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+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

Orange/__init__.py

+__import__('pkg_resources').declare_namespace(__name__)

Orange/bioinformatics/__init__.py

Empty file added.

Orange/bioinformatics/obiArrayExpress.py

+"""
+===============
+obiArrayExpress
+===============
+
+A python module for accessing the ArrayExpress web services and database.
+
+`Array Express Archive <http://www.ebi.ac.uk/arrayexpress/>`_ is a database of gene expression experiments that you
+can query and download.
+
+Example ::
+
+    >>> # Retrieve the object representing experiment with accession E-TABM-25 
+    >>> experiment = ArrayExpressExperiment("E-TABM-25")
+    >>> print experiment.accession
+    E-TABM-25
+    
+    >>> print experiment.name
+    Transcription profiling of aging in the primate brain
+    
+    >>> print experiment.species
+    ['Pan troglodytes']
+    
+    >>> print experiment.files
+    [{'kind': ...
+    
+    >>> # Retrieve the data matrix for experiment 'E-MEXP-2917'
+    >>> experiment = ArrayExpressExperiment("E-MEXP-2917")
+    >>> table = experiment.fgem_to_table() 
+
+
+Low level Array Express query using REST services::
+
+    >>> import obiArrayExpress
+    >>> obiArrayExpress.query_experiments(accession='E-MEXP-31')
+    {u'experiments': ...
+    
+    >>> obiArrayExpress.query_experiments(keywords='gliobastoma')
+    {u'experiments': ...
+    
+    >>> obiArrayExpress.query_files(accession='E-MEXP-32', format="xml")
+    <xml.etree.ElementTree.ElementTree object ...
+   
+.. note:: Currently querying ArrayExpress files only works with the xml format.
+
+.. note:: See the documentation of `query_experiments` for a full set of
+          parameters that these functions accept.
+
+"""
+
+import os, sys
+import urllib2
+
+import orngServerFiles
+import warnings
+import posixpath
+import shelve
+import shutil
+import posixpath
+import json
+from xml.etree.ElementTree import ElementTree
+from StringIO import StringIO
+
+from collections import defaultdict
+from functools import partial
+from contextlib import closing
+
+parse_json = json.load
+
+def parse_xml(stream):
+    """ Parse an xml stream into an instance of xml.etree.ElementTree.ElementTree.
+    """
+    return ElementTree(file=stream) 
+
+# All searchable fields of ArrayExpress (see query_experiments docstring
+# for a description of the fields)
+ARRAYEXPRESS_FIELDS = \
+    ["keywords",
+     "accession",
+     "array",
+     "ef",
+     "efv",
+     "expdesign",
+     "exptype",
+     "gxa",
+     "pmid",
+     "sa",
+     "species",
+     "expandefo",
+     "directsub",
+     "assaycount",
+     "efcount",
+     "samplecount",
+     "sacount",
+     "rawcount",
+     "fgemcount",
+     "miamescore",
+     "date",
+     "wholewords",
+    ]
+    
+
+class ArrayExpressConnection(object):
+    """ A connection to the ArrayExpress. Used to construct a REST query
+    and run it.
+    
+    .. todo:: Implement user login.
+    
+    """
+    
+    DEFAULT_ADDRESS = "http://www.ebi.ac.uk/arrayexpress/{format}/v2/"
+    DEFAULT_FORMAT = "json"
+    DEFAULT_CACHE = orngServerFiles.localpath("ArrayExpress", "ArrayExpressCache.shelve")
+    # Order of arguments in the query
+    _ARGS_ORDER = ["keywords", "species", "array"]
+    
+    def __init__(self, address=None, timeout=30, cache=None,
+                 username=None, password=None):
+        """ Initialize the connection object.
+        
+        :param address: Address of the ArrayExpress API
+        :param timeout: Timeout for the socket connection
+        
+        .. todo:: Implement user login (see Accessing Private Data in API docs)
+        
+        """
+        self.address = address if address is not None else self.DEFAULT_ADDRESS
+        self.timeout = timeout
+        self.cache = cache if cache is not None else self.DEFAULT_CACHE
+        self.username = username
+        self.password = password
+        
+    def format_query(self, **kwargs):
+        """ Format the query arguments.
+        
+        Example ::
+        
+            >>> conn.format_query(gxa=True, efcount=(1, 5))
+            'efcount=[1 TO 5]&gxa=true'
+            
+        """
+        # Formaters:
+        def format_default(val):
+            if isinstance(val, basestring):
+                return val
+            else:
+                return "+".join(val)
+        def format_species(val):
+            return '"%s"' % val.lower()
+        def format_gxa(val):
+            if val:
+                return "true"
+            else:
+                raise ValueError("gxa={0}".format(val))
+        def format_expandefo(val):
+            if val:
+                return "on"
+            else:
+                raise ValueError("expandefo={0}".format(val))
+        def format_true_false(val):
+            return "true" if val else "false"
+        def format_interval(val):
+            if isinstance(val, tuple):
+                return "[{0} TO {1}]".format(*val)
+            else:
+                raise ValueError("Must be an interval argument (min, max)!")
