hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore#

class hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore(app, workflow, path, fs)#

Bases: ZarrPersistentStore

A store designed mainly as an archive format that can be uploaded to e.g. Zenodo.

Methods

`add_EAR`	Add a new EAR to an element iteration.
`add_element`	Add a new element to a task.
`add_element_iteration`	Add a new iteration to an element.
`add_element_set`
`add_file`
`add_loop`	Add a new loop to the workflow.
`add_set_parameter`
`add_submission`	Add a new submission.
`add_submission_part`
`add_task`	Add a new task to the workflow.
`add_template_components`
`add_unset_parameter`
`cached_load`	Context manager to cache the root attributes.
`check_parameters_exist`	For each parameter ID, return True if it exists, else False
`copy`	Copy the workflow store.
`delete`	Delete the persistent workflow.
`delete_no_confirm`	Permanently delete the workflow data with no confirmation.
`get_EAR_skipped`
`get_EARs`
`get_creation_info`
`get_element_iterations`
`get_elements`
`get_fs_path`
`get_loops`	Retrieve all loops, including pending.
`get_loops_by_IDs`	Retrieve loops by index (ID), including pending.
`get_parameter_set_statuses`
`get_parameter_sources`
`get_parameters`	param kwargs:
`get_submissions`	Retrieve all submissions, including pending.
`get_submissions_by_ID`
`get_task`
`get_task_elements`	Get element data by an index slice within a given task.
`get_tasks`	Retrieve all tasks, including pending.
`get_tasks_by_IDs`
`get_template`
`get_template_components`	Get all template components, including pending.
`get_ts_fmt`
`get_ts_name_fmt`
`make_test_store_from_spec`	Generate an store for testing purposes.
`prepare_test_store_from_spec`	Generate a valid store from a specification in terms of nested elements/iterations/EARs.
`reinstate_replaced_dir`
`remove_path`	Try very hard to delete a directory or file.
`remove_replaced_dir`
`rename_path`	Revert the replaced workflow path to its original name.
`save`	Commit pending changes to disk, if not in batch-update mode.
`set_EAR_end`
`set_EAR_skip`
`set_EAR_start`
`set_EAR_submission_index`
`set_EARs_initialised`
`set_file`
`set_jobscript_metadata`
`set_parameter_value`
`unzip`
`update_loop_num_iters`
`update_param_source`
`using_resource`	Context manager for managing StoreResource objects associated with the store.
`write_empty_workflow`
`zip`

Attributes

`has_pending`
`is_submittable`	Does this store support workflow submission?
`logger`
`ts_fmt`
`zarr_store`

add_EAR(elem_iter_ID, action_idx, data_idx, metadata, save=True)#

Add a new EAR to an element iteration.

Parameters:

elem_iter_ID (int) –
action_idx (int) –
data_idx (Dict) –
metadata (Dict) –
save (bool) –

Return type:

int

add_element(task_ID, es_idx, seq_idx, src_idx, save=True)#

Add a new element to a task.

Parameters:

task_ID (int) –
es_idx (int) –
seq_idx (Dict) –
src_idx (Dict) –
save (bool) –

add_element_iteration(element_ID, data_idx, schema_parameters, loop_idx=None, save=True)#

Add a new iteration to an element.

Parameters:

element_ID (int) –
data_idx (Dict) –
schema_parameters (List[str]) –
loop_idx (Dict | None) –
save (bool) –

Return type:

int

add_element_set(task_id, es_js, save=True)#

Parameters:

task_id (int) –
es_js (Dict) –
save (bool) –

add_file(store_contents, is_input, source, path=None, contents=None, filename=None, save=True)#

Parameters:

store_contents (bool) –
is_input (bool) –
source (Dict) –
contents (str) –
filename (str) –
save (bool) –

add_loop(loop_template, iterable_parameters, iter_IDs, save=True)#

Add a new loop to the workflow.

Parameters:

loop_template (Dict) –
iter_IDs (List[int]) –
save (bool) –

add_set_parameter(data, source, save=True)#

Parameters:

data (Any) –
source (Dict) –
save (bool) –

Return type:

int

add_submission(sub_idx, sub_js, save=True)#

Add a new submission.

Parameters:

sub_idx (int) –
sub_js (Dict) –
save (bool) –

add_submission_part(sub_idx, dt_str, submitted_js_idx, save=True)#

Parameters:

sub_idx (int) –
dt_str (str) –
submitted_js_idx (List[int]) –
save (bool) –

add_task(idx, task_template, save=True)#

Add a new task to the workflow.

Parameters:

idx (int) –
task_template (Dict) –
save (bool) –

add_template_components(temp_comps, save=True)#

Parameters:

temp_comps (Dict) –
save (bool) –

Return type:

None

add_unset_parameter(source, save=True)#

Parameters:

source (Dict) –
save (bool) –

Return type:

int

cached_load()#

Context manager to cache the root attributes.

Return type:: Iterator[Dict]

check_parameters_exist(id_lst)#

For each parameter ID, return True if it exists, else False

Parameters:: id_lst (Iterable[int]) –
Return type:: List[bool]

copy(path=None)#

Copy the workflow store.

This does not work on remote filesystems.

Return type:: str

delete()#

Delete the persistent workflow.

Return type:: None

delete_no_confirm()#

Permanently delete the workflow data with no confirmation.

