manual changes

HISTORY.rst

@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+----------------------
+1.16.0 (2021-08-14)
+----------------------
+
+* Update bioblend to 0.16.0
+
 ----------------------
 1.15.0 (2021-04-08)
 ----------------------

parsec/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '1.15.0'
+__version__ = '1.16.0'
 
 PROJECT_NAME = "parsec"

parsec/cli.py

@@ -90,12 +90,14 @@ def list_commands(self, ctx):
         # We pre-calculate this so it works more nicely within packaged
         # versions of parsec. Please feel free to fix this?
 
-        commands = ['config', 'datasets', 'datatypes', 'folders', 'forms',
-                    'ftpfiles', 'genomes', 'groups', 'histories', 'jobs',
-                    'libraries', 'quotas', 'roles', 'tool_data', 'tools',
-                    'users', 'utils', 'visual', 'workflows',
-                    'toolshed_categories', 'toolshed_repositories',
-                    'toolshed_tools']
+        commands = ['config', 'dataset_collections', 'datasets', 'datatypes',
+                    'folders', 'forms', 'ftpfiles', 'genomes', 'groups',
+                    'histories', 'init', 'invocations', 'jobs', 'libraries',
+                    'quotas', 'roles', 'tool_data', 'tool_dependencies',
+                    'toolshed_categories', 'toolshed', 'toolShed',
+                    'toolshed_repositories', 'toolshed_tools', 'tools',
+                    'users', 'utils', 'visual', 'workflows']
+
         return commands
 
     def get_command(self, ctx, name):

parsec/commands/cmd_config.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.config.get_config import cli as get_config
 from parsec.commands.config.get_version import cli as get_version
-from parsec.commands.config.module import cli as module
 
 
 @click.group()
@@ -11,4 +10,3 @@ def cli():
 
 cli.add_command(get_config)
 cli.add_command(get_version)
-cli.add_command(module)

parsec/commands/cmd_dataset_collections.py

@@ -1,6 +1,5 @@
 import click
 from parsec.commands.dataset_collections.download_dataset_collection import cli as download_dataset_collection
-from parsec.commands.dataset_collections.module import cli as module
 from parsec.commands.dataset_collections.show_dataset_collection import cli as show_dataset_collection
 from parsec.commands.dataset_collections.wait_for_dataset_collection import cli as wait_for_dataset_collection
 
@@ -11,6 +10,5 @@ def cli():
 
 
 cli.add_command(download_dataset_collection)
-cli.add_command(module)
 cli.add_command(show_dataset_collection)
 cli.add_command(wait_for_dataset_collection)

parsec/commands/cmd_datasets.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.datasets.download_dataset import cli as download_dataset
 from parsec.commands.datasets.get_datasets import cli as get_datasets
-from parsec.commands.datasets.module import cli as module
 from parsec.commands.datasets.publish_dataset import cli as publish_dataset
 from parsec.commands.datasets.show_dataset import cli as show_dataset
 from parsec.commands.datasets.update_permissions import cli as update_permissions
@@ -15,7 +14,6 @@ def cli():
 
 cli.add_command(download_dataset)
 cli.add_command(get_datasets)
-cli.add_command(module)
 cli.add_command(publish_dataset)
 cli.add_command(show_dataset)
 cli.add_command(update_permissions)

parsec/commands/cmd_datatypes.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.datatypes.get_datatypes import cli as get_datatypes
 from parsec.commands.datatypes.get_sniffers import cli as get_sniffers
-from parsec.commands.datatypes.module import cli as module
 
 
 @click.group()
@@ -11,4 +10,3 @@ def cli():
 
 cli.add_command(get_datatypes)
 cli.add_command(get_sniffers)
-cli.add_command(module)

parsec/commands/cmd_folders.py

@@ -2,7 +2,6 @@
 from parsec.commands.folders.create_folder import cli as create_folder
 from parsec.commands.folders.delete_folder import cli as delete_folder
 from parsec.commands.folders.get_permissions import cli as get_permissions
-from parsec.commands.folders.module import cli as module
 from parsec.commands.folders.set_permissions import cli as set_permissions
 from parsec.commands.folders.show_folder import cli as show_folder
 from parsec.commands.folders.update_folder import cli as update_folder
@@ -16,7 +15,6 @@ def cli():
 cli.add_command(create_folder)
 cli.add_command(delete_folder)
 cli.add_command(get_permissions)
-cli.add_command(module)
 cli.add_command(set_permissions)
 cli.add_command(show_folder)
 cli.add_command(update_folder)

parsec/commands/cmd_forms.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.forms.create_form import cli as create_form
 from parsec.commands.forms.get_forms import cli as get_forms
-from parsec.commands.forms.module import cli as module
 from parsec.commands.forms.show_form import cli as show_form
 