+        def format_date(val):
+            # TODO check if val contains a datetime.date object, assert proper format
+            return format_interval(val)
+        def format_wholewords(val):
+            if val:
+                return "on"
+            else:
+                raise ValueError("wholewords={0}".format(val))
+        
+        formaters = {"species": format_species,
+                     "gxa": format_gxa,
+                     "expandefo": format_expandefo,
+                     "directsub": format_true_false,
+                     "assaycount": format_interval,
+                     "efcount": format_interval,
+                     "samplecount": format_interval,
+                     "sacount": format_interval,
+                     "rawcount": format_interval,
+                     "fgemcount": format_interval,
+                     "miamescore": format_interval,
+                     "date": format_date,
+                     "wholewords": format_wholewords,
+                     }
+        parts = []
+        arg_items = kwargs.items()
+        ordered = sorted(arg_items, key=lambda arg: self._ARGS_ORDER.index(arg[0]) \
+                         if arg[0] in self._ARGS_ORDER else 100)
+        
+        for key, value in kwargs.iteritems():
+            if key == "format":
+                continue # format is handled in query_url
+            if key not in ARRAYEXPRESS_FIELDS:
+                raise ValueError("Invalid argument name: '{0}'".format(key))
+            if value is not None and value != []:
+                fmt = formaters.get(key, format_default)
+                value = fmt(value)
+                parts.append("{0}={1}".format(key, value))
+                 
+        return "&".join(parts)
+        
+    def query_url(self, what="experiments", **kwargs):
+        """ Return a formated query URL for the query arguments
+        
+        Example ::
+            >>> conn.query_url(accession="E-MEXP-31")
+            'http://www.ebi.ac.uk/arrayexpress/json/v2/experiments?accession=E-MEXP-31'
+            
+        """
+        query = self.format_query(**kwargs)
+        url = posixpath.join(self.address, what)
+        url = url.format(format=kwargs.get("format", self.DEFAULT_FORMAT))
+        url = url + ("?" + query if query else "")
+        url = url.replace(" ", "%20")
+        return url
+    
+    def query_url_experiments(self, **kwargs):
+        """ Return a formated experiments query url for the calls arguments
+        """
+        return self.query_url("experiments", **kwargs)
+    
+    def query_url_files(self, **kwargs):
+        """ Return a formated experiments query url for the calls arguments
+        """
+        return self.query_url("files", **kwargs)
+    
+    def query_experiment(self, **kwargs):
+        """ Return an open stream to the experiments query results.
+        
+        .. note:: This member function takes the same arguments as the module
+                  level `query_experiemnts` function.
+          
+        """
+        url = self.query_url_experiments(**kwargs)
+        stream = self._cache_urlopen(url, timeout=self.timeout)
+        return stream
+    
+    def query_files(self, **kwargs):
+        """ Return an open stream to the files query results.
+        
+        .. note:: This member function takes the same arguments as the module
+                  level `query_files` function.
+        """
+        url = self.query_url_files(**kwargs)
+        stream = self._cache_urlopen(url, timeout=self.timeout)
+        return stream
+    
+    def open_file(self, accession, kind="raw", ext=None):
+        """ Return a file handle to experiment data.
+        Possible values for kind:
+            - raw: return the raw data if available
+            - fgem: return the processed data if available
+            - biosamples: a png or svg design image
+            - idf: investigation description
+            - adf: array design description
+            - mageml: MAGE-ML file
+            
+        Example ::
+        
+            >>> raw_file = conn.open_file("E-TABM-1087", kind="raw")
+            >>> processed_file = conn.open_file("E-TABM-1087", kind="fgem")
+             
+        """
+        stream = self.query_files(accession=accession, format="xml")
+        tree = ElementTree(file=stream)
+        files = tree.findall("experiment/file")
+        for file in files:
+            filekind = file.find("kind").text
+            fileext = file.find("extension").text
+            if filekind.strip() == kind and (fileext.strip() == ext or ext is None): 
+                url = file.find("url").text
+                return self._cache_urlopen(url.strip(), timeout=self.timeout)
+            
+    def _cache_urlopen(self, url, timeout=30):
+        if self.cache is not None:
+            with self.open_cache() as cache:
+                cached = url in cache
+            if not cached:
+                stream = urllib2.urlopen(url, timeout=timeout)
+                data = stream.read()
+                with self.open_cache() as cache:
+                    cache[url] = data
+            else:
+                with self.open_cache() as cache:
+                    data = cache[url]
+            return StringIO(data)
+        else:
+            return urllib2.urlopen(url, timeout=timeout)
+        
+    def open_cache(self):
+        if isinstance(self.cache, basestring):
+            return closing(shelve.open(self.cache))
+        elif hasattr(self.cache, "close"):
+            return closing(self.cache)
+        elif self.cache is None:
+            return fake_closing({})
+        else:
+            return fake_closing(self.cache)
+        
+from contextlib import contextmanager
+
+@contextmanager
+def fake_closing(obj):
+    yield obj
+    
+def query_experiments(keywords=None, accession=None, array=None, ef=None,
+                      efv=None, expdesign=None, exptype=None,
+                      gxa=None, pmid=None, sa=None, species=None,
+                      expandefo=None, directsub=None, assaycount=None,
+                      efcount=None, samplecount=None, rawcount=None,
+                      fgemcount=None, miamescore=None, date=None, 
+                      format="json", wholewords=None, connection=None):
+    """ Query Array Express experiments.
