class BioSQLDatabaseAddForm(AddFormBase):
"""Add form """
form_fields = form.Fields(IBioSQLDatabase)
label = _(u"Add BioSQLDatabase")
form_name = _(u"Edit BioSQLDatabase")
def create(self, data):
root = self.context.getBioSQLRoot()
dbserver = root.getDBServer()
biodb = dbserver.new_database(data['id'], description=data.get("description", None))
dbserver.commit()
object = root[data['id']]
# TODO: test catalog object
return object
def upload_data(self, data, dbtype):
error = ISeqRecordUploader(self.context).loadData(data, dbtype)
if error:
return error
else:
return _("Updated ${data} of ${dbtype} on ${date_time}",
mapping={'date_time': repr(datetime.utcnow()),
'data': repr(data),
'dbtype': dbtype})
def upload_data(self, data, dbtype):
error = ISeqRecordUploader(self.context).loadData(data, dbtype)
if error:
return error
else:
return _("Updated ${data} of ${dbtype} on ${date_time}",
mapping={
'date_time': repr(datetime.utcnow()),
'data': repr(data),
'dbtype': dbtype
})
class BioSQLSeqRecordAddForm(AddFormBase):
"""Add form """
label = _(u"Add BioSQLSeqRecord")
form_name = _(u"Edit BioSQLSeqRecord")
def create(self, data):
seqrecord = SeqRecord(title=data['title'])
form.applyChanges(seqrecord, self.form_fields, data)
# TODO: id policy
seqrecord.id = seqrecord.title
# root = self.context.getBioSQLRoot()
# dbserver = root.getDBServer()
db = aq_inner(self.context.context)
biodb = db.getDatabase(reload=True)
# aq_inner(self.context.context).getDatabase().adaptor.conn.is_valid
# dbserver.adaptor.conn.is_valid
if biodb.load([seqrecord.seqrecord,]) == 1:
bioentry_id = biodb.adaptor.last_id('bioentry')
biodb.adaptor.commit()
db.keys(reload=True)
obj = db[str(bioentry_id)]
obj._getSeqRecord(reload=True)
else:
obj = None
return obj
class BioSQLSeqRecordEditForm(EditFormBase):
"""Edit form """
form_fields = form.Fields(IBioSQLSeqRecord)
label = _(u"Edit BioSQLSeqRecord")
form_name = _(u"Edit BioSQLSeqRecord")
class BioSQLDatabaseEditForm(EditFormBase):
"""Edit form """
form_fields = form.Fields(IBioSQLDatabase)
label = _(u"Edit BioSQLDatabase")
form_name = _(u"Edit BioSQLDatabase")
return self.annotations['organism']
else:
return ""
organism = property(fget=getOrganism)
def getAccessions(self):
if self.annotations.has_key('accessions'):
return self.annotations['accessions']
else:
return ""
accessions = property(fget=getAccessions)
def getTaxonomy(self):
if self.annotations.has_key('taxonomy'):
return self.annotations['taxonomy']
else:
return []
taxonomy = property(fget=getTaxonomy)
def alphabetClass(self):
return self.seqrecord.seq.alphabet.__class__
InitializeClass(BioSQLSeqRecord)
bioSQLSeqRecordFactory = Factory(BioSQLSeqRecord,
title=_(u"Create a new BioSQL SeqRecord"))
atapi.StringField("dsn",
required=True,
widget=atapi.StringWidget(label="dsn",
label_msgid="dsn_label",
description="DSN "
"... "
"...",
description_msgid="dsn_help",
i18n_domain="plone4bio")),
atapi.StringField(
"seqrecord_key",
required=True,
enforceVocabulary=True,
default='bioentry_id',
vocabulary=[
("bioentry_id", _(u"bioentry_id")),
("accession", _(u"accession")),
("version", _(u"accession.version")),
],
widget=atapi.SelectionWidget(
label="seqrecord_key",
label_msgid="seqrecord_key_label",
description=_(u"select the field name key for seqrecord uris"),
description_msgid="seqrecord_key_help",
i18n_domain="plone4bio")),
))
class BioSQLRoot(ATCTContent):
portal_type = 'BioSQLRoot'
# If 'spec' is specified, returns objects whose meta_type
# matches 'spec'.
assert spec is None, 'spec argument unsupported'
return self.__iter__()
security.declareProtected(access_contents_information, 'objectValues')
def objectValues(self, spec=None):
