def test_protocol_iadd():
# The core functionality is tested by `test_protocol_merge()`; this just
# needs to make sure the `+=` syntax works.
p = Protocol()
assert p.steps == []
p += "A"
assert p.steps == ["A"]
assert p[-1] == "A"
# Do it again just to make sure the first addition didn't put the protocol
# into some kind of broken state.
p += "B"
assert p.steps == ["A", "B"]
assert p[-1] == "B"
p += ["C", "D"]
assert p.steps == ["A", "B", "C", "D"]
assert p[-1] == "D"
p += pl("E")
assert p.steps == ["A", "B", "C", "D", pl("E")]
assert p[-1] == pl("E")
p += [pl("F"), pl("G")]
assert p.steps == ["A", "B", "C", "D", pl("E"), pl("F"), pl("G")]
assert p[-1] == pl("G")
p += Protocol(steps=["H"], footnotes={1: "h"})
assert p.steps == ["A", "B", "C", "D", pl("E"), pl("F"), pl("G"), "H"]
assert p.footnotes == {1: "h"}
assert p[-1] == "H"
def test_protocol_add():
p1 = Protocol(steps=["Step 1"])
p2 = Protocol(steps=["Step 2"])
p3 = p1 + p2
assert p1.steps == ["Step 1"]
assert p2.steps == ["Step 2"]
assert p3.steps == ["Step 1", "Step 2"]
def test_api_add_categories(empty_db):
db = empty_db
assert stash_rows(db) == ul([])
assert stash_category_rows(db) == ul([])
assert category_rows(db) == ul([])
# - Add the protocol.
# - Add an association table entry.
# - Add a category.
add_protocol(db, Protocol(), categories=['A'])
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
])
assert stash_category_rows(db) == ul([
dict(stash_pk=1, category_pk=1),
])
assert category_rows(db) == ul([
dict(pk=1, name='A'),
])
# - Add the protocol.
# - Add an association table entry.
# - Reuse the existing category.
add_protocol(db, Protocol(), categories=['A'])
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
])
assert stash_category_rows(db) == ul([
dict(stash_pk=1, category_pk=1),
dict(stash_pk=2, category_pk=1),
])
assert category_rows(db) == ul([
dict(pk=1, name='A'),
])
# - Add the protocol.
# - Add two association table entrys.
# - Add one category, reuse the other.
add_protocol(db, Protocol(), categories=['A', 'B'])
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
dict(pk=3, id=3, is_complete=False),
])
assert stash_category_rows(db) == ul([
dict(stash_pk=1, category_pk=1),
dict(stash_pk=2, category_pk=1),
dict(stash_pk=3, category_pk=1),
dict(stash_pk=3, category_pk=2),
])
assert category_rows(db) == ul([
dict(pk=1, name='A'),
dict(pk=2, name='B'),
])
def test_api_edit_protocol(empty_db):
db = empty_db
add_protocol(db, Protocol(steps=["A"]))
assert get_protocol(db).protocol.steps == ["A"]
# Keep the existing protocol (since no new protocol is specified):
edit_protocol(db)
assert get_protocol(db).protocol.steps == ["A"]
# Replace the existing protocol:
edit_protocol(db, protocol=Protocol(steps=["B"]))
assert get_protocol(db).protocol.steps == ["B"]
def get_protocol(self):
rxn = self.reaction
p = Protocol()
p += """\
Prepare a HyBond N+ membrane [1]:
- Draw a 50x50 mm grid using a dull pencil.
- Float in distilled water and allow to sink.
- Leave soaking for 10 min.
"""
p += f"""\
Prepare {plural(rxn.num_reactions):# DNA sample/s} [1]:
{rxn}
- Incubate at 95°C for 10 min.
"""
p += """\
Spot DNA [1]:
- Suspend the wetted membrane (e.g. over the top
of an open plastic box).
- Spot 2 µL of prepared DNA into each grid cell.