+    
+    :param keywords: A list of keywords to search (e.g. ['gliobastoma']
+    :param accession: Search by experiment accession (e.g. 'E-MEXP-31')
+    :param array: Search by array design name or accession (e.g. 'A-AFFY-33')
+    :param ef: Experimental factor (names of main variables of experiments)
+    :param efv: Experimental factor value (Has EFO expansion)
+    :param expdesign: Experiment design type. (e.g. ["dose", "response"])
+    :param exptype: Experiment type (e.g. 'RNA-Seq', has EFO expansion)
+    :param gxa: If True limit the results to experiments from the Gene
+        Expreission Atlas only.
+    :param pmid: Search by PubMed identifier
+    :param sa: Sample attribute values (e.g. 'fibroblast', has EFO expansion)
+    :param species: Search by species (e.g. 'Homo sapiens', has EFO expansion)
+    
+    :param expandefo: If True expand the search terms with all its child terms
+        in the Experimental Factor Ontology (EFO_) (e.g. keywords="cancer"
+        will be expanded to include for synonyms and sub types of cancer).
+    :param directsub: If True return only experiments submited directly to
+        Array Express else if False return only experiments imported from GEO
+        database (default None, return both)
+    :param assaycount: A two tuple (min, max) for filter on the number of
+        assays (e.g. (1, 5) will return only experiments with at least one
+        and no more then 5 assays).
+    :param efcount: Filter on the number of experimental factors (e.g. (1, 5))
+    :param sacount: Filter on the number of sample attribute categories
+    :param rawcount: Filter on the number or raw files
+    :param fgemcount: Filter on the number of final gene expression matrix
+        (processed data) files
+    :param miamescore: Filter on the MIAME complience score (max 5)
+    :param date: Filter by release date
+    
+    Example ::
+    
+        >>> query_experiments(species="Homo sapiens", ef="organism_part", efv="liver")
+        {u'experiments': ...
+        
+    .. _EFO: http://www.ebi.ac.uk/efo/
+    
+    """
+    if connection is None:
+        connection = ArrayExpressConnection()
+        
+    stream = connection.query_experiment(keywords=keywords, accession=accession,
+                array=array, ef=ef, efv=efv, expdesign=expdesign, exptype=exptype,
+                gxa=gxa, pmid=pmid, sa=sa, species=species, expandefo=expandefo,
+                directsub=directsub, assaycount=assaycount, efcount=efcount,
+                samplecount=samplecount, rawcount=rawcount, fgemcount=fgemcount,
+                miamescore=miamescore, date=date,  format=format,
+                wholewords=wholewords)
+    
+    if format == "json":
+        return parse_json(stream)
+    else:
+        return parse_xml(stream)
+    
+    
+def query_files(keywords=None, accession=None, array=None, ef=None,
+               efv=None, expdesign=None, exptype=None,
+               gxa=None, pmid=None, sa=None, species=None,
+               expandefo=None, directsub=None, assaycount=None,
+               efcount=None, samplecount=None, rawcount=None,
+               fgemcount=None, miamescore=None, date=None, 
+               format="json", wholewords=None, connection=None):
+    """ Query Array Express files.
+    
+    This function accepts the same arguments as `query_experiments`.
+    
+    Example ::
+    
+        >>> query_files(species="Mus musculus", ef="developmental_stage", efv="embryo", format="xml")
+        <xml.etree.ElementTree.ElementTree object ...
+        
+    .. todo:: why does the json interface not work.
+                        
+    """
+    if connection is None:
+        connection = ArrayExpressConnection()
+    
+    stream = connection.query_files(keywords=keywords, accession=accession,
+                array=array, ef=ef, efv=efv, expdesign=expdesign, exptype=exptype,
+                gxa=gxa, pmid=pmid, sa=sa, species=species, expandefo=expandefo,
+                directsub=directsub, assaycount=assaycount, efcount=efcount,
+                samplecount=samplecount, rawcount=rawcount, fgemcount=fgemcount,
+                miamescore=miamescore, date=date,  format=format,
+                wholewords=wholewords)
+    
+    if format == "json":
+        return parse_json(stream)
+    else:
+        return parse_xml(stream)
+    
+    
+def open_file(accession, kind="raw", ext=None, repo_dir=None):
+    """ Open a file for the experiment. 
