Merge pull request #32 from simonbray/update_1.16

.command-engine-ts.yml

@@ -2,6 +2,7 @@ project_name: parsec
 strict: false
 module:
     base_module: bioblend.toolshed
+    instance_ctx: ti
     instance_cls: "<class 'bioblend.toolshed.ToolShedInstance'>"
     instance_func: ToolShedInstance
     prefix: toolshed_

.command-engine.yml

@@ -2,6 +2,7 @@ project_name: parsec
 strict: false
 module:
     base_module: bioblend.galaxy
+    instance_ctx: gi
     instance_cls: "<class 'bioblend.galaxy.GalaxyInstance'>"
     instance_func: GalaxyInstance
     instance_args:

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)
 ----------------------

README.rst

@@ -671,7 +671,7 @@ Or we can use one of the utility scripts to wait on that workflow to finish befo
 License
 -------
 
-Copyright 2016-2017 Galaxy IUC
+Copyright 2016-2021 Galaxy IUC
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

docs/commands.rst

@@ -12,6 +12,7 @@ describes these commands.
    :maxdepth: 0
 
    commands/config.rst
+   commands/dataset_collections.rst
    commands/datasets.rst
    commands/datatypes.rst
    commands/folders.rst
@@ -27,6 +28,7 @@ describes these commands.
    commands/roles.rst
    commands/toolShed.rst
    commands/tool_data.rst
+   commands/tool_dependencies.rst
    commands/tools.rst
    commands/toolshed.rst
    commands/toolshed_categories.rst

docs/commands/dataset_collections.rst

@@ -0,0 +1,108 @@
+dataset_collections
+===================
+
+This section is auto-generated from the help text for the parsec command
+``dataset_collections``.
+
+
+``download_dataset_collection`` command
+---------------------------------------
+
+**Usage**::
+
+    parsec dataset_collections download_dataset_collection 
+
+**Help**
+
+Download a history dataset collection as an archive.
+
+
+**Output**
+
+
+    Information about the downloaded archive.
+
+   .. note::
+     This method downloads a ``zip`` archive for Galaxy 21.01 and later.
+     For earlier versions of Galaxy this method downloads a ``tgz`` archive.
+     This method is only supported by Galaxy 18.01 or later.
+
+**Options**::
+
+
+      -h, --help  Show this message and exit.
+    
+
+``show_dataset_collection`` command
+-----------------------------------
+
+**Usage**::
+
+    parsec dataset_collections show_dataset_collection [OPTIONS]
+
+**Help**
+
+Get details of a given dataset collection of the current user
+
+
+**Output**
+
+
+    element view of the dataset collection
+
+**Options**::
+
+
+      --instance_type TEXT  instance type of the collection - 'history' or 'library'
+                            [default: history]
+    
+      -h, --help            Show this message and exit.
+    
+
+``wait_for_dataset_collection`` command
+---------------------------------------
+
+**Usage**::
+
+    parsec dataset_collections wait_for_dataset_collection 
+
+**Help**
+
+Wait until all or a specified proportion of elements of a dataset collection are in a terminal state.
+
+
+**Output**
+
+
+    Details of the given dataset collection.
+
+**Options**::
+
+
+      --maxwait FLOAT              Total time (in seconds) to wait for the dataset
+                                   states in the dataset collection to become
+                                   terminal. If not all datasets are in a terminal
+                                   state within this time, a
+                                   ``DatasetCollectionTimeoutException`` will be
+                                   raised.  [default: 12000]
+    
+      --interval FLOAT             Time (in seconds) to wait between two consecutive
+                                   checks.  [default: 3]
+    
+      --proportion_complete FLOAT  Proportion of elements in this collection that
+                                   have to be in a terminal state for this method to
+                                   return. Must be a number between 0 and 1. For
+                                   example: if the dataset collection contains 2
+                                   elements, and proportion_complete=0.5 is
+                                   specified, then wait_for_dataset_collection will
+                                   return as soon as 1 of the 2 datasets is in a
+                                   terminal state. Default is 1, i.e. all elements
+                                   must complete.  [default: 1.0]
+    
+      --check                      Whether to check if all the terminal states of
+                                   datasets in the dataset collection are 'ok'. This
+                                   will raise an Exception if a dataset is in a
+                                   terminal state other than 'ok'.  [default: True]
+    
+      -h, --help                   Show this message and exit.
+    

docs/commands/datasets.rst

@@ -63,23 +63,94 @@ Download a dataset to file or in memory. If the dataset state is not 'ok', a ``D
 
 **Help**
 
-Provide a list of all datasets. Since this may be very large, ``limit`` and ``offset`` parameters should be used to specify the desired range.
+Get the latest datasets, or select another subset by specifying optional arguments for filtering (e.g. a history ID).
 
