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chore: Convert str.format to f-strings #138

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merged 4 commits into from
Feb 5, 2024
Merged

chore: Convert str.format to f-strings #138

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4ecadf7
chore: Convert str.format to f-strings
sellth Jan 25, 2024
f5e0a1b
fix typo
sellth Jan 29, 2024
825d8e5
update snapshots for previously missing Description output
sellth Jan 29, 2024
fa8320d
adapt testing because of previously missing Description field
sellth Jan 29, 2024
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33 changes: 14 additions & 19 deletions altamisa/apps/isatab2dot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,18 +34,15 @@
):
print(indent + "/* materials */", file=outf)
for name, mat in obj.materials.items():
label = json.dumps("{}:\n{}\n({})".format(mat.type, mat.name if mat.name else "-", name))
label = json.dumps(f"{mat.type}:\n{mat.name if mat.name else '-'}\n({name})")
print(
"{}{} [label={},shape={},color={},fontcolor={}]".format(
indent, json.dumps(name), label, mat_shape, mat_color, mat_color
),
f"{indent}{json.dumps(name)} [label={label},shape={mat_shape},color={mat_color},fontcolor={mat_color}]",
file=outf,
)
print(indent + "/* processes */", file=outf)
for name, proc in obj.processes.items():
label = json.dumps(
"{}:\n{}\n{}\n({})".format(
"Process",
"Process:\n{}\n{}\n({})".format(
proc.protocol_ref if proc.protocol_ref else "-",
proc.name if proc.name else "-",
name,
Expand All @@ -59,7 +56,7 @@
)
print(indent + "/* arcs */", file=outf)
for arc in obj.arcs:
print("{}{} -> {};".format(indent, json.dumps(arc.tail), json.dumps(arc.head)), file=outf)
print(f"{indent}{json.dumps(arc.tail)} -> {json.dumps(arc.head)};", file=outf)


def run(args: Arguments):
Expand All @@ -79,27 +76,25 @@

for s, study_info in enumerate(investigation.studies):
if not study_info.info.path:
print(" /* no file for study {} */".format(s + 1), file=output_file)
print(f" /* no file for study {s + 1} */", file=output_file)

Check warning on line 79 in altamisa/apps/isatab2dot.py

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continue
with open(os.path.join(path, study_info.info.path), "rt") as inputf:
study = StudyReader.from_stream("S{}".format(s + 1), inputf).read()
print(" /* study {} */".format(study_info.info.path), file=output_file)
print(" subgraph clusterStudy{} {{".format(s), file=output_file)
print(' label = "Study: {}"'.format(study_info.info.path), file=output_file)
study = StudyReader.from_stream(f"S{s + 1}", inputf).read()
print(f" /* study {study_info.info.path} */", file=output_file)
print(f" subgraph clusterStudy{s} {{", file=output_file)
print(f' label = "Study: {study_info.info.path}"', file=output_file)
print_dot(study, output_file)
print(" }", file=output_file)

for a, assay_info in enumerate(study_info.assays):
if not assay_info.path:
print(" /* no file for assay {} */".format(a + 1), file=output_file)
print(f" /* no file for assay {a + 1} */", file=output_file)

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continue
with open(os.path.join(path, assay_info.path), "rt") as inputf:
assay = AssayReader.from_stream(
"S{}".format(s + 1), "A{}".format(a + 1), inputf
).read()
print(" /* assay {} */".format(assay_info.path), file=output_file)
print(" subgraph clusterAssayS{}A{} {{".format(s, a), file=output_file)
print(' label = "Assay: {}"'.format(assay_info.path), file=output_file)
assay = AssayReader.from_stream(f"S{s + 1}", f"A{a + 1}", inputf).read()
print(f" /* assay {assay_info.path} */", file=output_file)
print(f" subgraph clusterAssayS{s}A{a} {{", file=output_file)
print(f' label = "Assay: {assay_info.path}"', file=output_file)
print_dot(assay, output_file)
print(" }", file=output_file)

Expand Down
9 changes: 3 additions & 6 deletions altamisa/apps/isatab2isatab.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,7 @@ def run_warnings_caught(args: Arguments):
path_in = os.path.realpath(os.path.dirname(args.input_investigation_file))
path_out = os.path.realpath(os.path.dirname(args.output_investigation_file))
if path_in == path_out:
tpl = "Can't output ISA-tab files to same directory as as input: {} == {}"
msg = tpl.format(path_in, path_out)
msg = f"Can't output ISA-tab files to same directory as as input: {path_in} == {path_out}"
raise IsaException(msg)

