clean up / fix build system

.gitignore

@@ -91,3 +91,12 @@ ENV/
 
 # swagger in the python directory
 python/ga4gh/dos/data_objects_service.swagger.json
+
+# Documentation build system artifacts
+.gradle/
+docs/html5/
+docs/pdf/
+docs/asciidoc/swagger2markup/
+spec/
+web_deploy/
+node_modules/

.travis.yml

@@ -49,6 +49,8 @@ jobs:
       - "./scripts/fetchpages.sh"
       - "./gradlew installSwagger buildSwagger asciidoctor"
       - "./scripts/stagepages.sh"
+      before_deploy:
+      - "mv misc/.gitignore .gitignore"
       deploy:
         provider: pages
         skip_cleanup: true

misc/.gitignore

@@ -0,0 +1,119 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+# lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+# swagger in the python directory
+python/ga4gh/dos/data_objects_service.swagger.json
+
+# Documentation build system artifacts
+.gradle/
+docs/html5/
+docs/pdf/
+docs/asciidoc/swagger2markup/
+spec/
+web_deploy/
+node_modules/
+
+# Non-pages content
+docs/asciidoc/
+python
+setup.py
+requirements.txt
+gradle
+build.gradle
+settings.gradle
+gradlew
+scripts
+misc
+openapi
+package.json
+package-lock.json
+Makefile
+merge_yaml.py
+.travis.yml

openapi/data_repository_service.swagger.yaml

@@ -2,7 +2,7 @@ swagger: '2.0'
 basePath: '/ga4gh/drs/v1'
 info:
   title: Data Repository Service
-  version: 0.1.0
+  version: 0.1.1
   description: 'https://github.com/ga4gh/data-repository-service-schemas'
   termsOfService: 'https://www.ga4gh.org/terms-and-conditions/'
   contact:
@@ -76,7 +76,7 @@ paths:
       x-swagger-router-controller: ga4gh.drs.server
   '/objects/{object_id}/access/{access_id}':
     get:
-      summary: Get a URL for fetching bytes. 
+      summary: Get a URL for fetching bytes.
       description: >-
         Returns a URL that can be used to fetch the bytes of an `Object`.
 
@@ -200,33 +200,33 @@ definitions:
           $ref: '#/definitions/Checksum'
         description: >-
           The checksum of the `Object`. At least one checksum must be provided.
-          
+
           For blobs, the checksum is computed over the bytes in the blob.
-          
-          
-          For bundles, the checksum is computed over a sorted concatenation of the 
+
+
+          For bundles, the checksum is computed over a sorted concatenation of the
           checksums of its top-level contained objects (not recursive, names not included).
           The list of checksums is sorted alphabetically (hex-code) before concatenation
           and a further checksum is performed on the concatenated checksum value.
-          
-          
+
+
           For example, if a bundle contains blobs with the following checksums:
-          
+
           md5(blob1) = 72794b6d
-          
-          md5(blob2) = 5e089d29   
-          
-          
+
+          md5(blob2) = 5e089d29
+
+
           Then the checksum of the bundle is:
-          
+
           md5( concat( sort( md5(blob1), md5(blob2) ) ) )
-          
+
           = md5( concat( sort( 72794b6d, 5e089d29 ) ) )
-          
+
           = md5( concat( 5e089d29, 72794b6d ) )
-          
+
           = md5( 5e089d2972794b6d )
-          
+
           = f7a29a04
       access_methods:
         type: array
@@ -240,7 +240,7 @@ definitions:
         type: array
         description: >-
           If not set, this `Object` is a single blob.
-          
+
           If set, this `Object` is a bundle containing the listed `ContentsObject` s (some of which may be further nested).
         items:
           $ref: '#/definitions/ContentsObject'
@@ -253,7 +253,7 @@ definitions:
         items:
           type: string
         description: >-
-          A list of strings that can be used to find other metadata 
+          A list of strings that can be used to find other metadata
           about this `Object` from external metadata sources. These
           aliases can be used to represent secondary
           accession numbers or external GUIDs.
@@ -348,7 +348,7 @@ definitions:
         type: string
         description: >-
           A name declared by the bundle author that must be
-          used when materialising this object, 
+          used when materialising this object,
           overriding any name directly associated with the object itself.
           This string MUST NOT contain any slashes.
       id:

scripts/stagepages.sh

@@ -9,7 +9,8 @@ if [ "$TRAVIS_BRANCH" != "gh-pages" ]; then
   else
     branch=$(echo "$TRAVIS_BRANCH" | awk '{print tolower($0)}')
     branchpath="preview/$branch"
-  fi  
+  fi
+  echo $branchpath
   mkdir -p "$branchpath/docs"
   cp docs/html5/index.html "$branchpath/docs/"
   cp docs/pdf/index.pdf "$branchpath/docs/"