Merge pull request #31 from solvebio/feature/annotate-broken

Feature/annotate broken

requirements.txt

@@ -0,0 +1,2 @@
+ipython
+nose

solvebio/__init__.py

@@ -68,9 +68,7 @@ def emit(self, record):
 
 from . import version
 from .errors import SolveError
-from .resource import (User, Depository, DepositoryVersion, Dataset,  # noqa
-                       DatasetField, Annotation, Sample)
-from .query import Query, PagingQuery, BatchQuery, Filter, RangeFilter  # noqa
+from .query import Query, PagingQuery,  Filter, RangeFilter
 
 __all__ = ['version',
            'Annotation'

solvebio/resource/__init__.py

@@ -1,13 +1,14 @@
 """Glues together all SolveObjects"""
-# For the future...
-# from Dataset import Dataset
-# from DatasetField import DatasetField
-from depository import Depository
-from depositoryversion import DepositoryVersion
-from resource import Dataset, User, \
-    ListObject, DatasetField
+# __package__ = 'solvebio.resource'
+
+from .depository import Depository
+from .depositoryversion import DepositoryVersion
+from .resource import ListObject
 from .annotation import Annotation
-from .sample     import Sample
+from .sample import Sample
+from .user import User
+from .dataset import Dataset
+from .datasetfield import DatasetField
 
 
 types = {

solvebio/resource/dataset.py

@@ -0,0 +1,77 @@
+"""Dataset Class"""
+import re
+
+# __package__ = 'solvebio.resource'
+from ..client import client
+from ..help import open_help
+from ..query import Query, PagingQuery
+
+from .solveobject import convert_to_solve_object
+from .resource import CreateableAPIResource, ListableAPIResource, \
+    UpdateableAPIResource
+from .datasetfield import DatasetField
+
+
+class Dataset(CreateableAPIResource, ListableAPIResource,
+              UpdateableAPIResource):
+    """
+    Datasets are access points to data. Dataset names are unique
+    within versions of a depository.
+    """
+    ALLOW_FULL_NAME_ID = True
+    FULL_NAME_REGEX = r'^([\w\d\-\.]+/){2}[\w\d\-\.]+$'
+
+    @classmethod
+    def retrieve(cls, id, **params):
+        """Supports lookup by full name"""
+        if isinstance(id, unicode) or isinstance(id, str):
+            _id = unicode(id).strip()
+            id = None
+            if re.match(cls.FULL_NAME_REGEX, _id):
+                params.update({'full_name': _id})
+            else:
+                raise Exception('Unrecognized full name.')
+
+        return super(Dataset, cls).retrieve(id, **params)
+
+    def depository_version(self):
+        from .depositoryversion import DepositoryVersion
+        return DepositoryVersion.retrieve(self['depository_version'])
+
+    def depository(self):
+        from .depository import Depository
+        return Depository.retrieve(self['depository'])
+
+    def fields(self, name=None, **params):
+        if 'fields_url' not in self:
+            raise Exception(
+                'Please use Dataset.retrieve({ID}) before doing looking '
+                'up fields')
+
+        if name:
+            # construct the field's full_name if a field name is provided
+            return DatasetField.retrieve(
+                '/'.join([self['full_name'], name]))
+
+        response = client.request('get', self.fields_url, params)
+        return convert_to_solve_object(response)
+
+    def _data_url(self):
+        if 'data_url' not in self:
+            if 'id' not in self or not self['id']:
+                raise Exception(
+                    'No Dataset ID was provided. '
+                    'Please instantiate the Dataset '
+                    'object with an ID or full_name.')
+            # automatically construct the data_url from the ID
+            return self.instance_url() + u'/data'
+        return self['data_url']
+
+    def query(self, paging=False, **params):
+        self._data_url()  # raises an exception if there's no ID
+        query_klass = PagingQuery if paging else Query
+        q = query_klass(self['id'], **params)
+        return q.filter(params.get('filters')) if params.get('filters') else q
+
+    def help(self):
+        open_help(self['full_name'])

