Merge pull request #236 from tommydeboer/fix/debugger

Rename io to in_out to fix broken debug connection

mcmd/__main__.py

@@ -20,9 +20,9 @@
 from mcmd.core.context.home_context import HomeContext
 from mcmd.args.parser import parse_args
 from mcmd.config.loader import load_config
-from mcmd.io import io
-from mcmd.io.io import set_debug
-from mcmd.io.logging import set_level
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import set_debug
+from mcmd.in_out.logging import set_level
 
 
 def main():
@@ -69,7 +69,7 @@ def set_log_level(args):
 
 # noinspection PyUnusedLocal
 def interrupt_handler(sig, frame):
-    io.warn('Interrupted by user.')
+    in_out.warn('Interrupted by user.')
     sys.exit(0)
 
 

mcmd/commands/add.py

@@ -9,8 +9,8 @@
 from mcmd.core.compatibility import version, deprecated
 from mcmd.core.context import context
 from mcmd.core.errors import McmdError
-from mcmd.io import io
-from mcmd.io.io import highlight
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import highlight
 from mcmd.molgenis import api
 from mcmd.molgenis.client import post, get, post_files
 from mcmd.molgenis.principals import to_role_name
@@ -169,7 +169,7 @@ def add_arguments(subparsers):
 
 @command
 def add_user(args):
-    io.start('Adding user %s' % highlight(args.username))
+    in_out.start('Adding user %s' % highlight(args.username))
 
     password = args.set_password if args.set_password else args.username
     email = args.with_email if args.with_email else args.username + '@molgenis.org'
@@ -190,7 +190,7 @@ def add_user(args):
 @command
 def add_role(args):
     role_name = to_role_name(args.rolename)
-    io.start('Adding role {}'.format(highlight(role_name)))
+    in_out.start('Adding role {}'.format(highlight(role_name)))
 
     role = {'name': role_name,
             'label': role_name}
@@ -241,7 +241,7 @@ def _get_role_ids(role_names) -> List[str]:
 @command
 def add_group(args):
     group_name = _to_group_name(args.name)
-    io.start('Adding group %s' % highlight(group_name))
+    in_out.start('Adding group %s' % highlight(group_name))
     post(api.group(), data={'name': group_name, 'label': args.name})
 
 
@@ -259,7 +259,7 @@ def _to_group_name(group_input: str):
 
 @command
 def add_package(args):
-    io.start('Adding package %s' % highlight(args.id))
+    in_out.start('Adding package %s' % highlight(args.id))
 
     data = {'id': args.id,
             'label': args.id}
@@ -272,7 +272,7 @@ def add_package(args):
 
 @command
 def add_token(args):
-    io.start('Adding token %s for user %s' % (highlight(args.token), highlight(args.user)))
+    in_out.start('Adding token %s for user %s' % (highlight(args.token), highlight(args.user)))
 
     user = get(api.rest2('sys_sec_User'),
                params={
@@ -312,12 +312,12 @@ def add_theme(args):
         paths.append(bs4)
         names.append('bootstrap4-style')
         bs4_name = file_utils.get_file_name_from_path(bs4)
-        io.start(
+        in_out.start(
             'Adding bootstrap 3 theme {} and bootstrap 4 theme {} to bootstrap themes'.format(
                 highlight(bs3_name),
                 highlight(bs4_name)))
     else:
-        io.start(
+        in_out.start(
             'Adding bootstrap 3 theme {} to bootstrap themes'.format(
                 highlight(bs3_name)))
     if not args.from_path:
@@ -337,10 +337,10 @@ def add_logo(args):
     valid_types = {'image/jpeg', 'image/png', 'image/gif'}
     logo = [args.logo]
     if not args.from_path:
-        io.start('Adding logo from path {}'.format(highlight(args.logo)))
+        in_out.start('Adding logo from path {}'.format(highlight(args.logo)))
         logo = [_get_path_from_quick_folders(args.logo)]
     else:
-        io.start('Adding logo {}'.format(highlight(args.logo)))
+        in_out.start('Adding logo {}'.format(highlight(args.logo)))
     files = _prepare_files_for_upload(logo, ['logo'], valid_types)
     post_files(files, api_)
 