+     
+    Example ::
+    
+        >>> file = open_file("E-MTAB-369", kind="raw", repo_dir="~/.arrayexpress/")
+        
+    """
+    raise NotImplementedError
+
+"""\
+MAGE-TAB convinence functions, classes
+======================================
+"""
+
+IDF_SINGLE_TAGS = \
+    ["Investigation Title",
+     "Date of Experiment",
+     "Public Release Date",
+     "Experiment Description",
+    ]
+
+def parse_idf(file):
+    """ Parse an idf.txt (Investigation Description  Format) formated file.
+    Return a list of tuples where the first element is the tag (first column)
+    and the second element is a list of all tag values.
+    
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line and not line.startswith("#")]
+    parsed = [(line[0], line[1:]) for line in lines]
+    return parsed
+    
+def parse_sdrf(file):
+    """ Parse an sdfr formated file. Return a tuple with the first element
+    a list of header values and the second element is a list of all rows
+    (a row is a list of string values).
+    
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line.strip() and not line.startswith("#")]
+    header = [h for h in lines[0] if h]
+    rows = [line[:len(header)] for line in lines[1:]]
+    assert(all([len(r) == len(header) for r in rows]))
+    return header, rows
+    
+def parse_adf(file):
+    pass
+
+def parse_data_matrix(file):
+    """ Parse the MAGE-TAB processed data matrix. Return a tuple where the
+    elements are:
+        - a (header REF, header values) tuple (e.g. ("Hybridization REF", ["Stage1", "Stage2", ...]) )
+        - a list of quantitations for header values (e.g. ["log2 ratio", "log2 ratio", ...])
+        - a (row REF, row names list) tuple ("e.g. ("Reporter REF", ["Probe 1", "Probe 2", ...]) )
+        - a list of list matrix with values (as strings)
+        
+    """
+    if isinstance(file, basestring):
+        file = open(file, "rb")
+    data = file.read()
+    lines = data.splitlines()
+    lines = [line.split("\t") for line in lines if line.strip()]
+    header = lines[0]
+    header_ref, header = header[0], header[1:]
+    line2 = lines[1]
+    row_ref, quanifications = line2[0], line2[1:]
+    row_names, rows = [], []
+    for line in lines[2:]:
+        r_name, row = line[0], line[1:]
+        row_names.append(r_name)
+        rows.append(row)
+        
+    return ((header_ref, header),
+            quanifications,
+            (row_ref, row_names),
+            rows) 
+    
+class InvestigationDesign(dict):
+    """ Investigation design (contains the contents of the .idf).
+    
+    Example ::
+    
+        >>> idf = InvestigationDesign("foobar.idf")
+        >>> print idf.investigation_title
+        foo investigation
+        >>> print idf.experimental_design
+        ['fubar', 'snafu']
+        >>> print idf.sdrf_file
+        ['foobar.sdrf']
+        
+    """
+    def __init__(self, idf_file=None):
+        idf = parse_idf(idf_file)
+        self._idf = idf
+        self.update(dict(idf))
+        for tag, values in idf:
+            if tag in IDF_SINGLE_TAGS:
+                values = values[0] if values else None
+            ttag = self.transform_tag(tag)
+            setattr(self, ttag, values)
+        
+    def transform_tag(self, tag):
+        """ Transform the tag into a proper python attribute name by
+        replacing all spaces and special characters (e.g '[', ']' into
+        underscores).
+        
+        """
+        toreplace = [" ", "-", "[", "]"]
+        for s in toreplace:
+            tag = tag.replace(s, "_")
+        return tag.lower()
+            
+    def __getitem__(self, tag):
+        """ Return the tag values
+        
+        Example ::
+        
+            >>> idf["Investigation Title"]
+            'foo investigation'
+            
+        """
+        try:
+            return self._idf_dict[tag]
+        except KeyError:
+            pass
+        
+        ttag = self.transform_tag(tag)
+        if hasattr(self, ttag):
+            return getattr(self, ttag)
+        else:
+            raise KeyError(tag)
+        
+class SampleDataRelationship(object):
+    """ Sample-Data Relationship (contains the contents of the .sdrf file).
+    
+    Example ::
+    
+        >>> sdr = SampleDataRelationship("foobar.sdrf")
+        >>> sdr.source_name
+        ['foo', ...
+        
+        >>> sdr.sample_name
+        ['sampled foo', ...
+        
+        >>> sdr.extract_protocol_ref
+        ['bar the foo', ...