solvebio/resource/datasetfield.py

@@ -0,0 +1,39 @@
+"""DatasetField Class"""
+import re
+
+from ..client import client
+
+from .solveobject import convert_to_solve_object
+from .resource import CreateableAPIResource, ListableAPIResource, \
+    UpdateableAPIResource
+
+
+class DatasetField(CreateableAPIResource, ListableAPIResource,
+                   UpdateableAPIResource):
+    """
+    Each SolveBio dataset has a different set of fields, some of
+    which can be used as filters. Dataset field resources provide
+    users with documentation about each field.
+    """
+    ALLOW_FULL_NAME_ID = True
+    FULL_NAME_REGEX = r'^([\w\d\-\.]+/){3}[\w\d\-\.]+$'
+
+    @classmethod
+    def retrieve(cls, id, **params):
+        """Supports lookup by ID or full name"""
+        if isinstance(id, unicode) or isinstance(id, str):
+            _id = unicode(id).strip()
+            id = None
+            if re.match(cls.FULL_NAME_REGEX, _id):
+                params.update({'full_name': _id})
+            else:
+                raise Exception('Unrecognized full name.')
+
+        return super(DatasetField, cls).retrieve(id, **params)
+
+    def facets(self, **params):
+        response = client.request('get', self.facets_url, params)
+        return convert_to_solve_object(response)
+
+    def help(self):
+        return self.facets()

solvebio/resource/depository.py

@@ -1,10 +1,16 @@
 """Depository Class"""
-
-from resource import CreateableAPIResource, ListableAPIResource, \
-     SearchableAPIResource, UpdateableAPIResource
-from solveobject import convert_to_solve_object
+# __package__ = 'solvebio.resource'
 import re
 
+from ..client import client
+from ..help import open_help
+
+from .solveobject import convert_to_solve_object
+from .resource import CreateableAPIResource, ListableAPIResource, \
+    SearchableAPIResource, UpdateableAPIResource
+from .depositoryversion import DepositoryVersion
+
+
 class Depository(CreateableAPIResource, ListableAPIResource,
                  SearchableAPIResource, UpdateableAPIResource):
     """

solvebio/resource/depositoryversion.py

@@ -1,10 +1,15 @@
 """DepositoryVersion Class"""
-
-from resource import CreateableAPIResource, ListableAPIResource, \
-     UpdateableAPIResource
-from solveobject import convert_to_solve_object
 import re
 
+from ..client import client
+from ..help import open_help
+
+from .solveobject import convert_to_solve_object
+from .resource import CreateableAPIResource, ListableAPIResource, \
+    UpdateableAPIResource
+from .dataset import Dataset
+
+
 class DepositoryVersion(CreateableAPIResource, ListableAPIResource,
                         UpdateableAPIResource):
 

solvebio/resource/resource.py

@@ -1,18 +1,13 @@
 # -*- coding: utf-8 -*-
 import urllib
-import re
 
 from ..client import client
-from ..query import Query, PagingQuery
-from ..help import open_help
 
 from .util import class_to_api_name
 from .solveobject import SolveObject, convert_to_solve_object
 
 
 class APIResource(SolveObject):
-    #    from pydbgr.api import debug; debug()
-    #    types[self.__class__.__name__] = self
 
