Hierarchical namespace

.flake8

@@ -1,2 +1,2 @@
 [flake8]
-exclude = ga4gh/*_pb2.py,ga4gh/datamodel/obo_parser.py,docs,ez_setup.py
+exclude = ga4gh/server/datamodel/obo_parser.py,docs,ez_setup.py

.gitignore

@@ -12,7 +12,7 @@ scripts/auth.yml
 *.bak
 *.db-shm
 *.db-wal
-ga4gh/_version.py
+_version.py
 tests/data/registry.db
 
 # Below based off of https://gist.github.com/octocat/9257657

.travis.yml

@@ -11,7 +11,6 @@ install:
   - pip install pip --upgrade
 # RDFLib requres html5lib;  html5lib requires setuptools version 18.5 or above;
   - pip install setuptools==25.1.0
-  - pip install ga4gh-common # need ga4gh_common.setup for sdist
   - python setup.py sdist
   - pip install dist/ga4gh*.tar.gz
 # every installable in setup.py's entry_points should be tested here
@@ -33,7 +32,8 @@ script:
            ga2sam_dev.py ga2vcf_dev.py repo_dev.py server_dev.py
            setup.py
            tests ga4gh scripts
-  - nosetests --with-coverage --cover-package ga4gh
+  - python -mnose tests 
+              --with-coverage --cover-package ga4gh.server
               --cover-inclusive --cover-min-percentage 80
               --cover-branches --cover-erase
   - make clean -C docs

configtest_dev.py

@@ -1,7 +1,12 @@
 """
 Simple shim for running the configuration testing program during development.
 """
-import ga4gh.cli.configtest as cli_configtest
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import dev_glue  # NOQA
+import ga4gh.server.cli.configtest as cli_configtest
 
 if __name__ == "__main__":
     cli_configtest.configtest_main()

convert_error_code.py

@@ -8,7 +8,7 @@
 
 import argparse
 
-import ga4gh.exceptions as exceptions
+import ga4gh.server.exceptions as exceptions
 
 
 def parseArgs():

deploy/application.wsgi

@@ -1,5 +1,5 @@
 # This file is copied into place by the .whiskey/action_hooks/pre-build hook during Docker build
 
-from ga4gh.frontend import app as application
-import ga4gh.frontend as frontend
+from ga4gh.server.frontend import app as application
+import ga4gh.server.frontend as frontend
 frontend.configure("/srv/ga4gh/config.py")

dev_glue.py

@@ -0,0 +1,15 @@
+"""
+Glue for running server code during development
+
+Import this module before using any other module that imports ga4gh.server.
+Otherwise, python will look for server in the installed ga4gh package.
+
+See __path__ documentation at:
+    https://docs.python.org/2/tutorial/modules.html
+"""
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import ga4gh
+ga4gh.__path__.insert(0, 'ga4gh')

docs/conf.py

@@ -21,7 +21,12 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('..'))
 
+# the following two lines are similar ones to those in dev_glue.py
+# they enable python to find the ga4gh.server package
 import ga4gh
+ga4gh.__path__.insert(0, '../ga4gh')
+
+import ga4gh.server
 
 # -- General configuration ------------------------------------------------
 
@@ -62,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = ga4gh.__version__.split("+")[0]
+version = ga4gh.server.__version__.split("+")[0]
 # The full version, including alpha/beta/rc tags.
-release = ga4gh.__version__
+release = ga4gh.server.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/configuration.rst

@@ -43,7 +43,7 @@ file path. This is the first command that must be issued
 when creating a new GA4GH repository.
 
 .. argparse::
-    :module: ga4gh.cli.repomanager
+    :module: ga4gh.server.cli.repomanager
     :func: getRepoManagerParser
     :prog: ga4gh_repo
     :path: init
@@ -69,7 +69,7 @@ understand the structure of the repository that they are managing.
    of this command should improve considerably in the near future.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: list
@@ -99,7 +99,7 @@ well in their repository.
    of this command should improve considerably in the near future.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: verify
@@ -121,7 +121,7 @@ of ReadGroupSets, VariantSets, VariantAnnotationSets and FeatureSets. Each
 dataset has a name, which is used to identify it in the repository manager.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-dataset
@@ -149,7 +149,7 @@ number of metadata values (.e.g. ``ncbiTaxonId``) which can be set
 using command line options.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-referenceset
@@ -175,7 +175,7 @@ Adds a new biosample to the repository. The biosample argument is
 a JSON document according to the GA4GH JSON schema.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-biosample
@@ -198,7 +198,7 @@ Adds a new individual to the repository. The individual argument is
 a JSON document following the GA4GH JSON schema.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-individual
@@ -224,7 +224,7 @@ to ontology IDs. Sequence ontology definitions can be downloaded from
 the `Sequence Ontology site <https://github.com/The-Sequence-Ontology/SO-Ontologies>`_.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-ontology
@@ -254,7 +254,7 @@ provided using the ``-I`` option.
 .. todo:: Document adding VariantAnnotationSets using the -a option.
 