mcmd/commands/config.py

@@ -6,8 +6,8 @@
 from mcmd.commands._registry import arguments
 from mcmd.core.command import command, CommandType
 from mcmd.core.errors import McmdError
-from mcmd.io import io, ask
-from mcmd.io.io import highlight
+from mcmd.in_out import in_out, ask
+from mcmd.in_out.in_out import highlight
 
 
 # =========
@@ -126,7 +126,7 @@ def config_set_host(args):
         urls = [auth['url'] for auth in auths]
         url = ask.multi_choice('Please select a host:', urls)
 
-    io.start("Switching to host {}".format(highlight(url)))
+    in_out.start("Switching to host {}".format(highlight(url)))
 
     if config.host_exists(url):
         config.set_host(url)
@@ -143,21 +143,21 @@ def config_set_import_action(args):
         options = ['add', 'add_update_existing', 'update']
         action = ask.multi_choice('Choose the default import action:', options)
 
-    io.start("Setting import action to {}".format(highlight(action)))
+    in_out.start("Setting import action to {}".format(highlight(action)))
     config.set_import_action(action)
 
 
 # noinspection PyUnusedLocal
 @command
 def config_set_non_interactive(args):
-    io.start('Switching to non-interactive mode')
+    in_out.start('Switching to non-interactive mode')
     config.set_non_interactive(True)
 
 
 # noinspection PyUnusedLocal
 @command
 def config_set_interactive(args):
-    io.start('Switching to interactive mode')
+    in_out.start('Switching to interactive mode')
     config.set_non_interactive(False)
 
 
@@ -184,9 +184,9 @@ def config_add_host(args):
         password = ask.password("Password (Leave blank to use command line authentication)")
         password = None if len(password) == 0 else password
 
-    io.start("Adding host {}".format(highlight(url)))
+    in_out.start("Adding host {}".format(highlight(url)))
     config.add_host(url, username, password)
-    io.succeed()
+    in_out.succeed()
 
     if args.switch:
         _switch_to_new_host(url)
@@ -196,15 +196,15 @@ def config_add_host(args):
 
 @command
 def config_add_dataset_folder(args):
-    io.start('Adding resource folder {}'.format(highlight(args.folder)))
+    in_out.start('Adding resource folder {}'.format(highlight(args.folder)))
     if not Path(args.folder).is_dir():
         raise McmdError('Folder does not exist: {}'.format(args.folder))
     config.add_dataset_folder(args.folder)
 
 
 @command
 def config_add_resource_folder(args):
-    io.start('Adding resource folder {}'.format(highlight(args.folder)))
+    in_out.start('Adding resource folder {}'.format(highlight(args.folder)))
     if not Path(args.folder).is_dir():
         raise McmdError('Folder does not exist: {}'.format(args.folder))
     config.add_resource_folder(args.folder)

mcmd/commands/delete.py

@@ -1,11 +1,11 @@
 from urllib.parse import urljoin
 
-import mcmd.io.ask
+import mcmd.in_out.ask
 import mcmd.molgenis.client as client
 from mcmd.commands._registry import arguments
 from mcmd.core.command import command
-from mcmd.io import io
-from mcmd.io.io import highlight
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import highlight
 from mcmd.molgenis import api
 from mcmd.molgenis.resources import detect_resource_type, ensure_resource_exists, ResourceType
 