- Allow to dry.
"""
if self.transfer_type == 'alkaline':
p.steps[-1] += """\
- Rinse briefly in 2x SSC.
- Allow to dry.
"""
if self.transfer_type == 'saline':
p += f"""\
Denature and fix the DNA [1]:
- Place the membrane on sheets of Whatman 3MM
paper soaked in the following solutions:
- 1.5 M NaCl, 0.5 M NaOH for 10 min.
- 1.0 M NaCl, 0.5 M Tris HCl, pH=7.0 for 5 min.
- Not soaked, until dry.
- Irradiate with 254 nm UV light for {self.uv_time}.
"""
p.footnotes[1] = """\
Brown (1993). doi:10.1002/0471142727.mb0209bs21
The NaOH is to chemically hybridize the DNA to the
membrane.
"""
return p
def test_api_reset_dependencies_2(empty_db):
# Dependency graph: 1 → 2
# ↓ ↓
# 3 → 4
db = empty_db
p1 = add_protocol(db, Protocol())
p2 = add_protocol(db, Protocol(), dependencies=[p1.id])
p3 = add_protocol(db, Protocol(), dependencies=[p1.id])
p4 = add_protocol(db, Protocol(), dependencies=[p2.id, p3.id])
db.commit()
# Check that the tables were setup correctly:
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
dict(pk=3, id=3, is_complete=False),
dict(pk=4, id=4, is_complete=False),
])
assert stash_dependency_rows(db) == ul([
dict(upstream_pk=1, downstream_pk=2),
dict(upstream_pk=1, downstream_pk=3),
dict(upstream_pk=2, downstream_pk=4),
dict(upstream_pk=3, downstream_pk=4),
])
# Delete an upstream protocol, update id numbers.
# Delete two association table entries.
drop_protocols(db, [1])
reset_protocols(db)
assert stash_rows(db) == ul([
dict(pk=2, id=1, is_complete=False),
dict(pk=3, id=2, is_complete=False),
dict(pk=4, id=3, is_complete=False),
])
assert stash_dependency_rows(db) == ul([
dict(upstream_pk=2, downstream_pk=4),
dict(upstream_pk=3, downstream_pk=4),
])
# Delete a downstream protocol.
# Delete two association table entries.
drop_protocols(db, [3])
reset_protocols(db)
assert stash_rows(db) == ul([
dict(pk=2, id=1, is_complete=False),
dict(pk=3, id=2, is_complete=False),
])
assert stash_dependency_rows(db) == ul([])
def full_db(empty_db):
"""
Initialize a database with a reasonably diverse set of protocols.
"""
db = empty_db
p1 = add_protocol(db, Protocol(steps=["X"]), message='M')
p2 = add_protocol(db, Protocol(steps=["Y"]), categories=['A'])
p3 = add_protocol(db, Protocol(steps=["Z"]), dependencies=[1])
# Manually change the id numbers to catch bugs any bugs resulting from
# using ids where primary keys are expected or vice versa.
p1.id, p2.id, p3.id = 11, 12, 13
db.commit()
return db
def test_api_get_next_id(empty_db):
db = empty_db
assert get_next_id(db) == 1
p = add_protocol(db, Protocol())
assert get_next_id(db) == 2
p.id = 10
assert get_next_id(db) == 11
def test_protocol_prepend():
a = Protocol(
date=arrow.get(1988, 11, 8),
commands=['command-1'],
steps=['Step 1'],
footnotes={1: 'Footnote A'},
)
b = Protocol(
date=arrow.get(1989, 9, 19),
commands=['command-2'],
steps=['Step 2'],
footnotes={1: 'Footnote B'},
)
b.prepend(a)
assert b.date == arrow.get(1989, 9, 19)
assert b.commands == ['command-1', 'command-2']
assert b.steps == ['Step 1', 'Step 2']
assert b.footnotes == {1: 'Footnote A', 2: 'Footnote B'}
def test_api_reset_categories_1(empty_db):
db = empty_db
add_protocol(db, Protocol(), categories=['A'])
add_protocol(db, Protocol(), categories=['A'])
db.commit()
