diff util/subtools.py @ 1:2ae1e96a8380 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a8c47ae0025953ef398bdc689dc5df5516edf686-dirty

--- a/util/subtools.py	Tue Oct 17 17:28:05 2017 -0400
+++ b/util/subtools.py	Tue Oct 24 18:24:40 2017 -0400
@@ -63,13 +63,13 @@
         # If we detect an error from the subprocess, then we raise an exception
         # TODO: Manage if we raise an exception for everything, or use CRITICAL etc... but not stop process
         # TODO: The responsability of returning a sys.exit() should not be there, but up in the app.
+        #if p.returncode:
         if p.returncode:
             if stderr == subprocess.PIPE:
                 raise PopenError(cmd, error, p.returncode)
             else:
                 # TODO: To Handle properly with a design behind, if we received a option as a file for the error
-                raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}"
-                                .format(cmd, stderr.name, p.returncode))
+                raise Exception("Error when calling {0}. Error as been logged in your file {1}. Error code: {2}".format(cmd, stderr.name, p.returncode))
 
     except OSError as e:
         message = "The subprocess {0} has encountered an OSError: {1}".format(
@@ -94,248 +94,14 @@
         logging.exception(message)
 
         sys.exit(-1)
-    return p
-
-
-def write_features(field, attribute, gff3):
-    """
-    The function write the features to gff3 format (defined in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
-    field, attribute are ordered dictionary 
-    gff3 is the file handler
-    """
-    attr = []
-    for v in field.values():
-        gff3.write(str(v) + '\t')
-    for k, v in attribute.items():
-        s = str(k) + '=' + str(v)
-        attr.append(s)
-    gff3.write(';'.join(attr))
-    gff3.write('\n')
-
-def twoBitInfo(two_bit_file_name, two_bit_info_file):
-    """
-    Call twoBitInfo and write the result into twoBit_info_file
-    :param two_bit_file_name:
-    :param two_bit_info_file:
-    :return the subprocess.check_call return object:
-    """
-    array_call = ['twoBitInfo', two_bit_file_name, two_bit_info_file]
-    p = _handleExceptionAndCheckCall(array_call)
-    return p
-
-
-def faToTwoBit(fasta_file_name, twoBitFile):
-    """
-    This function call faToTwoBit UCSC tool, and return the twoBitFile
-    :param fasta_file_name:
-    :param mySpecieFolder:
-    :return:
-    """
-
-    array_call = ['faToTwoBit', fasta_file_name, twoBitFile]
-    _handleExceptionAndCheckCall(array_call)
-
-    return twoBitFile
-
-def sortChromSizes(two_bit_info_file_name, chrom_sizes_file_name):
-    """
-    Call sort with -k2rn on two_bit_info_file_name and write the result into chrom_sizes_file_name
-    :param two_bit_info_file_name:
-    :param chrom_sizes_file_name:
-    :return:
-    """
-    array_call = ['sort', '-k2rn', two_bit_info_file_name,
-                  '-o', chrom_sizes_file_name]
-    p = _handleExceptionAndCheckCall(array_call)
-    return p
-
-def getChromSizes(reference, tool_dir):
-    #TODO: find a better way instead of shipping the two exec files with the tool
-    faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
-    twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
-    try:
-        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
-        chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
-    except IOError as err:
-        print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
-    try:
-        subprocess.call(['faToTwoBit', reference, twoBitFile.name])
-    except OSError as err:
-        print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
-    try:
-        subprocess.call(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
-    except OSError as err:
-        print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
-    return chrom_sizes
-
-def sequence_region(chrom_sizes):
-    """
-    This function read from a chromatin size file generated by twoBitInfo and write the information to dict
-    return a dict
-    """
-    f = open(chrom_sizes, 'r')
-    sizes = f.readlines()
-    sizes_dict = {}
-    for line in sizes:
-        chrom_info = line.rstrip().split('\t')
-        sizes_dict[chrom_info[0]] = chrom_info[1]
-    return sizes_dict
-
-def child_blocks(parent_field, parent_attr, gff3, child_type):
-    num = 0
-    blockcount = int(parent_attr['blockcount'])
-    chromstart = parent_attr['chromstarts'].split(',')
-    blocksize = parent_attr['blocksizes'].split(',')
-    parent_start = parent_field['start']
-    while num < blockcount:
-        child_attr = OrderedDict()
-        child_field = parent_field
-        child_field['type'] = child_type
-        child_field['start'] = int(chromstart[num]) + int(parent_start)
-        child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
-        child_attr['ID'] = parent_attr['ID'] + '_part_' + str(num+1)
-        child_attr['Parent'] = parent_attr['ID']
-        write_features(child_field, child_attr, gff3)
-        num = num + 1
-
-def add_tracks_to_json(trackList_json, new_tracks, modify_type):
-    """
-    Add to track configuration (trackList.json)
-    # modify_type =  'add_tracks': add a new track like bam or bigwig, new_track = dict()
-    # modify_type = 'add_attr': add configuration to the existing track, new_track = dict(track_name: dict())
-    """
-    with open(trackList_json, 'r+') as f:
-        data = json.load(f)
-        if modify_type == 'add_tracks':
-            data['tracks'].append(new_tracks)
-        elif modify_type == 'add_attr':
