Merge pull request #11010 from jmchilton/app_fixes

Small improvements to try to get galaxy-app closer to working.

lib/galaxy/util/__init__.py

@@ -1177,7 +1177,7 @@ def read_dbnames(filename):
         name_to_db_base = {}
         if filename is None:
             # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test
-            filename = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample')
+            filename = os.path.join(galaxy_directory(), 'tool-data', 'shared', 'ucsc', 'builds.txt.sample')
         for line in open(filename):
             try:
                 if line[0:1] == "#":

packages/app/galaxy/files

@@ -0,0 +1 @@
+../../../lib/galaxy/files/

packages/app/galaxy/schema

@@ -0,0 +1 @@
+../../../lib/galaxy/schema

packages/app/pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = --ignore-glob 'galaxy/tools/bundled/*'

packages/app/requirements.txt

@@ -4,3 +4,16 @@ galaxy-job-metrics
 galaxy-tool-util
 galaxy-web-framework
 galaxy-web-stack
+
+kombu
+Beaker
+pykwalify
+pulsar-galaxy-lib==0.14.0.dev4
+gxformat2
+Mako
+sqlitedict
+svgwrite
+sortedcontainers
+Markdown
+refgenconf
+Fabric3

packages/app/setup.py

@@ -32,6 +32,8 @@ TEST_DIR = 'tests'
 PACKAGES = [
     'galaxy',
     'galaxy.actions',
+    'galaxy.files',
+    'galaxy.files.sources',
     'galaxy.forms',
     'galaxy.jobs',
     'galaxy.jobs.actions',
@@ -47,6 +49,7 @@ PACKAGES = [
     'galaxy.jobs.splitters',
     'galaxy.managers',
     'galaxy.openid',
+    'galaxy.schema',
     'galaxy.tools',
     'galaxy.tools.actions',
     'galaxy.tools.data',

packages/test.sh

@@ -33,7 +33,7 @@ PACKAGE_DIRS=(
 )
 # tool_util not yet working 100%,
 # data has many problems quota, tool shed install database, etc..
-RUN_TESTS=(1 1 1 1 1 1 1 1 1 1 0 0)
+RUN_TESTS=(1 1 1 1 1 1 1 1 1 1 1 0)
 RUN_MYPY=(1 1 1 1 1 1 1 1 1 1 0 0)
 for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
     package_dir=${PACKAGE_DIRS[$i]}