@@ -79,23 +79,23 @@ def delete(args):
 
 
 def _delete_entity_type(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete entity type {} including its data?'.format(args.resource))):
-        io.start('Deleting entity type {}'.format(highlight(args.resource)))
+        in_out.start('Deleting entity type {}'.format(highlight(args.resource)))
         _delete_rows(ResourceType.ENTITY_TYPE.get_entity_id(), [args.resource])
 
 
 def _delete_entity_type_data(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete all data in entity type {}?'.format(args.resource))):
-        io.start('Deleting all data from entity {}'.format(highlight(args.resource)))
+        in_out.start('Deleting all data from entity {}'.format(highlight(args.resource)))
         client.delete(api.rest1(args.resource))
 
 
 def _delete_entity_type_attribute(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete attribute {} of entity type {}?'.format(args.attribute, args.resource))):
-        io.start('Deleting attribute {} of entity {}'.format(highlight(args.attribute), highlight(args.resource)))
+        in_out.start('Deleting attribute {} of entity {}'.format(highlight(args.attribute), highlight(args.resource)))
         response = client.get(api.rest2('sys_md_Attribute'),
                               params={
                                   'q': 'entity=={};name=={}'.format(args.resource,
@@ -106,16 +106,16 @@ def _delete_entity_type_attribute(args):
 
 
 def _delete_package(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete package {} and all of its contents?'.format(args.resource))):
-        io.start('Deleting package {}'.format(highlight(args.resource)))
+        in_out.start('Deleting package {}'.format(highlight(args.resource)))
         _delete_rows(ResourceType.PACKAGE.get_entity_id(), [args.resource])
 
 
 def _delete_package_contents(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete the contents of package {}?'.format(args.resource))):
-        io.start('Deleting contents of package {}'.format(highlight(args.resource)))
+        in_out.start('Deleting contents of package {}'.format(highlight(args.resource)))
         _delete_entity_types_in_package(args.resource)
         _delete_packages_in_package(args.resource)
 
@@ -143,7 +143,7 @@ def _delete_packages_in_package(package_id):
 
 
 def _delete_group(args):
-    if args.force or (not args.force and mcmd.io.ask.confirm(
+    if args.force or (not args.force and mcmd.in_out.ask.confirm(
             'Are you sure you want to delete group {}?'.format(args.resource))):
         io.start('Deleting group {}'.format(highlight(args.resource)))
         client.delete(urljoin(api.group(), args.resource))

mcmd/commands/disable.py

@@ -1,8 +1,8 @@
 from mcmd.commands._registry import arguments
 from mcmd.core.command import command
-from mcmd.io import ask
-from mcmd.io import io
-from mcmd.io.io import highlight
+from mcmd.in_out import ask
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import highlight
 from mcmd.molgenis import api
 from mcmd.molgenis.client import put
 from mcmd.molgenis.resources import ensure_resource_exists, ResourceType
@@ -48,14 +48,14 @@ def disable_rls(args):
     if not ask.confirm('Are you sure you want to disable row level security on %s?' % args.entity):
         return
 
-    io.start('Disabling row level security on entity type %s' % highlight(args.entity))
+    in_out.start('Disabling row level security on entity type %s' % highlight(args.entity))
 
     ensure_resource_exists(args.entity, ResourceType.ENTITY_TYPE)
     security.disable_row_level_security(args.entity)
 
 
 @command
 def disable_language(args):
-    io.start('Disabling language {}'.format(highlight(args.language)))
+    in_out.start('Disabling language {}'.format(highlight(args.language)))
     url = api.rest1('sys_Language/{}/active'.format(args.language))
     put(url, 'false')

mcmd/commands/enable.py

@@ -5,8 +5,8 @@
 from mcmd.core.command import command
 from mcmd.core.compatibility import deprecated
 from mcmd.core.errors import McmdError
-from mcmd.io import io
-from mcmd.io.io import highlight
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import highlight
 from mcmd.molgenis import api
 from mcmd.molgenis.client import post, put
 from mcmd.molgenis.resources import one_resource_exists, ensure_resource_exists, ResourceType
@@ -70,7 +70,7 @@ def add_arguments(subparsers):
 