     @classmethod
     def retrieve(cls, id, **params):
@@ -159,93 +154,3 @@ class DeletableAPIResource(APIResource):
     def delete(self, **params):
         self.refresh_from(self.request('delete', self.instance_url(), params))
         return self
-
-
-# API resources
-
-class User(SingletonAPIResource):
-    pass
-
-class Dataset(CreateableAPIResource, ListableAPIResource,
-              UpdateableAPIResource):
-    ALLOW_FULL_NAME_ID = True
-    FULL_NAME_REGEX = r'^([\w\d\-\.]+/){2}[\w\d\-\.]+$'
-
-    @classmethod
-    def retrieve(cls, id, **params):
-        """Supports lookup by full name"""
-        if isinstance(id, unicode) or isinstance(id, str):
-            _id = unicode(id).strip()
-            id = None
-            if re.match(cls.FULL_NAME_REGEX, _id):
-                params.update({'full_name': _id})
-            else:
-                raise Exception('Unrecognized full name.')
-
-        return super(Dataset, cls).retrieve(id, **params)
-
-    def depository_version(self):
-        return DepositoryVersion.retrieve(self['depository_version'])
-
-    def depository(self):
-        return Depository.retrieve(self['depository'])
-
-    def fields(self, name=None, **params):
-        if 'fields_url' not in self:
-            raise Exception(
-                'Please use Dataset.retrieve({ID}) before doing looking '
-                'up fields')
-
-        if name:
-            # construct the field's full_name if a field name is provided
-            return DatasetField.retrieve(
-                '/'.join([self['full_name'], name]))
-
-        response = client.request('get', self.fields_url, params)
-        return convert_to_solve_object(response)
-
-    def _data_url(self):
-        if 'data_url' not in self:
-            if 'id' not in self or not self['id']:
-                raise Exception(
-                    'No Dataset ID was provided. '
-                    'Please instantiate the Dataset '
-                    'object with an ID or full_name.')
-            # automatically construct the data_url from the ID
-            return self.instance_url() + u'/data'
-        return self['data_url']
-
-    def query(self, paging=False, **params):
-        self._data_url()  # raises an exception if there's no ID
-        query_klass = PagingQuery if paging else Query
-        q = query_klass(self['id'], **params)
-        return q.filter(params.get('filters')) if params.get('filters') else q
-
-    def help(self):
-        open_help(self['full_name'])
-
-
-class DatasetField(CreateableAPIResource, ListableAPIResource,
-                   UpdateableAPIResource):
-    ALLOW_FULL_NAME_ID = True
-    FULL_NAME_REGEX = r'^([\w\d\-\.]+/){3}[\w\d\-\.]+$'
-
-    @classmethod
-    def retrieve(cls, id, **params):
-        """Supports lookup by ID or full name"""
-        if isinstance(id, unicode) or isinstance(id, str):
-            _id = unicode(id).strip()
-            id = None
-            if re.match(cls.FULL_NAME_REGEX, _id):
-                params.update({'full_name': _id})
-            else:
-                raise Exception('Unrecognized full name.')
-
-        return super(DatasetField, cls).retrieve(id, **params)
-
-    def facets(self, **params):
-        response = client.request('get', self.facets_url, params)
-        return convert_to_solve_object(response)
-
-    def help(self):
-        return self.facets()

solvebio/resource/sample.py

@@ -38,7 +38,8 @@ def create(cls, genome_build, **params):
         """
         if 'vcf_url' in params:
             if 'vcf_file' in params:
-                raise TypeError('Specified both vcf_url and vcf_file; use only one')
+                raise TypeError('Specified both vcf_url and vcf_file; ' +
+                                'use only one')
             return Sample.create_from_url(genome_build, params['vcf_url'])
         elif 'vcf_file' in params:
             return Sample.create_from_file(genome_build, params['vcf_file'])

solvebio/resource/solveobject.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 from ..client import client
+
 from .util import json
 
 

solvebio/resource/user.py

@@ -0,0 +1,6 @@
+# -*- coding: utf-8 -*-
+from .resource import SingletonAPIResource
+
+
+class User(SingletonAPIResource):
+    pass

solvebio/test/__init__.py

@@ -5,19 +5,27 @@
 
 
 def all_names():
-    for _, modname, _ in pkgutil.iter_modules(__path__):
+    for i, modname, j in pkgutil.iter_modules(__path__):
+        print i, j
+        print modname
         # FIXME: figure out why test loader can't resolve
         # solvebio.test.test_conversion
-        if modname == 'test_conversion':
-            continue
-        if modname.startswith('test_modify_'):
-            continue
+        # if modname in ('test_conversion',
+        #                # 'test_annotation_access',
+        #                # 'test_query',
+        #                # 'test_query_batch',
+        #                # 'test_query_paging',
+        #                # 'test_sample_access',
+        #                # 'test_sample',
+        #                'test_annotation'):
+        #     continue
         if modname.startswith('test_'):
             yield 'solvebio.test.' + modname
 
 
 def all():
-    return unittest.defaultTestLoader.loadTestsFromNames(all_names())
+    names = [name for name in all_names()]
+    return unittest.defaultTestLoader.loadTestsFromNames(names)
 
 # def unit():
 #     unit_names = [name for name in all_names() if 'integration' not in name]

solvebio/test/query_helper.py

@@ -2,6 +2,7 @@
 import os
 import re
 import unittest
+
 import solvebio
 
 TEST_DATASET_NAME = 'ClinVar/2.0.0-1/Variants'

solvebio/test/test_annotation.py

@@ -1,7 +1,8 @@
 import unittest
 import os
 
-from solvebio import Annotation, SolveError
+from solvebio.errors import SolveError
+from solvebio.resource import Annotation
 
 
 class AnnotationTest(unittest.TestCase):

solvebio/test/test_annotation_access.py

@@ -1,7 +1,7 @@
 import unittest
 import os
 
-from solvebio import Annotation
+from solvebio.resource import Annotation
 
 
 @unittest.skipUnless('TEST_SOLVEBIO_API_UPDATE' in os.environ,