 
@@ -12,5 +11,4 @@ def cli():
 
 cli.add_command(create_form)
 cli.add_command(get_forms)
-cli.add_command(module)
 cli.add_command(show_form)

parsec/commands/cmd_ftpfiles.py

@@ -1,6 +1,5 @@
 import click
 from parsec.commands.ftpfiles.get_ftp_files import cli as get_ftp_files
-from parsec.commands.ftpfiles.module import cli as module
 
 
 @click.group()
@@ -9,4 +8,3 @@ def cli():
 
 
 cli.add_command(get_ftp_files)
-cli.add_command(module)

parsec/commands/cmd_genomes.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.genomes.get_genomes import cli as get_genomes
 from parsec.commands.genomes.install_genome import cli as install_genome
-from parsec.commands.genomes.module import cli as module
 from parsec.commands.genomes.show_genome import cli as show_genome
 
 
@@ -12,5 +11,4 @@ def cli():
 
 cli.add_command(get_genomes)
 cli.add_command(install_genome)
-cli.add_command(module)
 cli.add_command(show_genome)

parsec/commands/cmd_groups.py

@@ -7,7 +7,6 @@
 from parsec.commands.groups.get_group_roles import cli as get_group_roles
 from parsec.commands.groups.get_group_users import cli as get_group_users
 from parsec.commands.groups.get_groups import cli as get_groups
-from parsec.commands.groups.module import cli as module
 from parsec.commands.groups.show_group import cli as show_group
 from parsec.commands.groups.update_group import cli as update_group
 
@@ -25,6 +24,5 @@ def cli():
 cli.add_command(get_group_roles)
 cli.add_command(get_group_users)
 cli.add_command(get_groups)
-cli.add_command(module)
 cli.add_command(show_group)
 cli.add_command(update_group)

parsec/commands/cmd_histories.py

@@ -14,7 +14,6 @@
 from parsec.commands.histories.get_published_histories import cli as get_published_histories
 from parsec.commands.histories.get_status import cli as get_status
 from parsec.commands.histories.import_history import cli as import_history
-from parsec.commands.histories.module import cli as module
 from parsec.commands.histories.open_history import cli as open_history
 from parsec.commands.histories.show_dataset import cli as show_dataset
 from parsec.commands.histories.show_dataset_collection import cli as show_dataset_collection
@@ -48,7 +47,6 @@ def cli():
 cli.add_command(get_published_histories)
 cli.add_command(get_status)
 cli.add_command(import_history)
-cli.add_command(module)
 cli.add_command(open_history)
 cli.add_command(show_dataset)
 cli.add_command(show_dataset_collection)

parsec/commands/cmd_init.py

@@ -56,10 +56,10 @@ def cli(ctx, url=None, api_key=None, admin=False, **kwds):
     while True:
         galaxy_url = url
         if url is None or len(url) == 0 :
-            galaxy_url = click.prompt("Please entry your Galaxy's URL")
+            galaxy_url = click.prompt("Please enter your Galaxy's URL")
         galaxy_key = api_key
         if api_key is None or len(api_key) == 0 :
-            galaxy_key = click.prompt("Please entry your Galaxy API Key")
+            galaxy_key = click.prompt("Please enter your Galaxy API Key")
         info("Testing connection...")
         gi = galaxy.GalaxyInstance(galaxy_url, galaxy_key)
         try:

parsec/commands/cmd_invocations.py

@@ -6,7 +6,6 @@
 from parsec.commands.invocations.get_invocation_step_jobs_summary import cli as get_invocation_step_jobs_summary
 from parsec.commands.invocations.get_invocation_summary import cli as get_invocation_summary
 from parsec.commands.invocations.get_invocations import cli as get_invocations
-from parsec.commands.invocations.module import cli as module
 from parsec.commands.invocations.rerun_invocation import cli as rerun_invocation
 from parsec.commands.invocations.run_invocation_step_action import cli as run_invocation_step_action
 from parsec.commands.invocations.show_invocation import cli as show_invocation
@@ -26,7 +25,6 @@ def cli():
 cli.add_command(get_invocation_step_jobs_summary)
 cli.add_command(get_invocation_summary)
 cli.add_command(get_invocations)
-cli.add_command(module)
 cli.add_command(rerun_invocation)
 cli.add_command(run_invocation_step_action)
 cli.add_command(show_invocation)

