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"""Configuration information about NCBI's databases"""
# Used to figure out if efetch supports the start, stop, strand, and
# complexity fields
PUBLICATION_TYPE = 0
SEQUENCE_TYPE = 1
# Map from database name to database type
class DatabaseInfo:
"""stores NCBI's name for the database and its type"""
def __init__(self, db, dbtype):
self.db = db
self.dbtype = dbtype
class DatabaseDict(dict):
"""map from name to DatabaseInfo for that database name
Entries are also available through attributes like PUBMED,
OMIM, and NUCLEOTIDE.
"""
def gettype(self, db, dbtype = None):
"""Given a database name and optional type, return the database type"""
if dbtype not in (None, SEQUENCE_TYPE, PUBLICATION_TYPE):
raise TypeError("Unknown database type: %r" % (dbtype,))
if dbtype is None:
dbtype = self[db].dbtype
return dbtype
databases = DatabaseDict()
def _add_db(x):
databases[x.db] = x
return x.db
# XXX Try these
# <option value="structure">Structure</option>
# <option value="pmc">PMC</option>
# <option value="taxonomy">Taxonomy</option>
# <option value="books">Books</option>
# <option value="geo">ProbeSet</option>
# <option value="domains">3D Domains</option>
# <option value="UniSts">UniSTS</option>
# <option value="cdd">Domains</option>
# <option value="snp">SNP</option>
# <option value="popset">PopSet</option>
databases.PUBMED = _add_db(DatabaseInfo("pubmed", 0))
databases.OMIM = _add_db(DatabaseInfo("omim", 0))
databases.JOURNALS = _add_db(DatabaseInfo("journals", 0))
databases.GENOME = _add_db(DatabaseInfo("genome", 1))
databases.NUCLEOTIDE = _add_db(DatabaseInfo("nucleotide", 1))
databases.PROTEIN = _add_db(DatabaseInfo("protein", 1))
databases.POPSET = _add_db(DatabaseInfo("popset", 1))
databases.SEQUENCES = _add_db(DatabaseInfo("sequences", 1))
databases.UNIGENE = _add_db(DatabaseInfo("unigene", 1))
databases.GENE = _add_db(DatabaseInfo("gene", 1))
# Someday I want to make it easier to get a given format. I would
# rather not have to specify the retmode/rettype pair, but I don't
# know what people want from this feature, so skip for now. Plus,
# it's harder than I thought.
##class FormatInfo:
## def __init__(self, name, retmode):
## self.name = name
## self.retmode = retmode
## self.rettype = rettype
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