# Check that the tables were setup correctly.
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
])
assert stash_category_rows(db) == ul([
dict(stash_pk=1, category_pk=1),
dict(stash_pk=2, category_pk=1),
])
assert category_rows(db) == ul([
dict(pk=1, name='A'),
])
# - Delete the protocol, update id numbers.
# - Delete the association table entry.
# - Keep the category.
drop_protocols(db, [1])
reset_protocols(db)
assert stash_rows(db) == ul([
dict(pk=2, id=1, is_complete=False),
])
assert stash_category_rows(db) == ul([
dict(stash_pk=2, category_pk=1),
])
assert category_rows(db) == ul([
dict(pk=1, name='A'),
])
# - Delete the protocol.
# - Delete the association table entry.
# - Delete the category.
drop_protocols(db, [1])
reset_protocols(db)
assert stash_rows(db) == ul([])
assert stash_category_rows(db) == ul([])
assert category_rows(db) == ul([])
def test_api_find_protocols_dependencies(empty_db):
# Extra tests for the specific case where a protocol has two dependencies,
# one of which is completed. This is a bit tricky to get right.
db = empty_db
p1 = add_protocol(db, Protocol())
p2 = add_protocol(db, Protocol())
p3 = add_protocol(db, Protocol(), dependencies=[p1.id, p2.id])
p1.id, p2.id, p3.id = 11, 12, 13
db.commit()
hits = find_protocols(db)
assert {x.id for x in hits} == {p1.id, p2.id}
drop_protocols(db, [p1.id])
hits = find_protocols(db)
assert {x.id for x in hits} == {p2.id}
drop_protocols(db, [p2.id])
hits = find_protocols(db)
assert {x.id for x in hits} == {p3.id}
def test_protocol_format_everything():
"""
Just make sure the spacing between all the elements looks right.
"""
p = Protocol()
p.date = arrow.get(1988, 11, 8)
p.commands = ['sw cmd-1', 'sw cmd-2']
p.steps = ['Step 1', 'Step 2']
p.footnotes = {1: 'Footnote 1', 2: 'Footnote 2'}
assert p.format_text(inf) == """\
def test_api_add(empty_db):
db = empty_db
rows = query_helper(
Stash.id,
Stash.is_complete,
Stash.message,
)
assert rows(db) == ul([])
p1 = add_protocol(db, Protocol(steps=["X"]))
assert get_protocol(db, 1).protocol.steps == ["X"]
assert rows(db) == ul([
dict(id=1, is_complete=False, message=None),
])
p2 = add_protocol(db, Protocol(steps=["Y"]), message="A")
assert get_protocol(db, 2).protocol.steps == ["Y"]
assert rows(db) == ul([
dict(id=1, is_complete=False, message=None),
dict(id=2, is_complete=False, message="A"),
])
def test_api_add_dependencies(empty_db):
db = empty_db
assert stash_rows(db) == ul([])
assert stash_dependency_rows(db) == ul([])
# No dependencies:
add_protocol(db, Protocol())
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
])
assert stash_dependency_rows(db) == ul([])
# One dependency:
add_protocol(db, Protocol(), dependencies=[1])
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
])
assert stash_dependency_rows(db) == ul([
dict(upstream_pk=1, downstream_pk=2),
])
# Two dependencies:
add_protocol(db, Protocol(), dependencies=[1, 2])
assert stash_rows(db) == ul([
dict(pk=1, id=1, is_complete=False),
dict(pk=2, id=2, is_complete=False),
dict(pk=3, id=3, is_complete=False),
])
assert stash_dependency_rows(db) == ul([
dict(upstream_pk=1, downstream_pk=2),
dict(upstream_pk=1, downstream_pk=3),
dict(upstream_pk=2, downstream_pk=3),
])
# Fail to create self-dependency:
with pytest.raises(UsageError, match="No stashed protocol with id '11'"):