+        
+        >>> sdr.derived_array_data_matrix_file
+        ['foobar.data.txt', ...
+        
+        >>>
+         
+    """
+    
+    # Nodes an edges
+    NODES_EDGES = ["Source Name", "Sample Name", "Extract Name",
+                   "Labeled Extract Name", "Hybridization Name",
+                   "Assay Name", "Scan Name", "Normalization Name",
+                   "Array Data File", "Derived Array Data File",
+                   "Array Data Matrix File", "Derived Array Data Matrix File",
+                   "Image File", "Protocol REF"]
+    
+    # Attributes for nodes and edges
+    NODE_EDGE_ATTRIBUTES = \
+    {"Source Name": ["Characteristics", "Provider", "Material Type", "Description", "Comment"],
+     "Sample Name": ["Characteristics", "Material Type", "Description", "Comment"],
+     "Extract Name":["Characteristics", "Material Type", "Description", "Comment"],
+     "Labeled Extract Name": ["Characteristics", "Material Type", "Description", "Label", "Comment"],
+     "Hybridization Name": ["Array Design File", "Array Design REF", "Comment"],
+     "Assay Name": ["Technology Type", "Comment"],
+     "Scan Name": ["Comment"],
+     "Normalization Name": ["Comment"],
+     "Array Data File": ["Comment"],
+     "Derived Array Data File": ["Comment"],
+     "Array Data Matrix File": ["Comment"],
+     "Derived Array Data Matrix File": ["Comment"],
+     "Image File": ["Comment"],
+     "Protocol REF": ["Term Source REF", "Parameter", "Performer", "Date", "Comment"]
+     }
+    
+    # Attributes
+    ATTRIBUTE_COLUMNS = \
+    {"Characteristics []": ["Unit", "Term Source REF"],
+     "Provider": ["Comment"],
+     "Material Type": ["Term Source REF"],
+     "Label": ["Term Source REF"],
+     "Array Design File": ["Comment"],
+     "Array Design REF": ["Term Source REF", "Comment"],    
+     "Technology Type": ["Term Source REF"],
+     "Factor Value [] ()": ["Unit", "Term Source REF"],
+     "Performer": ["Comment"],
+     "Date": [],
+     "Parameter Value []": ["Unit", "Comment"],
+     "Unit []": ["Term Source REF"],
+     "Description": [],
+     "Term Source REF": ["Term Accession Number"],
+     "Term Accession Number": [],
+     "Comment []": []
+     }
+    def __init__(self, sdrf_file=None):
+        header, rows = parse_sdrf(sdrf_file)
+        self.header = header
+        self.rows = rows 
+        
+    def transform_tag(self, tag):
+        """ Transform the tag into a proper python attribute name by
+        replacing all spaces and special characters (e.g '[', ']' into
+        underscores).
+        
+        """
+        toreplace = [" ", "-", "[", "]"]
+        for s in toreplace:
+            tag = tag.replace(s, "_")
+        return tag.lower()
+    
+    def _subsection(self, name):
+        """ Return the named subsection (name must be from the
+        NODES_EDGES list).
+        
+        """
+        idx = self.NODES_EDGES.index(name)
+        start = self.header.index(name)
+        end = -1
+        for name in self.NODES_EDGES[idx + 1:]:
+            if name in self.header[start + 1:]:
+                end = self.header.index(name, start + 1)
+                break
+        return self.header[start:end], [r[start:end] for r in self.rows]
+    
+    def _column(self, name):
+        """ Return the named column.
+        """
+        index = self.header.index(name)
+        return [r[index] for r in self.rows]
+        
+    def source(self):
+        """ Return the Source subsection
+        """
+        return self._subsection("Source Name")
+        
+    def source_name(self):
+        """ Return the Source Name subsection
+        """
+        return self._column("Source Name")
+        
+    def sample(self):
+        """ Return the Sample subsection
+        """
+        return self._subsection("Sample Name")
+        
+    def sample_name(self):
+        """ Return the Sample Name subsection
+        """
+        return self._column("Sample Name")
+        
+    def extract(self):
+        """ Return the Extract subsection
+        """
+        return self._subsection("Extract Name")
+        
+    def extract_name(self):
+        """ Return the Extract Name subsection
+        """
+        return self._column("Extract Name")
+        
+    def labeled_extract(self):
+        """ Return the Labeled Extract subsection
+        """
+        return self._subsection("Labeled Extract Name")
+        
+    def labeled_extract_name(self):
+        """ Return the Labeled Extract Name subsection
+        """
+        return self._column("Labeled Extract Name")
+        
+    def hybridization(self):
+        """ Return the Hibridization subsection.
+        """
+        return self._subsection("Hibridization Name")
+        
+    def hybridization_name(self):
+        """ Return the Hibridization Name subsection.