with ExitStack() as stack:
Expand Down Expand Up @@ -98,15 +97,13 @@ def run_reading(
for s, study_info in enumerate(investigation.studies):
if study_info.info.path:
with open(os.path.join(path_in, study_info.info.path), "rt") as inputf:
studies[s] = StudyReader.from_stream("S{}".format(s + 1), inputf).read()
studies[s] = StudyReader.from_stream(f"S{s + 1}", inputf).read()
if study_info.assays:
assays[s] = {}
for a, assay_info in enumerate(study_info.assays):
if assay_info.path:
with open(os.path.join(path_in, assay_info.path), "rt") as inputf:
assays[s][a] = AssayReader.from_stream(
"S{}".format(s + 1), "A{}".format(a + 1), inputf
).read()
assays[s][a] = AssayReader.from_stream(f"S{s + 1}", f"A{a + 1}", inputf).read()

# Validate studies and assays
for s, study_info in enumerate(investigation.studies):
Expand Down
6 changes: 2 additions & 4 deletions altamisa/apps/isatab_validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,15 +82,13 @@ def run_warnings_caught(args: Arguments):
for s, study_info in enumerate(investigation.studies):
if study_info.info.path:
with open(os.path.join(path_in, study_info.info.path), "rt") as inputf:
studies[s] = StudyReader.from_stream("S{}".format(s + 1), inputf).read()
studies[s] = StudyReader.from_stream(f"S{s + 1}", inputf).read()
if study_info.assays:
assays[s] = {}
for a, assay_info in enumerate(study_info.assays):
if assay_info.path:
with open(os.path.join(path_in, assay_info.path), "rt") as inputf:
assays[s][a] = AssayReader.from_stream(
"S{}".format(s + 1), "A{}".format(a + 1), inputf
).read()
assays[s][a] = AssayReader.from_stream(f"S{s + 1}", f"A{a + 1}", inputf).read()

# Validate studies and assays
for s, study_info in enumerate(investigation.studies):
Expand Down
6 changes: 2 additions & 4 deletions altamisa/isatab/headers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -446,8 +446,7 @@ def _parse_next(self):
raise ParseIsatabException(msg)
return self._parse_labeled_column_header(val, label, type_)
# None of the if-statements above was taken
tpl = 'Header "{}" unknown, processing unclear'
msg = tpl.format(val)
msg = f'Header "{val}" unknown, processing unclear'
raise ParseIsatabException(msg)

def _parse_term_source_ref(self):
Expand All @@ -471,8 +470,7 @@ def _parse_simple_column_header(self, type_):
def _parse_labeled_column_header(self, val, key, type_):
tok = val[len(key) :] # strip '^{key}'
if not tok or tok[0] != "[" or tok[-1] != "]":
tpl = "Problem parsing labeled header {}"
msg = tpl.format(val)
msg = f"Problem parsing labeled header {val}"
raise ParseIsatabException(msg)
self.col_no += 1
return type_(self.col_no - 1, tok[1:-1])
Expand Down
3 changes: 1 addition & 2 deletions altamisa/isatab/helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ def list_strip(line: List[str]) -> List[str]:
"""Remove trailing space from strings in a list (e.g. a csv line)"""
new_line = [field.strip() for field in line]
if new_line != line:
tpl = "Removed trailing whitespaces in fields of line: {}"
msg = tpl.format(line)
msg = f"Removed trailing whitespaces in fields of line: {line}"
warnings.warn(msg, ParseIsatabWarning)
return new_line
2 changes: 1 addition & 1 deletion altamisa/isatab/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -509,7 +509,7 @@ def __getitem__(self, idx):
elif idx == 1:
return self.head
else:
raise IndexError("Invalid index: %d" % idx) # pragma: no cover
raise IndexError(f"Invalid index: {idx}") # pragma: no cover


@attr.s(auto_attribs=True, frozen=True)
Expand Down
76 changes: 33 additions & 43 deletions altamisa/isatab/parse_assay_study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,8 +130,10 @@ def _assign_column_headers(self): # noqa: C901
header.column_type not in self.name_headers
and header.column_type not in self.allowed_column_types
):
tpl = 'Invalid column type occured "{}" not in {}'
msg = tpl.format(header.column_type, self.allowed_column_types)
msg = (
"Invalid column type occured "
f'"{header.column_type}" not in {self.allowed_column_types}'
)
raise ParseIsatabException(msg)
# Most headers are not secondary, so make this the default state.
is_secondary = False
Expand Down Expand Up @@ -206,7 +208,7 @@ def _assign_column_headers(self): # noqa: C901
): # pragma: no cover
tpl = (
"Ontologies not supported for primary annotation "
"'{}' (in col {}).".format(prev.column_type, "{}")
f"'{prev.column_type}' (in col {{}})."
)
elif prev.term_source_ref_header: # pragma: no cover
tpl = 'Seen "Term Source REF" header for same entity ' "in col {}"
Expand All @@ -232,8 +234,7 @@ def _assign_column_headers(self): # noqa: C901

