From 9862fac8cf556a68d1d270f675792de6bca4fb14 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 29 Dec 2020 00:12:47 -0500
Subject: [PATCH] Small improvements to try to get galaxy-app closer to
 working.

---
 lib/galaxy/util/__init__.py    |  2 +-
 packages/app/galaxy/files      |  1 +
 packages/app/galaxy/schema     |  1 +
 packages/app/pytest.ini        |  2 ++
 packages/app/requirements.txt  | 13 +++++++++++++
 packages/app/setup.py          |  3 +++
 packages/app/tests/__init__.py |  0
 packages/test.sh               |  2 +-
 8 files changed, 22 insertions(+), 2 deletions(-)
 create mode 120000 packages/app/galaxy/files
 create mode 120000 packages/app/galaxy/schema
 create mode 100644 packages/app/pytest.ini
 create mode 100644 packages/app/tests/__init__.py

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 50a763775e4..e65c00dc1f2 100644
--- a/lib/galaxy/util/__init__.py
+++ b/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] == "#":
diff --git a/packages/app/galaxy/files b/packages/app/galaxy/files
new file mode 120000
index 00000000000..85c2c6baf4a
--- /dev/null
+++ b/packages/app/galaxy/files
@@ -0,0 +1 @@
+../../../lib/galaxy/files/
\ No newline at end of file
diff --git a/packages/app/galaxy/schema b/packages/app/galaxy/schema
new file mode 120000
index 00000000000..14df7cabc56
--- /dev/null
+++ b/packages/app/galaxy/schema
@@ -0,0 +1 @@
+../../../lib/galaxy/schema
\ No newline at end of file
diff --git a/packages/app/pytest.ini b/packages/app/pytest.ini
new file mode 100644
index 00000000000..6b5e4056f66
--- /dev/null
+++ b/packages/app/pytest.ini
@@ -0,0 +1,2 @@
+[pytest]
+addopts = --ignore-glob 'galaxy/tools/bundled/*'
diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt
index e51c3b80fbc..af5570aad57 100644
--- a/packages/app/requirements.txt
+++ b/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
diff --git a/packages/app/setup.py b/packages/app/setup.py
index 76c6ed8926a..1617366236e 100644
--- a/packages/app/setup.py
+++ b/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',
diff --git a/packages/app/tests/__init__.py b/packages/app/tests/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/packages/test.sh b/packages/test.sh
index fefe5f00423..8d17b6f2003 100755
--- a/packages/test.sh
+++ b/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]}