+        """
+        return self._column("Hibridization Name")
+        
+    def assay(self):
+        """ Return the Assay subsection
+        """
+        return self._subsection("Assay Name")
+        
+    def assay_name(self):
+        """ Return the Assay Name subsection
+        """
+        return self._column("Assay Name")
+        
+    def scan(self):
+        """ Return the Scan subsection
+        """
+        return self._subsection("Scan Name")
+        
+    def scan_name(self):
+        """ Return the Scan name subsection
+        """
+        return self._column("Scan Name")
+        
+    def normalization(self):
+        """ Return the Normalization subsection.
+        """
+        return self._subsection("Normalization Name")
+        
+    def normalization_name(self):
+        """ Return the Normalization Name subsection.
+        """
+        return self._column("Normalization Name")
+         
+    def array_data(self):
+        """ Return the Array Data subsection
+        """
+        return self._subsection("Array Data File")
+    
+    def array_data_file(self):
+        """ Return the Array Data File subsection
+        """
+        return self._column("Array Data File")
+        
+    def derived_array_data(self):
+        """ Return the Derived Array Data subsection
+        """
+        return self._subsection("Derived Array Data File")
+    
+    def derived_array_data_file(self):
+        """ Return the Derived Array Data File subsection
+        """
+        return self._column("Derived Array Data File")
+        
+    def array_data_matrix(self):
+        """ Return the Array Data Matrix subsection.
+        """
+        return self._subsection("Array Data Matrix File")
+    
+    def array_data_matrix_file(self):
+        """ Return the Array Data Matrix File subsection.
+        """
+        return self._column("Array Data Matrix File")
+        
+    def derived_array_data_matrix(self):
+        """ Return the Derived Array Data Matrix subsection.
+        """
+        return self._subsection("Derived Array Data Matrix File")
+    
+    def derived_array_data_matrix_file(self):
+        """ Return the Derived Array Data Matrix File subsection.
+        """
+        return self._column("Derived Array Data Matrix File")
+        
+    def image(self):
+        """ Return the Image subsection
+        """
+        return self._subsection("Image File")
+    
+    def image_file(self):
+        """ Return the Image File subsection.
+        """
+        return self._column("Image File")
+        
+class ArrayDesign(object):
+    """ Arary design (contains the contents of the .adf file).
+    """
+    def __init__(self, adf_file=None):
+        adf = parse_adf(adf_file)
+        self._adf = adf
+    
+def _is_float(str):
+    try:
+        float(str)
+        return True
+    except ValueError:
+        return False
+    
+def _is_continuous(items, check_count=100):
+    """ Are the strings in items continous numbers. 
+    """
+    count = 0
+    i = 0
+    for i, item in enumerate(items):
+        if _is_float(item):
+            count += 1
+        if i >= check_count:
+            break
+    return count >= i * 0.5
+    
+def processed_matrix_to_orange(matrix_file):
+    """ Load a single processed matrix file in to an Orange.data.Table
+    instance. 
+    """
+    import numpy
+    import Orange
+    
+    if isinstance(matrix_file, basestring):
+        matrix_file = open(matrix_file, "rb")
+        
+#    data_matrix = matrix_file.read()
+    header, quantification, rows, matrix = parse_data_matrix(matrix_file)
+    header_ref, header = header
+    row_ref, rows = rows
+    
+    matrix = numpy.array(matrix, dtype=object)
+    
+    
+    features = []
+    is_float = numpy.frompyfunc(_is_float, 1, 1) # an numpy ufunc
+         
+    for header_name, quant, column in zip(header, quantification, matrix.T):
+        if _is_continuous(column):
+            feature = Orange.feature.Continuous(header_name)
+            column[numpy.where(1 - is_float(column))] = "?" # relace all non parsable floats with '?'
+        else:
+            values = set(column)
+            feature = Orange.feature.Discrete(header_name, values=sorted(values))
+        feature.attributes["quantification"] = quant
+        features.append(feature)
+        
+    row_ref_feature = Orange.feature.String(row_ref)
+    domain = Orange.data.Domain(features, None)
+    domain.addmeta(Orange.feature.Descriptor.new_meta_id(), row_ref_feature)
+    
+    table = Orange.data.Table(domain, [list(row) for row in matrix])
+    
+    # Add row identifiers
+    for instance, row in zip(table, rows):
+        instance[row_ref_feature] = row
+    
+    return table
+    
+
+def mage_tab_to_orange(idf_filename):
+    """ Convert an MAGE-TAB annotated experiment into an Orange.data.Table
+    instance (assumes all the associated MAGE-TAB files are in the same
+    directory.
