Quota / Folder support

parsec/commands/cmd_folders.py

@@ -1,10 +1,18 @@
 import click
-from parsec.commands.folders.show_folder import cli as func0
-from parsec.commands.folders.delete_folder import cli as func1
+from parsec.commands.folders.create_folder import cli as func0
+from parsec.commands.folders.show_folder import cli as func1
+from parsec.commands.folders.update_folder import cli as func2
+from parsec.commands.folders.set_permissions import cli as func3
+from parsec.commands.folders.get_permissions import cli as func4
+from parsec.commands.folders.delete_folder import cli as func5
 
 @click.group()
 def cli():
 	pass
 
 cli.add_command(func0)
 cli.add_command(func1)
+cli.add_command(func2)
+cli.add_command(func3)
+cli.add_command(func4)
+cli.add_command(func5)

parsec/commands/cmd_quotas.py

@@ -1,10 +1,18 @@
 import click
 from parsec.commands.quotas.get_quotas import cli as func0
 from parsec.commands.quotas.show_quota import cli as func1
+from parsec.commands.quotas.delete_quota import cli as func2
+from parsec.commands.quotas.update_quota import cli as func3
+from parsec.commands.quotas.create_quota import cli as func4
+from parsec.commands.quotas.undelete_quota import cli as func5
 
 @click.group()
 def cli():
 	pass
 
 cli.add_command(func0)
 cli.add_command(func1)
+cli.add_command(func2)
+cli.add_command(func3)
+cli.add_command(func4)
+cli.add_command(func5)

parsec/commands/folders/create_folder.py

@@ -0,0 +1,21 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('create_folder')
+@click.argument("parent_folder_id", type=str)
+@click.argument("name", type=str)
+
+@click.option(
+    "--description",
+    help="folder's description",
+    type=str
+)
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, parent_folder_id, name, description=""):
+    """Create a folder.
+    """
+    return ctx.gi.folders.create_folder(parent_folder_id, name, description=description)

parsec/commands/folders/get_permissions.py

@@ -0,0 +1,16 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('get_permissions')
+@click.argument("folder_id", type=str)
+@click.argument("scope", type=str)
+
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, folder_id, scope):
+    """Get the permissions of a folder.
+    """
+    return ctx.gi.folders.get_permissions(folder_id, scope)

parsec/commands/folders/set_permissions.py

@@ -0,0 +1,32 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('set_permissions')
+@click.argument("folder_id", type=str)
+
+@click.option(
+    "--action",
+    help="action to execute, only "set_permissions" is supported.",
+    type=str
+)
+@click.option(
+    "--add_ids",
+    help="list of role IDs which can add datasets to the folder"
+)
+@click.option(
+    "--manage_ids",
+    help="list of role IDs which can manage datasets in the folder"
+)
+@click.option(
+    "--modify_ids",
+    help="list of role IDs which can modify datasets in the folder"
+)
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, folder_id, action="", add_ids="", manage_ids="", modify_ids=""):
+    """Set the permissions of a folder.
+    """
+    return ctx.gi.folders.set_permissions(folder_id, action=action, add_ids=add_ids, manage_ids=manage_ids, modify_ids=modify_ids)

parsec/commands/folders/update_folder.py

@@ -0,0 +1,21 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('update_folder')
+@click.argument("folder_id", type=str)
+@click.argument("name", type=str)
+
+@click.option(
+    "--description",
+    help="folder's description",
+    type=str
+)
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, folder_id, name, description=""):
+    """Update folder information.
+    """
+    return ctx.gi.folders.update_folder(folder_id, name, description=description)

parsec/commands/quotas/create_quota.py

@@ -0,0 +1,31 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('create_quota')
+@click.argument("name", type=str)
+@click.argument("description", type=str)
+@click.argument("amount", type=str)
+@click.argument("operation", type=str)
+
+@click.option(
+    "--default",
+    help="Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. None is equivalent to ``no``.",
+    type=str
+)
+@click.option(
+    "--in_users",
+    help="A list of user IDs or user emails."
+)
+@click.option(
+    "--in_groups",
+    help="A list of group IDs or names."
+)
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, name, description, amount, operation, default="", in_users="", in_groups=""):
+    """Create a new quota
+    """
+    return ctx.gi.quotas.create_quota(name, description, amount, operation, default=default, in_users=in_users, in_groups=in_groups)