add_protocol(db, Protocol(), dependencies=[11])
def test_protocol_clear_footnotes(steps_before, steps_after, footnotes_before):
p = Protocol()
p.steps = steps_before
p.footnotes = footnotes_before
p.clear_footnotes()
assert p.steps == steps_after
assert p.footnotes == {}
def test_protocol_prune_footnotes(steps_before, footnotes_before, steps_after, footnotes_after):
p = Protocol()
p.steps = steps_before
p.footnotes = footnotes_before
p.prune_footnotes()
assert p.steps == steps_after
assert p.footnotes == footnotes_after
def test_protocol_renumber_footnotes(new_ids, steps_before, footnotes_before, steps_after, footnotes_after):
p = Protocol()
p.steps = steps_before
p.footnotes = footnotes_before
p.renumber_footnotes(new_ids)
assert p.steps == steps_after
assert p.footnotes == footnotes_after
def test_protocol_insert_footnotes(steps_before, footnotes_before, footnotes_new, pattern, steps_after, footnotes_after, error):
p = Protocol()
p.steps = steps_before
p.footnotes = footnotes_before
with error:
p.insert_footnotes(*footnotes_new, pattern=pattern)
assert p.steps == steps_after
assert p.footnotes == footnotes_after
def test_protocol_format_footnotes(footnotes, expected):
p = Protocol()
p.footnotes = footnotes
assert p.format_text(inf) == expected.rstrip()
def test_protocol_format_steps(steps, expected):
p = Protocol()
p.steps = steps
assert p.format_text(inf) == expected.rstrip()
def test_protocol_format_commands(commands, expected):
p = Protocol()
p.commands = commands
assert p.format_text(inf) == expected.rstrip()
def test_protocol_format_date(date, expected):
p = Protocol()
p.date = arrow.get(date)
assert p.format_text(inf) == expected.rstrip()
def test_protocol_format_text_empty():
p = Protocol()
assert p.format_text(inf) == ''
def test_protocol_pick_slug(date, commands, expected):
p = Protocol(date=date, commands=commands)
assert p.pick_slug() == expected
def test_protocol_merge_footnotes(steps_before, steps_after):
p = Protocol()
p.steps = steps_before
p.merge_footnotes()
assert p.steps == steps_after
def test_protocol_repr():
p = Protocol()
assert repr(p) == 'Protocol(date=None, commands=[], steps=[], footnotes={})'
#!/usr/bin/env python3
import stepwise
from inform import plural
from stepwise import Protocol, Step, Footnote, MasterMix
p = Protocol()
n = 6
loading_buf = MasterMix("""\
Reagent Stock Volume MM?
====================== ===== ========= ===
water to 5.0 µL y
Bolt LDS sample buffer 4x 2.5 µL y
Bolt reducing agent 10x 1.0 µL y
""")
loading_buf.num_reactions = 2 * n
loading_buf.extra_percent = 50
protein_samples = MasterMix("""\
Reagent Stock Volume MM?
========================= ========= ========== ===
water to 10.0 µL y
loading buffer master mix 2x 5.0 µL y
BSA 500 ng/µL 1.0 µL y
""")
protein_samples.num_reactions = n
protein_samples.extra_percent = 10
dna_samples = MasterMix("""\
Reagent Stock Volume MM?
def test_protocol_merge_err():
with raises(ParseError, match="cannot interpret 42 as a protocol"):
Protocol.merge(42)
def get_protocol(self):
p = Protocol()
p += "Miniprep."
return p
def test_protocol_add_footnotes(footnotes_new, footnotes_before, footnotes_after, formatted_ids):
p = Protocol()
p.footnotes = footnotes_before
assert p.add_footnotes(*footnotes_new) == formatted_ids
assert p.footnotes == footnotes_after