+    
+    .. todo:: Add Characteristics, Factor Values ... to the feature.attributes dict
+    
+    """
+    import Orange
+    dirname = os.path.dirname(idf_filename)
+    idf = InvestigationDesign(idf_filename)
+    
+    sdrf_filename = os.path.join(dirname, idf.sdrf_file[0])
+    sdrf = SampleDataRelationship(sdrf_filename)
+    
+    data_matrices = set(sdrf.derived_array_data_matrix_file())
+    data_matrices = [name for name in data_matrices if name.strip()]
+    
+    tables = []
+    for filename in data_matrices:
+        matrix_file = os.path.join(dirname, filename)
+        table = processed_matrix_to_orange(matrix_file)
+        tables.append(table)
+        
+    return hstack_tables(tables)
+    
+def hstack_tables(tables):
+    """ Stack the tables horizontaly.
+    """
+    import Orange
+    max_len = max([len(table) for table in tables])
+    stacked_features = []
+    stacked_values = [[] for i in range(max_len)]
+    stacked_meta_features = []
+    stacked_meta_values = [{} for i in range(max_len)]
+    
+    for table in tables:
+        stacked_features.extend(table.domain.variables)
+        stacked_meta_features.extend(table.domain.getmetas().items())
+        
+        for i, instance in enumerate(table):
+            stacked_values[i].extend(list(instance))
+            stacked_meta_values[i].update(instance.getmetas())
+            
+        # Fill extra lines with unknowns
+        for i in range(len(table), max_len):
+            stacked_values[i].extend(["?"] * len(table.domain.variables))
+        
+    domain = Orange.data.Domain(stacked_features, tables[-1].domain.class_var)
+    domain.addmetas(dict(set(stacked_meta_features)))
+    table = Orange.data.Table(domain, stacked_values)
+    
+    # Add meta attributes
+    for instance, metas in zip(table, stacked_meta_values):
+        for m, val in metas.iteritems():
+            instance[m] = val
+            
+    return table
+    
+def _dictify(element):
+    """ 'Dictify' and xml.etree.Element.Element instance by taking all
+    subnode tags as keys and the corresponding text values as items i.e. turn
+    `<node><bla>foo</bla><a>b</b></node>` into a {"bla":"foo", "a":b"}
+        
+    """
+    if element is None:
+        element = []
+    dict = {}
+    strip = lambda s: s.strip() if s else s
+    for node in element:
+        dict[node.tag] = strip(getattr(node, "text", None))
+    return dict
+    
+class SearchableList(list):
+    """ A list with a `search` method
+    """
+    def search(self, **kwargs):
+        """ Search the list for elements with members that correspond the
+        supplied keyword arguments.
+        
+            >>> foo.bar = "foo"
+            >>> list = SearchableList([foo, bar])
+            >>> list.search(bar="foo") # Search for objects which have a member named "bar" and that member equals "foo"
+            [<__main__.foo object ...
+            
+        """
+        ret = []
+        for obj in self:
+            for member, value in kwargs.items():
+                if hasattr(obj, member) and getattr(obj, member) == value:
+                    ret.append(obj)
+        return ret
+    
+class ArrayExpressExperiment(object):
+    """ An convinience class representing an Array Express Experiment.
+    
+    Example ::
+    
+        >>> ae = ArrayExpressExperiment("E-MEXP-2917")
+        >>> print ae.name
+        Characterization of Data Variation in Gene Expression Profiling of Human Peripheral Blood Samples
+        
+        >>> for file in ae.files:
+        ...     print file["name"], file["url"]
+        E-MEXP-2917.sdrf.txt http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2917/E-MEXP-2917.sdrf.txt
+        ...
+        
+        >>> table = ae.fgem_to_table() # Retieve the experiment data table 
+            
+    """
+    
+    def __init__(self, accession, connection=None):
+        self.accession = accession
+        self.connection = connection
+        self._etree = tree = query_experiments(accession=accession, connection=self.connection, format="xml")
+        experiments = tree.findall("experiment")
+        # find the exact match (more then one experiment can be listed in the query result)
+        experiments = [e for e in experiments if e.find("accession").text.strip() == accession]
+        self._experiment = experiment = experiments[0]
+        
+        self.species = [e.text for e in experiment.findall("species")]
+        bool_values = {"true": True, "false": False}
+        self.rawdatafiles = bool_values[experiment.find("rawdatafiles").get("available","false")]
+        self.fgemdatafiles = bool_values[experiment.find("fgemdatafiles").get("available", "false")]
+        
+        self.sampleattributes = []
+        for sa in experiment.findall("sampleattribute"):
+            category = sa.find("category").text.strip()
+            values = [val.text for val in sa.findall("value")]
+            self.sampleattributes.append((category, values))
+            
+        self.experimentalfactors = []
+        for ef in experiment.findall("experimentalfactor"):
+            name = ef.find("name").text.strip()
+            values = [val.text.strip() for val in ef.findall("values")]
+            self.experimentalfactors.append((name, values))
+            
+        self.miamescores = _dictify(experiment.find("miamescores"))
