a44e3254174152b2d4b3f241d1935654cd139181
vsmalladi
  Tue May 8 10:11:21 2012 -0700
Renamed library from ucscgenomics to ucscGb. Redmine #7029.
diff --git python/lib/ucscgenomics/geo.py python/lib/ucscgenomics/geo.py
deleted file mode 100644
index 90d0e22..0000000
--- python/lib/ucscgenomics/geo.py
+++ /dev/null
@@ -1,96 +0,0 @@
-import urllib2, re, datetime
-
-# if the molecule is RNA, we need to map our data into !Sample_molecule, which only takes certain fields
-# first we check rnaExtractMapping. If its not there, we use the localization. This is because (at current)
-# polyA is the most important trait, otherwise its going to be nonPolyA which GEO doesn't accept. 
-rnaExtractMapping = {
-    'shortPolyA': 'polyA RNA', 
-    'longPolyA': 'polyA RNA', 
-    'polyA': 'polyA RNA'
-}
-
-localizationMapping = {
-    'cytosol': 'cytoplasmic RNA', 
-    'polysome': 'cytoplasmic RNA',
-    'membraneFraction': 'cytoplasmic RNA',
-    'mitochondria': 'cytoplasmic RNA',
-    'nucleus': 'nuclear RNA', 
-    'nucleolus': 'nuclear RNA', 
-    'nucleoplasm': 'nuclear RNA', 
-    'nuclearMatrix': 'nuclear RNA', 
-    'chromatin': 'nuclear RNA',
-    'cell': 'total RNA'
-}
-
-# map our instrument names to GEO's names
-instrumentModels = {
-    'Illumina_GA2x': 'Illumina Genome Analyzer II',
-    'Illumina_GA2': 'Illumina Genome Analyzer II',
-    'Illumina_HiSeq_2000': 'Illumina HiSeq 2000',
-    'Illumina_GA1': 'Illumina Genome Analyzer',
-    'Illumina_GA1_or_GA2': 'Illumina Genome Analyzer, Illumina Genome Analyzer II',
-    'SOLiD_Unknown': 'SOLiD',
-    'AB_SOLiD_3.5': 'AB SOLiD 3.5',
-    'Unknown': 'Illumina Genome Analyzer'
-}
-
-class Submission(object):
-    
-    @property
-    def accessions(self):
-        return self._accessions
-        
-    @property
-    def dateSubmitted(self):
-        return self._submitted
-    
-    @property
-    def dateUpdated(self):
-        return self._updated
-    
-    def __init__(self, geoId):
-        html = getHtml(geoId)
-        self._accessions = getGSE(html)
-        self._submitted = getDateSubmitted(html)
-        self._updated = getDateUpdated(html)
-        
-    def getSample(self, geoId):
-        html = getHtml(geoId)
-        return getGSM(html)
-
-def getHtml(geoId):
-    try:
-        response = urllib2.urlopen('http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=%s' % geoId)
-    except:
-        return None
-    return response.read()
-    
-def getGSE(html):
-    gsms = re.findall('(GSM[0-9]+)</a></td>\n<td valign="top">([^<]+)</td>', html)
-    d = dict()
-    for gsm in gsms:
-        d[gsm[1]] = gsm[0]
-    return d
-    
-def getGSM(html):
-    suppfiles = re.findall('<tr valign="top"><td bgcolor="#[0-9A-F]+">([^<]+)</td>', html)
-    d = dict()
-    for f in suppfiles:
-        print f
-        fname = f.rsplit('_', 1)[1]
-        d[fname] = fname
-    return d
-        
-    
-def getDateSubmitted(html):
-    datestr = re.search('<td>Submission date</td>\n<td>([^<]+)</td>', html)
-    if datestr == None:
-        return None
-    return datetime.datetime.strptime(datestr.group(1), '%b %d, %Y')
-    
-def getDateUpdated(html):
-    datestr = re.search('<td>Last update date</td>\n<td>([^<]+)</td>', html)
-    if datestr == None:
-        return None
-    return datetime.datetime.strptime(datestr.group(1), '%b %d, %Y')
-