parsec/commands/quotas/delete_quota.py

@@ -0,0 +1,15 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('delete_quota')
+@click.argument("quota_id", type=str)
+
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, quota_id):
+    """Delete a quota
+    """
+    return ctx.gi.quotas.delete_quota(quota_id)

parsec/commands/quotas/undelete_quota.py

@@ -0,0 +1,15 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('undelete_quota')
+@click.argument("quota_id", type=str)
+
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, quota_id):
+    """Unelete a quota
+    """
+    return ctx.gi.quotas.undelete_quota(quota_id)

parsec/commands/quotas/update_quota.py

@@ -0,0 +1,48 @@
+import click
+from parsec.cli import pass_context, json_loads
+from parsec.decorators import bioblend_exception, dict_output
+
+@click.command('update_quota')
+@click.argument("quota_id", type=str)
+
+@click.option(
+    "--name",
+    help="Name for the new quota. This must be unique within a Galaxy instance.",
+    type=str
+)
+@click.option(
+    "--description",
+    help="Quota description. If you supply this parameter, but not the name, an error will be thrown.",
+    type=str
+)
+@click.option(
+    "--amount",
+    help="Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``, ``unlimited``)",
+    type=str
+)
+@click.option(
+    "--operation",
+    help="One of (``+``, ``-``, ``=``). If you wish to change this value, you must also provide the ``amount``, otherwise it will not take effect.",
+    type=str
+)
+@click.option(
+    "--default",
+    help="Whether or not this is a default quota. Valid values are ``no``, ``unregistered``, ``registered``. Calling update twice with a default of ``no`` will throw an error. Not passing this parameter is equivalent to passing ``no``.",
+    type=str
+)
+@click.option(
+    "--in_users",
+    help="A list of user IDs or user emails."
+)
+@click.option(
+    "--in_groups",
+    help="A list of group IDs or names."
+)
+
+@pass_context
+@bioblend_exception
+@dict_output
+def cli(ctx, quota_id, name="", description="", amount="", operation="", default="", in_users="", in_groups=""):
+    """Update an existing quota
+    """
+    return ctx.gi.quotas.update_quota(quota_id, name=name, description=description, amount=amount, operation=operation, default=default, in_users=in_users, in_groups=in_groups)

parsec/commands/toolshed/install_repository_revision.py

@@ -10,12 +10,12 @@
 
 @click.option(
     "--install_tool_dependencies",
-    help="Whether or not to automatically handle tool dependencies (see http://wiki.galaxyproject.org/AToolOrASuitePerRepository for more details)",
+    help="Whether or not to automatically handle tool dependencies (see https://galaxyproject.org/toolshed/tool-dependency-recipes/ for more details)",
     is_flag=True
 )
 @click.option(
     "--install_repository_dependencies",
-    help="Whether or not to automatically handle repository dependencies (see http://wiki.galaxyproject.org/DefiningRepositoryDependencies for more details)",
+    help="Whether or not to automatically handle repository dependencies (see https://galaxyproject.org/toolshed/defining-repository-dependencies/ for more details)",
     is_flag=True
 )
 @click.option(

scripts/autobuilder.py

@@ -7,7 +7,7 @@
 import glob
 import argparse
 import logging
-logging.basicConfig(level=logging.DEBUG)
+logging.basicConfig(level=logging.INFO)
 log = logging.getLogger()
 
 
@@ -311,7 +311,6 @@ def process_arg(k, v, param_type, real_type):
                 except Exception as e:
                     param_type = []
                     real_type = None
-                    print(candidate, e)
                 process_arg(k, v, param_type, real_type)
 
             had_weird_kwargs = False