modified cli to export panels and created a test for it

scout/commands/base.py

@@ -121,7 +121,7 @@ def cli(context, mongodb, username, password, authdb, host, port, loglevel, conf
 app_cli.add_command(wipe) # Done!
 app_cli.add_command(setup_command) # Done!
 app_cli.add_command(delete) # Done!
-cli.add_command(export)
+app_cli.add_command(export) # in progress
 cli.add_command(convert)
 cli.add_command(view_command)
 

scout/commands/export/export_command.py

@@ -27,14 +27,14 @@
 
 
 @click.group()
-@click.pass_context
-def export(ctx):
+def export():
     """
     Export objects from the mongo database.
     """
     LOG.info("Running scout export")
+    pass
 
-export.add_command(panel)
+export.add_command(panel) # in progress
 export.add_command(genes)
 export.add_command(transcripts)
 export.add_command(variants)

scout/commands/export/panel.py

@@ -1,11 +1,14 @@
+# -*- coding: utf-8 -*-
 import logging
 
 import click
+from flask.cli import with_appcontext
 
 from scout.commands.utils import builds_option
-
 from scout.export.panel import (export_gene_panels, export_panels)
+from scout.server.extensions import store
 
+logging.basicConfig(level=logging.DEBUG)
 LOG = logging.getLogger(__name__)
 
 @click.command('panel', short_help='Export gene panels')
@@ -14,43 +17,44 @@
                 metavar='<panel_name>'
 )
 @builds_option
-@click.option('--version', 
+@click.option('--version',
     type=float,
-    help="Specify panel version, only works if one panel"
+    help="Specify panel version, only works if one panel is provided"
 )
 @click.option('--bed',
     help="Export genes in bed like format",
     is_flag=True,
 )
-@click.pass_context
-def panel(context, panel, build, bed, version):
+@with_appcontext
+def panel(panel, build, bed, version):
     """Export gene panels to .bed like format.
-    
+
         Specify any number of panels on the command line
     """
     LOG.info("Running scout export panel")
-    adapter = context.obj['adapter']
+    adapter = store
+
     # Save all chromosomes found in the collection if panels
     chromosomes_found = set()
-    
+
     if not panel:
         LOG.warning("Please provide at least one gene panel")
-        context.abort()
+        raise click.Abort()
 
     LOG.info("Exporting panels: {}".format(', '.join(panel)))
     if bed:
         if version:
             version = [version]
         lines = export_panels(
-            adapter=adapter, 
-            panels=panel, 
-            versions=version, 
+            adapter=adapter,
+            panels=panel,
+            versions=version,
             build=build,
         )
     else:
         lines = export_gene_panels(
-            adapter=adapter, 
-            panels=panel, 
+            adapter=adapter,
+            panels=panel,
             version=version,
             )
     for line in lines:

tests/commands/export/test_export_panel_cmd.py

@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+
+from scout.commands import app_cli
+from scout.server.extensions import store
+
+def test_export_panel(mock_app):
+    """Test the CLI command that exports a gene panel"""
+
+    runner = mock_app.test_cli_runner()
+    assert runner
+
+    panel_obj = store.panel_collection.find_one()
+    assert panel_obj
+
+    # Test the export panel cli without passing any data
+    result =  runner.invoke(app_cli, ['export', 'panel'])
+
+    # The CLI command should return an error message then return abort code
+    assert result.exit_code == 1
+    assert 'Please provide at least one gene panel' in result.output
+
+    # Try to pass a non-valid panel name
+    result =  runner.invoke(app_cli, ['export', 'panel', 'unknown_panel'])
+
+    # The CLI command should not return abort code but error message
+    assert result.exit_code == 0
+    assert 'WARNING Panel unknown_panel could not be found' in result.output
+
+    # Try to pass a valid panel name, without a valid version
+    result =  runner.invoke(app_cli, ['export', 'panel',
+        panel_obj['panel_name'],
+        '--version', 5.0
+        ])
+
+    # The CLI command should not return abort code but error message
+    assert result.exit_code == 0
+    assert 'WARNING Panel {} could not be found'.format(panel_obj['panel_name']) in result.output
+
+    # Pass a valid panel name, valid version
+    result =  runner.invoke(app_cli, ['export', 'panel',
+        panel_obj['panel_name'],
+        '--version', 1.0
+        ])
+
+    # The CLI command shoud return gene panel
+    assert result.exit_code == 0
+    assert '2397\tCRYBB1\t\t\t\t\n9394\tPICK1\t\t\t\t\n' in result.output
+
+    # Pass a valid panel name, valid version, bed file format option
+    result =  runner.invoke(app_cli, ['export', 'panel',
+        panel_obj['panel_name'],
+        '--version', 1.0,
+        '--bed'
+        ])
+
+    # The CLI command shoud return gene panel formatted in the expexted way
+    assert result.exit_code == 0
+    assert '22\t26995242\t27014052\t2397\tCRYBB1\n22\t38452318\t38471708\t9394\tPICK1\n' in result.output