Remove protocol.py

Issue BD2KGenomics/ga4gh-integration-deprecated#53

ga4gh/server/backend.py

@@ -8,8 +8,10 @@
 
 import ga4gh.server.datamodel as datamodel
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
 import ga4gh.server.paging as paging
+import ga4gh.server.response_builder as response_builder
+
+import ga4gh.schemas.protocol as protocol
 
 
 class Backend(object):
@@ -579,7 +581,7 @@ def runSearchRequest(
             request.page_size = self._defaultPageSize
         if request.page_size < 0:
             raise exceptions.BadPageSizeException(request.page_size)
-        responseBuilder = protocol.SearchResponseBuilder(
+        responseBuilder = response_builder.SearchResponseBuilder(
             responseClass, request.page_size, self._maxResponseLength)
         nextPageToken = None
         for obj, nextPageToken in objectGenerator(request):

ga4gh/server/cli/__init__.py

@@ -6,7 +6,8 @@
 from __future__ import unicode_literals
 
 import ga4gh.server
-import ga4gh.server.protocol as protocol
+
+import ga4gh.schemas.protocol as protocol
 
 # the maximum value of a long type in avro = 2**63 - 1
 # (64 bit signed integer)

ga4gh/server/converters.py

@@ -11,7 +11,8 @@
 import pysam
 
 import ga4gh.server.datamodel.reads as reads
-import ga4gh.server.protocol as protocol
+
+import ga4gh.schemas.protocol as protocol
 
 
 class AbstractConverter(object):

ga4gh/server/datamodel/__init__.py

@@ -13,7 +13,8 @@
 import os
 
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
+
+import ga4gh.schemas.protocol as protocol
 
 
 class PysamFileHandleCache(object):

ga4gh/server/datamodel/bio_metadata.py

@@ -9,9 +9,10 @@
 import json
 
 import ga4gh.server.datamodel as datamodel
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 
+import ga4gh.schemas.protocol as protocol
+
 
 class Biosample(datamodel.DatamodelObject):
     """

ga4gh/server/datamodel/datasets.py

@@ -10,12 +10,12 @@
 import ga4gh.server.datamodel.sequence_annotations as sequence_annotations
 import ga4gh.server.datamodel.variants as variants
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
 import ga4gh.server.datamodel.bio_metadata as biodata
 import ga4gh.server.datamodel.genotype_phenotype as g2p
 import ga4gh.server.datamodel.rna_quantification as rnaQuantification
 
 import ga4gh.schemas.pb as pb
+import ga4gh.schemas.protocol as protocol
 
 
 class Dataset(datamodel.DatamodelObject):

ga4gh/server/datamodel/genotype_phenotype.py

@@ -11,7 +11,8 @@
 
 import ga4gh.server.datamodel as datamodel
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
+
+import ga4gh.schemas.protocol as protocol
 
 # annotation keys
 TYPE = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'

ga4gh/server/datamodel/genotype_phenotype_featureset.py

@@ -12,10 +12,11 @@
 from rdflib import RDF
 
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
 import ga4gh.server.datamodel.sequence_annotations as sequence_annotations
 import ga4gh.server.datamodel.genotype_phenotype as g2p
 
+import ga4gh.schemas.protocol as protocol
+
 # annotation keys
 TYPE = 'http://www.w3.org/1999/02/22-rdf-syntax-ns#type'
 LABEL = 'http://www.w3.org/2000/01/rdf-schema#label'

ga4gh/server/datamodel/ontologies.py

@@ -8,10 +8,11 @@
 import collections
 import os.path
 
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 import ga4gh.server.datamodel.obo_parser as obo_parser
 
+import ga4gh.schemas.protocol as protocol
+
 
 SEQUENCE_ONTOLOGY_PREFIX = "SO"
 

ga4gh/server/datamodel/reads.py

@@ -16,9 +16,9 @@
 import ga4gh.server.datamodel as datamodel
 import ga4gh.server.datamodel.references as references
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
 
 import ga4gh.schemas.pb as pb
+import ga4gh.schemas.protocol as protocol
 
 
 def parseMalformedBamHeader(headerDict):

ga4gh/server/datamodel/references.py

@@ -13,10 +13,10 @@
 import pysam
 
 import ga4gh.server.datamodel as datamodel
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 
 import ga4gh.schemas.pb as pb
+import ga4gh.schemas.protocol as protocol
 
 
 DEFAULT_REFERENCESET_NAME = "Default"

ga4gh/server/datamodel/rna_quantification.py

@@ -7,10 +7,11 @@
 from __future__ import unicode_literals
 
 import ga4gh.server.datamodel as datamodel
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 import ga4gh.server.sqlite_backend as sqlite_backend
 
+import ga4gh.schemas.protocol as protocol
+
 
 """
     The RNA Quantifications associated with a GA4GH dataset reside in a sqlite

ga4gh/server/datamodel/sequence_annotations.py

@@ -9,12 +9,12 @@
 import json
 import random
 
-import ga4gh.server.protocol as protocol
 import ga4gh.server.datamodel as datamodel
 import ga4gh.server.sqlite_backend as sqlite_backend
 import ga4gh.server.exceptions as exceptions
 
 import ga4gh.schemas.pb as pb
+import ga4gh.schemas.protocol as protocol
 
 # Note to self: There's the Feature ID as understood in a GFF3 file,
 # the Feature ID that is its server-assigned compoundId, and the

ga4gh/server/datamodel/variants.py

@@ -16,12 +16,12 @@
 
 import pysam
 
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 import ga4gh.server.datamodel as datamodel
 
 import ga4gh.schemas.pb as pb
 import ga4gh.schemas.ga4gh.common_pb2 as common_pb2
+import ga4gh.schemas.protocol as protocol
 
 
 ANNOTATIONS_VEP_V82 = "VEP_v82"

ga4gh/server/datarepo.py

@@ -22,10 +22,11 @@
 import ga4gh.server.datamodel.genotype_phenotype_featureset as g2pFeatureset
 import ga4gh.server.datamodel.rna_quantification as rna_quantification
 import ga4gh.server.exceptions as exceptions
-import ga4gh.server.protocol as protocol
 
 import repo.models as m
 
+import ga4gh.schemas.protocol as protocol
+
 MODE_READ = 'r'
 MODE_WRITE = 'w'
 

ga4gh/server/exceptions.py

@@ -11,7 +11,7 @@
 import inspect
 import json
 
-import ga4gh.server.protocol as protocol
+import ga4gh.schemas.protocol as protocol
 
 
 def getExceptionClass(errorCode):

ga4gh/server/frontend.py

@@ -28,12 +28,12 @@
 import ga4gh.server
 import ga4gh.server.backend as backend
 import ga4gh.server.datamodel as datamodel
-import ga4gh.server.protocol as protocol
 import ga4gh.server.exceptions as exceptions
 import ga4gh.server.datarepo as datarepo
-
 import ga4gh.server.auth as auth
 
+import ga4gh.schemas.protocol as protocol
+
 
 MIMETYPE = "application/json"
 SEARCH_ENDPOINT_METHODS = ['POST', 'OPTIONS']