parsec/commands/cmd_jobs.py

@@ -7,7 +7,6 @@
 from parsec.commands.jobs.get_metrics import cli as get_metrics
 from parsec.commands.jobs.get_outputs import cli as get_outputs
 from parsec.commands.jobs.get_state import cli as get_state
-from parsec.commands.jobs.module import cli as module
 from parsec.commands.jobs.report_error import cli as report_error
 from parsec.commands.jobs.rerun_job import cli as rerun_job
 from parsec.commands.jobs.resume_job import cli as resume_job
@@ -31,7 +30,6 @@ def cli():
 cli.add_command(get_metrics)
 cli.add_command(get_outputs)
 cli.add_command(get_state)
-cli.add_command(module)
 cli.add_command(report_error)
 cli.add_command(rerun_job)
 cli.add_command(resume_job)

parsec/commands/cmd_libraries.py

@@ -8,7 +8,6 @@
 from parsec.commands.libraries.get_folders import cli as get_folders
 from parsec.commands.libraries.get_libraries import cli as get_libraries
 from parsec.commands.libraries.get_library_permissions import cli as get_library_permissions
-from parsec.commands.libraries.module import cli as module
 from parsec.commands.libraries.set_dataset_permissions import cli as set_dataset_permissions
 from parsec.commands.libraries.set_library_permissions import cli as set_library_permissions
 from parsec.commands.libraries.show_dataset import cli as show_dataset
@@ -37,7 +36,6 @@ def cli():
 cli.add_command(get_folders)
 cli.add_command(get_libraries)
 cli.add_command(get_library_permissions)
-cli.add_command(module)
 cli.add_command(set_dataset_permissions)
 cli.add_command(set_library_permissions)
 cli.add_command(show_dataset)

parsec/commands/cmd_quotas.py

@@ -2,7 +2,6 @@
 from parsec.commands.quotas.create_quota import cli as create_quota
 from parsec.commands.quotas.delete_quota import cli as delete_quota
 from parsec.commands.quotas.get_quotas import cli as get_quotas
-from parsec.commands.quotas.module import cli as module
 from parsec.commands.quotas.show_quota import cli as show_quota
 from parsec.commands.quotas.undelete_quota import cli as undelete_quota
 from parsec.commands.quotas.update_quota import cli as update_quota
@@ -16,7 +15,6 @@ def cli():
 cli.add_command(create_quota)
 cli.add_command(delete_quota)
 cli.add_command(get_quotas)
-cli.add_command(module)
 cli.add_command(show_quota)
 cli.add_command(undelete_quota)
 cli.add_command(update_quota)

parsec/commands/cmd_roles.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.roles.create_role import cli as create_role
 from parsec.commands.roles.get_roles import cli as get_roles
-from parsec.commands.roles.module import cli as module
 from parsec.commands.roles.show_role import cli as show_role
 
 
@@ -12,5 +11,4 @@ def cli():
 
 cli.add_command(create_role)
 cli.add_command(get_roles)
-cli.add_command(module)
 cli.add_command(show_role)

parsec/commands/cmd_toolShed.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.toolShed.get_repositories import cli as get_repositories
 from parsec.commands.toolShed.install_repository_revision import cli as install_repository_revision
-from parsec.commands.toolShed.module import cli as module
 from parsec.commands.toolShed.show_repository import cli as show_repository
 from parsec.commands.toolShed.uninstall_repository_revision import cli as uninstall_repository_revision
 
@@ -13,6 +12,5 @@ def cli():
 
 cli.add_command(get_repositories)
 cli.add_command(install_repository_revision)
-cli.add_command(module)
 cli.add_command(show_repository)
 cli.add_command(uninstall_repository_revision)

parsec/commands/cmd_tool_data.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.tool_data.delete_data_table import cli as delete_data_table
 from parsec.commands.tool_data.get_data_tables import cli as get_data_tables
-from parsec.commands.tool_data.module import cli as module
 from parsec.commands.tool_data.reload_data_table import cli as reload_data_table
 from parsec.commands.tool_data.show_data_table import cli as show_data_table
 
