parse out the encoded new datasets for galaxy
    newfiles = [x.strip().split('\t')[1:] for x in newfiles] # get rid of #ymakenewgalaxy
    for (file_path,file_name,file_type) in newfiles:
        # note, this gets created - pass extra args?
        #class DatasetInstance( object ):
        #    """A base class for all 'dataset instances', HDAs, LDAs, etc"""
        #    states = Dataset.states
        #    permitted_actions = Dataset.permitted_actions
        #    def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None,
        #                  dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None,
        #                  parent_id=None, validation_errors=None, visible=True, create_dataset = False ):
        file_path = file_path.strip()
        newname = file_name.strip()
        info = '%s, %s' % (job_name, newname)
        iphenofile = file_path
        pk = '' # file(iphenofile,'r').read()
        newdata = app.model.HistoryDatasetAssociation(extension=file_type,dbkey=dbkey,info=info,
            name=newname,peek = pk, create_dataset = True, sa_session = app.model.context)
        # as noted in encode_import_code.py on which this was based :)
        # This import should become a library
        #newdata.metadata.base_name = geoid
        efp = newdata.extra_files_path
        try:
            os.makedirs(efp)
        except:
            pass
        phenoname = os.path.split(iphenofile)[-1] # name
        iid = os.path.splitext(phenoname)[0]
        newppath = os.path.join(efp,phenoname)
        shutil.copy(iphenofile,newppath) # save pheno for metadata
        newdata.metadata.pheno_path = newppath
        newdata.metadata.base_name = iid
        #kevin
        #newdata.metadata.pheno='Name\tGroup\na.cel\t1\nb.cel\t1\nc.cel\t0\nd.cel\t0\n'
        try:
            app.security_agent.set_dataset_permissions( newdata.dataset, base_dataset.dataset.groups )
        except:
            pass # old pre-security?
        app.model.context.add(newdata)
        app.model.context.flush()
        try:
            shutil.copyfile(file_path,newdata.file_name)
            newdata.set_dataset_state ( states.OK )
        except:
            s = "The requested file %s is missing from the system." % file_path
            lf = file(logpath,'a')
            lf.write(s)
            lf.write('\n')
            lf.write('Trying to write to %s\n' % (newdata.file_name))
            lf.close()
            newdata.info = s
            newdata.set_dataset_state ( states.ERROR )
        newdata.dbkey = dbkey
        newdata.set_peek()
        newdata.set_meta() # must set peek first
        lf = file(logpath,'a')
        lf.write('## saving %s as %s\n' % (newname, newdata.file_name))
        s = '# newdata %s peek = %s\n' % (newname,newdata.peek)
        lf.write(s)
        s = '# newdata %s metadata pheno_path = %s\n' % (newname,newdata.metadata.pheno_path)
        lf.write(s)
        lf.write('\n')
        lf.close()
        newdata.set_size()
        history.add_dataset( newdata )
        app.model.context.flush()

    tmpDir = [x for x in loglist if x.split('\t')[0] == tmpString]
    if len(tmpDir) > 0:
        tmpDir = [x.strip().split('\t')[1:] for x in tmpDir]
        if len(tmpDir) > 0:
            for (tdir) in tmpDir[0]:
                for (f) in os.listdir(tdir):
                    os.unlink(tdir + '/' + f)
                os.rmdir(tdir)