 
 **Output**
 
 
-    Return a list of dataset dicts.
+
 
 **Options**::
 
 
-      --limit INTEGER   Maximum number of datasets to return.  [default: 500]
-      --offset INTEGER  Return datasets starting from this specified position. For
-                        example, if ``limit`` is set to 100 and ``offset`` to 200,
-                        datasets 200-299 will be returned.
+      --limit INTEGER         Maximum number of datasets to return.  [default: 500]
+      --offset INTEGER        Return datasets starting from this specified position.
+                              For example, if ``limit`` is set to 100 and ``offset``
+                              to 200, datasets 200-299 will be returned.
     
-      -h, --help        Show this message and exit.
+      --name TEXT             Dataset name to filter on.
+      --extension TEXT        Dataset extension (or list of extensions) to filter
+                              on.
+    
+      --state TEXT            Dataset state (or list of states) to filter on.
+      --visible               Optionally filter datasets by their ``visible``
+                              attribute.
+    
+      --deleted               Optionally filter datasets by their ``deleted``
+                              attribute.
+    
+      --purged                Optionally filter datasets by their ``purged``
+                              attribute.
+    
+      --tool_id TEXT          Tool ID to filter on.
+      --tag TEXT              Dataset tag to filter on.
+      --history_id TEXT       Encoded history ID to filter on.
+      --create_time_min TEXT  Show only datasets created after the provided time and
+                              date, which should be formatted as ``YYYY-MM-DDTHH-MM-
+                              SS``.
+    
+      --create_time_max TEXT  Show only datasets created before the provided time
+                              and date, which should be formatted as ``YYYY-MM-
+                              DDTHH-MM-SS``.
+    
+      --update_time_min TEXT  Show only datasets last updated after the provided
+                              time and date, which should be formatted as ``YYYY-MM-
+                              DDTHH-MM-SS``.
+    
+      --update_time_max TEXT  Show only datasets last updated before the provided
+                              time and date, which should be formatted as ``YYYY-MM-
+                              DDTHH-MM-SS``.
+    
+      --order TEXT            One or more of the following attributes for ordering
+                              datasets: ``create_time`` (default), ``extension``,
+                              ``hid``, ``history_id``, ``name``, ``update_time``.
+                              Optionally, ``-asc`` or ``-dsc`` (default) can be
+                              appended for ascending and descending order
+                              respectively. Multiple attributes can be stacked as a
+                              comma-separated list of values, e.g. ``create_time-
+                              asc,hid-dsc``.  [default: create_time-dsc]
+    
+      -h, --help              Show this message and exit.
+    
+
+``publish_dataset`` command
+---------------------------
+
+**Usage**::
+
+    parsec datasets publish_dataset [OPTIONS] DATASET_ID
+
+**Help**
+
+Make a dataset publicly available or private. For more fine-grained control (assigning different permissions to specific roles), use the ``update_permissions()`` method.
+
+
+**Output**
+
+
+    Current roles for all available permission types.
+
+   .. note::
+     This method can only be used with Galaxy ``release_19.05`` or later.
+
+**Options**::
+
+
+      --published  Whether to make the dataset published (``True``) or private
+                   (``False``).
+    
+      -h, --help   Show this message and exit.
     
 
 ``show_dataset`` command
@@ -108,3 +179,72 @@ Get details about a given dataset. This can be a history or a library dataset.
     
       -h, --help       Show this message and exit.
     
+
+``update_permissions`` command
+------------------------------
+
+**Usage**::
+
+    parsec datasets update_permissions [OPTIONS] DATASET_ID
+
+**Help**
+
+Set access, manage or modify permissions for a dataset to a list of roles.
+
+
+**Output**
+
+
+    Current roles for all available permission types.
+
+   .. note::
+     This method can only be used with Galaxy ``release_19.05`` or later.
+
+**Options**::
+
+
+      --access_ids TEXT  role IDs which should have access permissions for the
+                         dataset.
+    
+      --manage_ids TEXT  role IDs which should have manage permissions for the
+                         dataset.
+    
+      --modify_ids TEXT  role IDs which should have modify permissions for the
+                         dataset.
+    
+      -h, --help         Show this message and exit.
+    
+
+``wait_for_dataset`` command
+----------------------------
+
+**Usage**::
+
+    parsec datasets wait_for_dataset [OPTIONS] DATASET_ID
+
+**Help**
+
+Wait until a dataset is in a terminal state.
+
+
+**Output**
+
+
+    Details of the given dataset.
+
+**Options**::
+
+
+      --maxwait FLOAT   Total time (in seconds) to wait for the dataset state to
+                        become terminal. If the dataset state is not terminal within
+                        this time, a ``DatasetTimeoutException`` will be raised.
+                        [default: 12000]
+    
+      --interval FLOAT  Time (in seconds) to wait between 2 consecutive checks.
+                        [default: 3]
+    
+      --check           Whether to check if the dataset terminal state is 'ok'.
+                        [default: True]
+    
+      -h, --help        Show this message and exit.
+