-            for k in new_tracks:
-                for track in data['tracks']:
-                    if k.lower() in track['urlTemplate'].lower():
-                        attr = new_tracks[k]
-                        for k, v in attr.items():
-                            track[k] = v
-        f.seek(0, 0)
-        f.write(json.dumps(data, separators=(',' , ':'), indent=4))
-        f.truncate()
-        f.close()
-
-
-def createBamIndex(bamfile):
-    subprocess.call(['samtools', 'index', bamfile])
-    filename = bamfile + '.bai'
-    if os.path.exists(filename):
-        return filename
-    else:
-        raise ValueError('Did not find bai file')
-
-def flatfile_to_json(inputFile, dataType, trackType, trackLabel, outputFolder, options=None, compress=False):
-    if "bed" in dataType:
-        fileType = "--bed"
-    elif "gff" in dataType:
-        fileType = "--gff"
-    else:
-        raise ValueError("%s is not a valid filetype for flatfile_to_json" % dataType)
-       
-
-    array_call = ['flatfile-to-json.pl', 
-                   fileType, inputFile, 
-                   '--trackType', trackType, 
-                   '--trackLabel', trackLabel,
-                   '--out', outputFolder]
-    if compress:
-        array_call.append('--compress')
-    if options:
-        config = options.get("config")
-        clientConfig = options.get("clientConfig")
-        renderClassName = options.get('renderClassName')
-        subfeatureClasses = options.get('subfeatureClasses')
-        load_type = options.get("type")
-        if clientConfig:
-            array_call.append('--clientConfig')
-            array_call.append(clientConfig)
-        if config:
-            array_call.append('--config')
-            array_call.append(config)
-        if load_type:
-            array_call.append('--type')
-            array_call.append(load_type)
-        if renderClassName:
-            array_call.append('--renderClassName')
-            array_call.append(renderClassName)
-        if subfeatureClasses:
-            array_call.append('--subfeatureClasses')
-            array_call.append(json.dumps(subfeatureClasses))
-
-    p = _handleExceptionAndCheckCall(array_call)
-    return p
-
-def bam_to_json(inputFile, trackLabel, outputFolder, options=None, compress=False):
-    
-    array_call = ['bam-to-json.pl', 
-                   '--bam', inputFile, 
-                   '--trackLabel', trackLabel,
-                   '--out', outputFolder]
-    if compress:
-        array_call.append('--compress')
-    if options:
-        config = options.get('config')
-        clientConfig = options.get('clientConfig')
-        if clientConfig:
-            array_call.append('--clientConfig')
-            array_call.append(clientConfig)
-        if config:
-            array_call.append('--config')
-            array_call.append(config)
-
-    p = _handleExceptionAndCheckCall(array_call)
-    return p
-
-def add_track_json(trackList, track_json):
-    track_json = json.dumps(track_json)
-    new_track = subprocess.Popen(['echo', track_json], stdout=subprocess.PIPE)
-    p = subprocess.call(['add-track-json.pl', trackList], stdin=new_track.stdout)
-    return p
-
-def prepare_refseqs(fasta_file_name, outputFolder):
-    array_call = ['prepare-refseqs.pl', '--fasta', fasta_file_name, '--out', outputFolder]
-    p = _handleExceptionAndCheckCall(array_call)
-    return p       
-
-def generate_names(outputFolder):
-    array_call = ['generate-names.pl', '-v', '--out', outputFolder]
-    p = _handleExceptionAndCheckCall(array_call)
-    return p  
-   
-def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
-    """
-    Call validateFiles on input_file, using chrom_sizes_file_name and file_type
-    :param input_file:
-    :param chrom_sizes_file_name:
-    :param file_type:
-    :return:
-    """
-    
-    array_call = ['validateFiles', '-chromInfo=' + chrom_sizes_file_name, '-type='+ file_type, input_file]
-    if options:
-        tab = options.get("tab")
-        autoSql = options.get("autoSql")
-        logging.debug("tab: {0}".format(tab))
-        logging.debug("autoSql: {0}".format(autoSql))
-        if autoSql:
-            autoSql = ''.join(['-as=', autoSql])
-            array_call.append(autoSql)
-        if tab:
-            array_call.append('-tab')
-    p = _handleExceptionAndCheckCall(array_call)
-    return p
+    return output
 
 def arrow_add_organism(organism_name, organism_dir, public=False):
     array_call = ['arrow', 'organisms', 'add_organism', organism_name, organism_dir]
     if public:
         array_call.append('--public')
-    print array_call
-    p = subprocess.check_output(array_call)
+    p = _handleExceptionAndCheckCall(array_call)
+    #p = subprocess.check_output(array_call)
     return p
 
 def arrow_create_user(user_email, firstname, lastname, password, admin=False):
@@ -377,3 +143,19 @@
             return d['userId']
     logging.error("Cannot find user %s", user_email)
 
+def verify_user_login(username, password):
+    user_info = {'username': username, 'password': password}
+    array_call = ['curl', 
+                  '-b', 'cookies.txt', 
+                  '-c', 'cookies.txt', 
+                  '-H', 'Content-Type:application/json',
+                  '-d', json.dumps(user_info),
+                  'http://localhost:8080/apollo/Login?operation=login'
+                  ]
+    p = _handleExceptionAndCheckCall(array_call)
+    msg = json.loads(p)
+    if 'error' in msg:
+        logging.error("The Authentication for user %s failed. Get error message %s", username, msg['error'])
+        exit(-1)
+    
+