 @command
 def enable_rls(args):
-    io.start('Enabling row level security on entity type %s' % highlight(args.entity))
+    in_out.start('Enabling row level security on entity type %s' % highlight(args.entity))
 
     ensure_resource_exists(args.entity, ResourceType.ENTITY_TYPE)
     security.enable_row_level_security(args.entity)
@@ -90,7 +90,7 @@ def enable_theme(args):
     :return None
     """
     theme = args.theme.replace('.css', '').replace('.min', '')
-    io.start('Applying theme {}'.format(highlight(theme)))
+    in_out.start('Applying theme {}'.format(highlight(theme)))
     # Resource can be bootstrap-name.min.css (if molgenis theme), or name.min.css (if uploaded .min.css), or
     # name.css (if uploaded as .css).
     if one_resource_exists([theme + '.min.css', theme + '.css', 'bootstrap-' + theme + '.min.css'], ResourceType.THEME):
@@ -106,6 +106,6 @@ def enable_theme(args):
 
 @command
 def enable_language(args):
-    io.start('Enabling language {}'.format(highlight(args.language)))
+    in_out.start('Enabling language {}'.format(highlight(args.language)))
     url = api.rest1('sys_Language/{}/active'.format(args.language))
     put(url, 'true')

mcmd/commands/give.py

@@ -10,8 +10,8 @@
 from mcmd.core.command import command
 from mcmd.core.compatibility import version
 from mcmd.core.errors import McmdError
-from mcmd.io import io
-from mcmd.io.io import highlight
+from mcmd.in_out import in_out
+from mcmd.in_out.in_out import highlight
 from mcmd.molgenis.principals import PrincipalType, get_principal_type_from_args
 from mcmd.molgenis.resources import detect_resource_type, ensure_resource_exists, ResourceType
 from mcmd.molgenis.security import security
@@ -127,7 +127,7 @@ def _validate_args(args):
 
 def _grant(principal_type: PrincipalType, principal_name: str, resource_type: ResourceType, entity_type_id: str,
            permission: Permission):
-    io.start('Giving %s %s permission to %s on %s %s' % (principal_type.value,
+    in_out.start('Giving %s %s permission to %s on %s %s' % (principal_type.value,
                                                          highlight(principal_name),
                                                          highlight(permission.value),
                                                          resource_type.get_label().lower(),
@@ -138,7 +138,7 @@ def _grant(principal_type: PrincipalType, principal_name: str, resource_type: Re
 
 def _grant_rls(principal_type: PrincipalType, principal_name: str, entity_type_id: str,
                entity_id: str, permission: Permission):
-    io.start('Giving %s %s permission to %s on row %s of entity type %s' % (principal_type.value,
+    in_out.start('Giving %s %s permission to %s on row %s of entity type %s' % (principal_type.value,
                                                                             highlight(principal_name),
                                                                             highlight(permission.value),
                                                                             highlight(entity_id),

mcmd/commands/history.py

@@ -1,8 +1,8 @@
 from mcmd.commands._registry import arguments
 from mcmd.core import history as hist
 from mcmd.core.command import command, CommandType
-from mcmd.io import io
-from mcmd.io.logging import get_logger
+from mcmd.in_out import in_out
+from mcmd.in_out.logging import get_logger
 
 
 # =========
@@ -38,15 +38,15 @@ def add_arguments(subparsers):
 @command
 def history(args):
     if args.clear:
-        io.start('Clearing history')
+        in_out.start('Clearing history')
         hist.clear()
     else:
         lines = hist.read(args.number, include_fails=True)
         if len(lines) == 0:
             log.info('History is empty.')
         for line in lines:
-            io.start(line[1])
+            in_out.start(line[1])
             if line[0]:
-                io.succeed()
+                in_out.succeed()
             else:
-                io.error(None)
+                in_out.error(None)