# Returns a list of actual subobjects of the current object.
# If 'spec' is specified, returns only objects whose meta_type
# match 'spec'.
assert spec is None, 'spec argument unsupported'
return self.itervalues()
security.declareProtected(access_contents_information, 'objectItems')
def objectItems(self, spec=None):
# Returns a list of (id, subobject) tuples of the current object.
# If 'spec' is specified, returns only objects whose meta_type match
# 'spec'
assert spec is None, 'spec argument unsupported'
return self.iteritems()
# mix in selected methods from DictMixin
# We don't want *everything* because some cause problems for us
for m in ('__contains__', 'iterkeys', 'itervalues', 'values', 'items', 'get'):
setattr(BioSQLDatabase, m, getattr(DictMixin, m).im_func)
InitializeClass(BioSQLDatabase)
bioSQLDatabaseFactory = Factory(BioSQLDatabase, title=_(u"Create a new BioSQL Database"))
class IPlone4BioConfigurationSchema(Interface):
dbxref_patterns = List(title=u'Dbxref patterns',
description=_(u'help_dbxref_patterns', ),
value_type=Object(IDbxrefPattern,
title=u"dbxref pattern"))
class Plone4BioControlPanel(ControlPanelForm):
form_fields = FormFields(IPlone4BioConfigurationSchema)
form_fields['dbxref_patterns'].custom_widget = DbxrefPatternsWidget
label = _('Dbxrefs Patterns settings')
description = _('Dbxrefs Patterns.')
form_name = _('Dbxrefs Patterns')
atapi.StringField("dsn",
required = True,
widget = atapi.StringWidget(
label = "dsn",
label_msgid = "dsn_label",
description = "DSN "
"... "
"...",
description_msgid = "dsn_help",
i18n_domain = "plone4bio")
),
atapi.StringField("seqrecord_key",
required = True,
enforceVocabulary = True,
default = 'bioentry_id',
vocabulary = [("bioentry_id", _(u"bioentry_id")),
("accession", _(u"accession")),
("version", _(u"accession.version")),
],
widget = atapi.SelectionWidget(
label = "seqrecord_key",
label_msgid = "seqrecord_key_label",
description = _(u"select the field name key for seqrecord uris"),
description_msgid = "seqrecord_key_help",
i18n_domain = "plone4bio")
),
))
class BioSQLRoot(ATCTContent):
portal_type='BioSQLRoot'
class IBioSQLDatabase(IBioSQLProxy):
""" IReadContainer """
id = schema.TextLine(title=_(u"biodatabase_id"), required=True)
# authority = schema.TextLine(title=_(u"authority"))
description = schema.Text(title=_(u"description"))
return []
references = property(fget=getReferences)
def getOrganism(self):
if self.annotations.has_key('organism'):
return self.annotations['organism']
else:
return ""
organism = property(fget=getOrganism)
def getAccessions(self):
if self.annotations.has_key('accessions'):
return self.annotations['accessions']
else:
return ""
accessions = property(fget=getAccessions)
def getTaxonomy(self):
if self.annotations.has_key('taxonomy'):
return self.annotations['taxonomy']
else:
return []
taxonomy = property(fget=getTaxonomy)
def alphabetClass(self):
return self.seqrecord.seq.alphabet.__class__
InitializeClass(BioSQLSeqRecord)
bioSQLSeqRecordFactory = Factory(BioSQLSeqRecord, title=_(u"Create a new BioSQL SeqRecord"))