@@ -13,6 +12,5 @@ def cli():
 
 cli.add_command(delete_data_table)
 cli.add_command(get_data_tables)
-cli.add_command(module)
 cli.add_command(reload_data_table)
 cli.add_command(show_data_table)

parsec/commands/cmd_tool_dependencies.py

@@ -1,5 +1,4 @@
 import click
-from parsec.commands.tool_dependencies.module import cli as module
 from parsec.commands.tool_dependencies.summarize_toolbox import cli as summarize_toolbox
 
 
@@ -8,5 +7,4 @@ def cli():
     pass
 
 
-cli.add_command(module)
 cli.add_command(summarize_toolbox)

parsec/commands/cmd_tools.py

@@ -3,7 +3,6 @@
 from parsec.commands.tools.get_tool_panel import cli as get_tool_panel
 from parsec.commands.tools.get_tools import cli as get_tools
 from parsec.commands.tools.install_dependencies import cli as install_dependencies
-from parsec.commands.tools.module import cli as module
 from parsec.commands.tools.paste_content import cli as paste_content
 from parsec.commands.tools.put_url import cli as put_url
 from parsec.commands.tools.requirements import cli as requirements
@@ -23,7 +22,6 @@ def cli():
 cli.add_command(get_tool_panel)
 cli.add_command(get_tools)
 cli.add_command(install_dependencies)
-cli.add_command(module)
 cli.add_command(paste_content)
 cli.add_command(put_url)
 cli.add_command(requirements)

parsec/commands/cmd_toolshed.py

@@ -1,7 +1,6 @@
 import click
 from parsec.commands.toolshed.get_repositories import cli as get_repositories
 from parsec.commands.toolshed.install_repository_revision import cli as install_repository_revision
-from parsec.commands.toolshed.module import cli as module
 from parsec.commands.toolshed.show_repository import cli as show_repository
 from parsec.commands.toolshed.uninstall_repository_revision import cli as uninstall_repository_revision
 
@@ -13,6 +12,5 @@ def cli():
 
 cli.add_command(get_repositories)
 cli.add_command(install_repository_revision)
-cli.add_command(module)
 cli.add_command(show_repository)
 cli.add_command(uninstall_repository_revision)

parsec/commands/cmd_users.py

@@ -6,7 +6,6 @@
 from parsec.commands.users.get_current_user import cli as get_current_user
 from parsec.commands.users.get_user_apikey import cli as get_user_apikey
 from parsec.commands.users.get_users import cli as get_users
-from parsec.commands.users.module import cli as module
 from parsec.commands.users.show_user import cli as show_user
 from parsec.commands.users.update_user import cli as update_user
 
@@ -23,6 +22,5 @@ def cli():
 cli.add_command(get_current_user)
 cli.add_command(get_user_apikey)
 cli.add_command(get_users)
-cli.add_command(module)
 cli.add_command(show_user)
 cli.add_command(update_user)

parsec/commands/cmd_visual.py

@@ -1,6 +1,5 @@
 import click
 from parsec.commands.visual.get_visualizations import cli as get_visualizations
-from parsec.commands.visual.module import cli as module
 from parsec.commands.visual.show_visualization import cli as show_visualization
 
 
@@ -10,5 +9,4 @@ def cli():
 
 
 cli.add_command(get_visualizations)
-cli.add_command(module)
 cli.add_command(show_visualization)

parsec/commands/cmd_workflows.py

@@ -11,7 +11,6 @@
 from parsec.commands.workflows.import_workflow_dict import cli as import_workflow_dict
 from parsec.commands.workflows.import_workflow_from_local_path import cli as import_workflow_from_local_path
 from parsec.commands.workflows.invoke_workflow import cli as invoke_workflow
-from parsec.commands.workflows.module import cli as module
 from parsec.commands.workflows.refactor_workflow import cli as refactor_workflow
 from parsec.commands.workflows.run_invocation_step_action import cli as run_invocation_step_action
 from parsec.commands.workflows.run_workflow import cli as run_workflow
@@ -39,7 +38,6 @@ def cli():
 cli.add_command(import_workflow_dict)
 cli.add_command(import_workflow_from_local_path)
 cli.add_command(invoke_workflow)
-cli.add_command(module)
 cli.add_command(refactor_workflow)
 cli.add_command(run_invocation_step_action)
 cli.add_command(run_workflow)