Return type:: None

get_EAR_skipped(EAR_ID)#

Parameters:: EAR_ID (int) –
Return type:: bool

get_EARs(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[AnySEAR]

get_creation_info()#

get_element_iterations(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[AnySElementIter]

get_elements(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[AnySElement]

get_fs_path()#

get_loops()#

Retrieve all loops, including pending.

Return type:: Dict[int, Dict]

get_loops_by_IDs(id_lst)#

Retrieve loops by index (ID), including pending.

Parameters:: id_lst (Iterable[int]) –
Return type:: Dict[int, Dict]

get_parameter_set_statuses(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[bool]

get_parameter_sources(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[Dict]

get_parameters(id_lst, **kwargs)#

Parameters:

kwargs (Dict) –

dataset_copybool
For Zarr stores only. If True, copy arrays as NumPy arrays.
id_lst (Iterable[int]) –

Return type:

List[AnySParameter]

get_submissions()#

Retrieve all submissions, including pending.

Return type:: Dict[int, Dict]

get_submissions_by_ID(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: Dict[int, Dict]

get_task(task_idx)#

Parameters:: task_idx (int) –
Return type:: AnySTask

get_task_elements(task_id, idx_sel)#

Get element data by an index slice within a given task.

Element iterations and EARs belonging to the elements are included.

Parameters:: idx_sel (slice) –
Return type:: List[Dict]

get_tasks()#

Retrieve all tasks, including pending.

Return type:: List[AnySTask]

get_tasks_by_IDs(id_lst)#

Parameters:: id_lst (Iterable[int]) –
Return type:: List[AnySTask]

get_template()#

Return type:: Dict

get_template_components()#

Get all template components, including pending.

Return type:: Dict

get_ts_fmt()#

get_ts_name_fmt()#

property has_pending#

property is_submittable#: Does this store support workflow submission?

property logger#

classmethod make_test_store_from_spec(spec, dir=None, path='test_store', overwrite=False)#: Generate an store for testing purposes.

static prepare_test_store_from_spec(task_spec)#: Generate a valid store from a specification in terms of nested elements/iterations/EARs.

reinstate_replaced_dir()#

Return type:: None

remove_path(path, fs)#

Try very hard to delete a directory or file.

Dropbox (on Windows, at least) seems to try to re-sync files if the parent directory is deleted soon after creation, which is the case on a failed workflow creation (e.g. missing inputs), so in addition to catching PermissionErrors generated when Dropbox has a lock on files, we repeatedly try deleting the directory tree.

Parameters:: path (str) –
Return type:: None

remove_replaced_dir()#

Return type:: None

rename_path(replaced, original, fs)#

Revert the replaced workflow path to its original name.

This happens when new workflow creation fails and there is an existing workflow with the same name; the original workflow which was renamed, must be reverted.

Parameters:

replaced (str) –
original (str) –

Return type:

None

save()#: Commit pending changes to disk, if not in batch-update mode.

set_EAR_end(EAR_ID, exit_code, success, save=True)#

Parameters:

EAR_ID (int) –
exit_code (int) –
success (bool) –
save (bool) –

Return type:

datetime

set_EAR_skip(EAR_ID, save=True)#

Parameters:

EAR_ID (int) –
save (bool) –

Return type:

None

set_EAR_start(EAR_ID, save=True)#

Parameters:

EAR_ID (int) –
save (bool) –

Return type:

datetime

set_EAR_submission_index(EAR_ID, sub_idx, save=True)#

Parameters:

EAR_ID (int) –
sub_idx (int) –
save (bool) –

Return type:

None

set_EARs_initialised(iter_ID, save=True)#

Parameters:

iter_ID (int) –
save (bool) –

Return type:

None

set_file(store_contents, is_input, param_id=None, path=None, contents=None, filename=None, clean_up=False, save=True)#

Parameters:

store_contents (bool) –
is_input (bool) –
param_id (int) –
contents (str) –
filename (str) –
clean_up (bool) –
save (bool) –

set_jobscript_metadata(sub_idx, js_idx, version_info=None, submit_time=None, submit_hostname=None, submit_machine=None, submit_cmdline=None, os_name=None, shell_name=None, scheduler_name=None, scheduler_job_ID=None, process_ID=None, save=True)#

Parameters:

sub_idx (int) –
js_idx (int) –
version_info (Dict | None) –
submit_time (str | None) –
submit_hostname (str | None) –
submit_machine (str | None) –
submit_cmdline (List[str] | None) –
os_name (str | None) –
shell_name (str | None) –
scheduler_name (str | None) –
scheduler_job_ID (str | None) –
process_ID (int | None) –
save (bool) –

set_parameter_value(param_id, value, is_file=False, save=True)#

Parameters:

param_id (int) –
value (Any) –
is_file (bool) –
save (bool) –

property ts_fmt: str#

unzip(log=None)#

update_loop_num_iters(index, num_iters, save=True)#

Parameters:

index (int) –
num_iters (int) –
save (bool) –

Return type:

None

update_param_source(param_id, source, save=True)#

Parameters:

param_id (int) –
source (Dict) –
save (bool) –

Return type:

None

using_resource(res_label, action)#: Context manager for managing StoreResource objects associated with the store.

classmethod write_empty_workflow(app, template_js, template_components_js, wk_path, fs, fs_path, replaced_wk, ts_fmt, ts_name_fmt, creation_info)#

Parameters:

template_js (Dict) –
template_components_js (Dict) –
wk_path (str) –
fs_path (str) –
replaced_wk (str) –
ts_fmt (str) –
ts_name_fmt (str) –
creation_info (Dict) –

Return type:

None

property zarr_store: Store#

zip()#