+            
+        self.id = experiment.find("id").text
+        self.secondaryaccession = getattr(experiment.find("secondaryaccession"), "text", None)
+        self.name = experiment.find("name").text
+        self.experimenttype = experiment.find("experimenttype").text.strip()
+        self.releasedate = experiment.find("releasedate").text
+        self.lastupdatedate = getattr(experiment.find("lastupdatedate"), "text", None)
+        self.samples = int(experiment.find("samples").text)
+        self.assays = int(experiment.find("assays").text)
+        
+        self.arraydesign = [_dictify(e) for e in experiment.findall("arraydesign")]
+            
+        self.bioassaydatagroups = [_dictify(group) for group in experiment.findall("bioassaydatagroup")]
+        self.bibliography = [_dictify(e) for e in experiment.findall("bibliography")]
+        self.provider = [_dictify(e) for e in experiment.findall("provider")]
+        
+        self.experimentdesign = []
+        for expd in experiment.findall("experimentdesign"):
+            self.experimentdesign.append(expd.text)
+            
+        self.description = [_dictify(e) for e in experiment.findall("description")]
+        
+        tree = query_files(accession=self.accession, format="xml", connection=self.connection)
+        experiments = tree.findall("experiment")
+        experiments = [e for e in experiments if e.find("accession").text.strip() == accession]
+        experiment = experiments[0]
+        files = experiment.findall("file")
+        self.files = [_dictify(file) for file in files]
+        
+    def _download_processed(self):
+        """ Download the processed matrix file, and associated MAGE-TAB files (idf, sdrf, adf)
+        
+        .. todo:: What about the raw data files (we need converters for other file types) 
+        """
+        assert(self.fgemdatafiles)
+        exp_files = [(f["kind"], f) for f in self.files if f.get("kind") in ["idf", "sdrf"] and f.get("extension") == "txt"]
+        exp_files += [(f["kind"], f) for f in self.files if f.get("kind") == "fgem"]
+        array_files = [(f["kind"], f) for f in self.files if f.get("kind") == "adf" and f.get("extension") == "txt"]
+        assert(len(files) == 3)
+        
+        for type, file in files.iteritems():
+            url = file["url"].strip()
+            rest, basename = os.path.split(url)
+            _, dirname = os.path.split(rest)
+            
+            repo_dir = orngServerFiles.localpath("ArrayExpress", dirname)
+            try:
+                os.makedirs(repo_dir)
+            except OSError:
+                pass
+            local_filename = os.path.join(repo_dir, basename)
+            stream = urllib2.urlopen(url)
+            shutil.copyfileobj(stream, open(local_filename, "wb"))
+            
+            if file["extension"] == "zip":
+                import zipfile
+                zfile = zlib.ZipFile(local_filename)
+                zfile.extractall(repo_dir)
+            elif file["extension"] == "gz":
+                import gzip
+                gzfile = gzip.open(local_filename)
+                gzfile.extractall(repo_dir)
+            elif file["extension"] in ["tgz", "tar"]:
+                import tarfile
+                tfile = tarfile.TarFile(local_filename)
+                tfile.extractall(repo_dir)
+            elif file["extension"] == "txt":
+                pass
+            else:
+                raise ValueError("Unknown extension ('{0}').".format(basename))
+            
+    def _download_file(self, url, extract=True):
+        """ Download the `file` from the ArrayExpress saving it to a local
+        repository directory.
+         
+        """
+        rest, basename = posixpath.split(url)
+        dirname = posixpath.basename(rest)
+        repo_dir = orngServerFiles.localpath("ArrayExpress", dirname)
+        try:
+            os.makedirs(repo_dir)
+        except OSError:
+            pass
+        stream = urllib2.urlopen(url)
+        local_filename = os.path.join(repo_dir, basename)
+        shutil.copyfileobj(stream, open(local_filename, "wb"))
+        
+        if extract:
+            _, extension = os.path.splitext(local_filename)
+            if extension == ".zip":
+                import zipfile
+                zfile = zipfile.ZipFile(local_filename)
+                zfile.extractall(repo_dir)
+            elif extension == ".gz":
+                import gzip
+                gzfile = gzip.open(local_filename)
+                gzfile.extractall(repo_dir)
+            elif extension in [".tgz"]:
+                import tarfile
+                tfile = tarfile.TarFile(local_filename)
+                tfile.extractall(repo_dir)
+            elif extension == ".txt":
+                pass
+            else:
+                raise ValueError("Unknown extension ('{0}').".format(basename))
+            
+    def _is_local(self, url):
+        """ Is the `url` stored in the local repository.
+        """
+        return os.path.exists(self._local_filepath(url))
+    
+    def _local_filepath(self, url):
+        """ Return the local file path for url.
+        """
+        rest, basename = posixpath.split(url)
+        dirname = posixpath.basename(rest)
+        return orngServerFiles.localpath("ArrayExpress", os.path.join(dirname, basename))