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Add --table option in contents #33

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Merged
dwhswenson merged 4 commits into from
Dec 11, 2020
Merged

Add --table option in contents #33

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695ed8b
Add support for --table option in `contents`
dwhswenson Dec 8, 2020
47e41af
Tests for --table arg to contents
dwhswenson Dec 8, 2020
dd4ec60
Some cleanup in contents; complete testing
dwhswenson Dec 9, 2020
586e6e4
add test for tags table
dwhswenson Dec 9, 2020
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Add support for --table option in contents
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@dwhswenson
dwhswenson committed Dec 8, 2020
commit 695ed8b973f73e6c28899316de0d6dc3e6272ea3
36 changes: 29 additions & 7 deletions paths_cli/commands/contents.py
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Original file line number Diff line number Diff line change
@@ -1,19 +1,45 @@
import click
from paths_cli.parameters import INPUT_FILE

UNNAMED_SECTIONS = {
'Steps': lambda storage: storage.steps,
'Move Changes': lambda storage: storage.movechanges,
'SampleSets': lambda storage: storage.samplesets,
'Trajectories': lambda storage: storage.trajectories,
'Snapshots': lambda storage: storage.snapshots
}

@click.command(
'contents',
short_help="list named objects from an OPS .nc file",
)
@INPUT_FILE.clicked(required=True)
def contents(input_file):
@click.option('--table', type=str, required=False,
help="table to show results from")
def contents(input_file, table):
"""List the names of named objects in an OPS .nc file.

This is particularly useful when getting ready to use one of simulation
scripts (i.e., to identify exactly how a state or engine is named.)
"""
storage = INPUT_FILE.get(input_file)
print(storage)
if table is None:
report_all_tables(storage)
else:
table_attr = table.lower()
try:
store = getattr(storage, table_attr)
except AttributeError:
print("This needs to raise a good error; bad table name")
else:
if table_attr in UNNAMED_SECTIONS:
print(get_unnamed_section_string(table_attr, store))
else:
print(get_section_string_nameable(table_attr, store,
_get_named_namedobj))

def report_all_tables(storage):
store_section_mapping = {
'CVs': storage.cvs, 'Volumes': storage.volumes,
'Engines': storage.engines, 'Networks': storage.networks,
Expand All @@ -26,12 +52,8 @@ def contents(input_file):
print(get_section_string_nameable('Tags', storage.tags, _get_named_tags))

print("\nData Objects:")
unnamed_sections = {
'Steps': storage.steps, 'Move Changes': storage.movechanges,
'SampleSets': storage.samplesets,
'Trajectories': storage.trajectories, 'Snapshots': storage.snapshots
}
for section, store in unnamed_sections.items():
for section, store_func in UNNAMED_SECTIONS.items():
store = store_func(storage)
print(get_unnamed_section_string(section, store))

def _item_or_items(count):
Expand Down