 .. argparse::
-    :module: ga4gh.cli.repomanager
+    :module: ga4gh.server.cli.repomanager
     :func: getRepoManagerParser
     :prog: ga4gh_repo
     :path: add-variantset
@@ -324,7 +324,7 @@ then the readgroup set will be associated with it automatically. If it does not
 name of the reference set using the ``--referenceSetName`` option.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-readgroupset
@@ -372,7 +372,7 @@ init-rnaquantificationset
 Initializes a rnaquantification set.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: init-rnaquantificationset
@@ -393,7 +393,7 @@ init-rnaquantificationset
 Initializes a rnaquantification set.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: init-rnaquantificationset
@@ -416,7 +416,7 @@ Adds a rnaquantification to a RNA quantification set.
 RNA quantification formats supported are currently kallisto and RSEM.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-rnaquantification
@@ -443,7 +443,7 @@ When the desired RNA quantification have been added to the set, use this command
 to add them to the registry.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-rnaquantificationset
@@ -469,7 +469,7 @@ Clinical Genomics Knowledge Base http://nif-crawler.neuinfo.org/monarch/ttl/cgd.
 published by the Monarch project, is the supported format for Evidence.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: add-phenotypeassociationset
@@ -491,7 +491,7 @@ Removes a dataset from the repository and recursively removes all
 objects (ReadGroupSets, VariantSets, etc) within this dataset.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-dataset
@@ -515,7 +515,7 @@ to remove a reference set that is referenced by other objects in the
 repository will result in an error.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-referenceset
@@ -537,7 +537,7 @@ remove-biosample
 Removes a biosample from the repository.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-biosample
@@ -559,7 +559,7 @@ remove-individual
 Removes an individual from the repository.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-individual
@@ -583,7 +583,7 @@ to remove an ontology that is referenced by other objects in the
 repository will result in an error.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-ontology
@@ -606,7 +606,7 @@ Removes a variant set from the repository. This also deletes all
 associated call sets and variant annotation sets from the repository.
 
 .. argparse::
-    :module: ga4gh.cli.repomanager
+    :module: ga4gh.server.cli.repomanager
     :func: getRepoManagerParser
     :prog: ga4gh_repo
     :path: remove-variantset
@@ -628,7 +628,7 @@ remove-readgroupset
 Removes a read group set from the repository.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-readgroupset
@@ -650,7 +650,7 @@ remove-rnaquantificationset
 Removes a rna quantification set from the repository.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-rnaquantificationset
@@ -672,7 +672,7 @@ remove-phenotypeassociationset
 Removes an rdf object store.
 
 .. argparse::
-   :module: ga4gh.cli.repomanager
+   :module: ga4gh.server.cli.repomanager
    :func: getRepoManagerParser
    :prog: ga4gh_repo
    :path: remove-phenotypeassociationset

docs/demo.rst

@@ -185,7 +185,7 @@ performed above, we can use the following code:
 
     from __future__ import print_function
 
-    import ga4gh_client.client as client
+    import ga4gh.client.client as client
 
     httpClient = client.HttpClient("http://localhost:8000")
     # Get the datasets on the server.
@@ -439,6 +439,6 @@ client's libraries for use in your own programs:
 
 .. code-block:: python
 
-    >>> import ga4gh_client.client as client
+    >>> import ga4gh.client.client as client
     >>> client.HttpClient
     <class 'ga4gh_client.client.HttpClient'>

docs/installation.rst

@@ -70,8 +70,8 @@ contents:
 
 .. code-block:: python
 
-    from ga4gh.frontend import app as application
-    import ga4gh.frontend as frontend
+    from ga4gh.server.frontend import app as application
+    import ga4gh.server.frontend as frontend
     frontend.configure("/srv/ga4gh/config.py")
 
 Create the configuration file at ``/srv/ga4gh/config.py``, and write the

ga2sam_dev.py

@@ -5,7 +5,8 @@
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import ga4gh.cli.ga2sam as ga2sam
+import dev_glue  # NOQA
+import ga4gh.server.cli.ga2sam as ga2sam
 
 if __name__ == "__main__":
     ga2sam.ga2sam_main()

ga2vcf_dev.py

@@ -5,7 +5,8 @@
 from __future__ import print_function
 from __future__ import unicode_literals
 
-import ga4gh.cli.ga2vcf as cli_ga2vcf
+import dev_glue  # NOQA
+import ga4gh.server.cli.ga2vcf as cli_ga2vcf
 
 if __name__ == "__main__":
     cli_ga2vcf.ga2vcf_main()

ga4gh/__init__.py

@@ -1,10 +1,8 @@
 """
-Reference implementation of the GA4GH APIs.
+GA4GH server
 """
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
 
-__version__ = "undefined"
-try:
-    from . import _version
-    __version__ = _version.version
-except ImportError:
-    pass
+__import__('pkg_resources').declare_namespace(__name__)

ga4gh/server/__init__.py

@@ -0,0 +1,12 @@
+"""
+Reference implementation of the GA4GH APIs.
+"""
+# Don't include future imports here; we don't want to export them as
+# part of the package
+
+__version__ = "undefined"
+try:
+    from . import _version
+    __version__ = _version.version
+except ImportError:
+    pass