DBD: Transcription factor prediction database

Release 2.0
www.transcriptionfactor.org
Sequence ID search:
An error occured in context "Search/Domain" cell "1.00"
in the section containing the code:
001 
002 
003 import dbd, sys
004 
005 cellhead()
006 
007 params = dbd.parse_params()
008 
009 domainlike = None
010 domain = None
011 
012 if params.has_key("domainlike") and params.has_key("cat"):
013 	domainlike = params["domainlike"]
014 	cat = params["cat"]
015 elif params.has_key("domainlike"):
016 	domainlike = params["domainlike"]
017 	cat = 'DBD'
018 elif session.has_key("domainlike") and session.has_key("cat"):
019 	domainlike = session["domainlike"]
020 	cat = session["cat"]
021 elif session.has_key("domainlike"):
022 	domainlike = session["domainlike"]
023 	cat = 'DBD'
024 elif params.has_key("id") and params.has_key("cat"):
025 	domain = params["id"]
026 	cat = params["cat"]
027 elif params.has_key("id"):
028 	domain = params["id"]
029 	cat = 'DBD'
030 elif session.has_key("id") and session.has_key("cat"):
031 	domain = session["id"]
032 	cat = session["cat"]
033 elif session.has_key("id"):
034 	domain = session["id"]
035 	cat = 'DBD'
036 elif params.has_key("domain") and params.has_key("cat"):
037 	domain = params["domain"]
038 	cat = params["cat"]
039 elif params.has_key("domain"):
040 	domain = params["domain"]
041 	cat = 'DBD'
042 elif session.has_key("domain") and session.has_key("cat"):
043 	domain = session["domain"]
044 	cat = session["cat"]
045 elif session.has_key("domain"):
046 	domain = session["domain"]
047 	cat = 'DBD'
048 else:
049 	print "Error"
050 	cellbody()
051 	dbd.print_error_cell("Please specify a model id and model category")
052 	cellend()
053 	sys.exit()
054 
055 page = 0
056 limit = dbd.RECORDS_PER_PAGE
057 if params.has_key("page"):
058         page = int(params["page"])
059 if params.has_key("limit"):
060         limit = int(params["limit"])
061 
062 
063 if domainlike:
064 	print "Binding category: %s Domain search: %s" %(cat, domainlike)
065 	cellbody()
066 	dbd.print_domain_table(globals.HomeURLBase, dbd.IMAGE_GEN_DIR, dbd.model_by_search_domain, cat, domainlike)
067 else:
068 	for row in dbd.get_family_name_by_model(domain):
069 		[family_name] = row
070 		print """Binding category: %s. Domain search: %s.""" %(cat, family_name)
071 	cellbody()
072         print """<blockquote><p> Each predicted transcription factor is displayed with its SUPERFAMILY (SF) as well as PFAM (PF) architecture. <br> """ 
073         print """ The domain architectures are represented as colored rectangles and oblongs on a black line corresponding to the polypeptide chain. <br> """
074 	print """ The oblongs represent DNA-binding domains, and the rectangles represent domains with other functions. <br> """
075         print """ The numbers inside the SF rectangles represent the SF database identifier for that protein superfamily, and are linked to a description. <br> """
076         print """ The PFAM identifiers inside the boxes are also linked to descriptions of the family. <br> """
077         print """ All the domains belonging to one family have the same colored rectangle. <br> """
078         print """ Colors are reused for different families, so that two different families can be represented by the same color. </p> """
079         print """<p> The full repertoire of transcription factors may be distributed across several pages of results. <br> """
080         print """ These can be accessed by clicking on the individual page numbers, or downloading the entire set of results from the <a href="%s?Download">Download</a> section. </p><br> """ %globals.HomeURLBase
081 	dbd.print_tfs_table(globals.HomeURLBase, globals.Context, dbd.IMAGE_GEN_DIR, dbd.tfs_by_model, cat, domain, limit=limit, page=page)
082 
083 
084 cellend()
085 
086 
Traceback (most recent call last):
  File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/web.py", line 148, in gen_cell
    exec _code in _globals_d, _locals_d
  File "<string>", line 68, in <module>
  File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/dbd.py", line 518, in get_family_name_by_model
    c = get_db_cursor()
  File "/net/isilonP/public/rw/research/teichmann/apache/test/DBD/dbd.py", line 68, in get_db_cursor
    db = MySQLdb.connect(host="mysql-teichmann-web.ebi.ac.uk", port=4412, user="admin", passwd="z2Kd6OvN", db="DBD2")
  File "/usr/lib64/python2.6/site-packages/MySQLdb/__init__.py", line 81, in Connect
    return Connection(*args, **kwargs)
  File "/usr/lib64/python2.6/site-packages/MySQLdb/connections.py", line 187, in __init__
    super(Connection, self).__init__(*args, **kwargs2)
OperationalError: (2003, "Can't connect to MySQL server on 'mysql-teichmann-web.ebi.ac.uk' (111)")