@staticmethod
def _raise_seen_before(name, col_no): # pragma: no cover
tpl = 'Seen "{}" header for same entity in col {}'
msg = tpl.format(name, col_no)
msg = f'Seen "{name}" header for same entity in col {col_no}'
raise ParseIsatabException(msg)

def _build_complex(
Expand All @@ -256,7 +257,7 @@ def _build_complex(
unit = self._build_freetext_or_term_ref(header.unit_header, line)
if unit is not None and not isinstance(unit, (str, models.OntologyTermRef)):
raise ParseIsatabException(
"Unit must be a string or an OntologyTermRef, not {}".format(type(unit))
f"Unit must be a string or an OntologyTermRef, not {type(unit)}"
)
# Then, constructing ``klass`` is easy
return klass(header.label, value, unit)
Expand Down Expand Up @@ -284,11 +285,10 @@ def _build_freetext_or_term_ref(
]
return term_refs
else: # pragma: no cover
tpl = (
msg = (
"Irregular numbers of fields in ontology term columns"
"(i.e. ';'-separated fields): {}"
f"(i.e. ';'-separated fields): {line[header.col_no : header2.col_no + 2]}"
)
msg = tpl.format(line[header.col_no : header2.col_no + 2])
raise ParseIsatabException(msg)

# Else, just create single ontology term references
Expand Down Expand Up @@ -348,24 +348,22 @@ def build(self, line: List[str]) -> models.Material:
# First, build the individual components
if not self.name_header:
raise ParseIsatabException(
"No name header found for material found for file {}".format(self.filename)
f"No name header found for material found for file {self.filename}"
)
type_ = self.name_header.column_type
assay_id = "-{}".format(self.assay_id) if self.assay_id else ""
assay_id = f"-{self.assay_id}" if self.assay_id else ""
name = line[self.name_header.col_no]
if name:
# make material/data names unique by column
if self.name_header.column_type == table_headers.SOURCE_NAME:
unique_name = "{}-{}-{}".format(self.study_id, "source", name)
unique_name = f"{self.study_id}-source-{name}"
elif self.name_header.column_type == table_headers.SAMPLE_NAME:
# use static column identifier "sample-", since the same
# samples occur in different columns in study and assay
unique_name = "{}-{}-{}".format(self.study_id, "sample", name)
unique_name = f"{self.study_id}-sample-{name}"
else:
# anything else gets the column id
unique_name = "{}{}-{}-COL{}".format(
self.study_id, assay_id, name, self.name_header.col_no + 1
)
unique_name = f"{self.study_id}{assay_id}-{name}-COL{self.name_header.col_no + 1}"
else:
name_val = "{}{}-{} {}-{}-{}".format(
self.study_id,
Expand Down Expand Up @@ -434,8 +432,7 @@ def build(self, line: List[str]) -> models.Process:
try:
date = datetime.strptime(line[self.date_header.col_no], "%Y-%m-%d").date()
except ValueError as e: # pragma: no cover
tpl = 'Invalid ISO8601 date "{}"' # pragma: no cover
msg = tpl.format(line[self.date_header.col_no])
msg = f'Invalid ISO8601 date "{line[self.date_header.col_no]}"' # pragma: no cover
raise ParseIsatabException(msg) from e
else:
date = ""
Expand Down Expand Up @@ -479,14 +476,11 @@ def _build_protocol_ref_and_name(
) -> Tuple[str, Union[models.AnnotatedStr, str], Optional[str], Optional[str]]:
# At least one of these headers has to be specified
if not self.name_header and not self.protocol_ref_header: # pragma: no cover
raise ParseIsatabException(
"No protocol reference header found for process found for file {}".format(
self.filename
)
)
msg = f"No protocol reference header found for process found for file {self.filename}"
raise ParseIsatabException(msg)
# Perform case distinction on which case is actually true
counter_value = self._next_counter()
assay_id = "-{}".format(self.assay_id) if self.assay_id else ""
assay_id = f"-{self.assay_id}" if self.assay_id else ""
name = None
name_type = None
if not self.name_header: # and self.protocol_ref_header:
Expand All @@ -509,9 +503,7 @@ def _build_protocol_ref_and_name(
name = line[self.name_header.col_no]
name_type = self.name_header.column_type
if name: # Use name if available
unique_name = "{}{}-{}-{}".format(
self.study_id, assay_id, name, self.name_header.col_no + 1
)
unique_name = f"{self.study_id}{assay_id}-{name}-{self.name_header.col_no + 1}"
else: # Empty! # pragma: no cover
name_val = "{}{}-{} {}-{}-{}".format(
self.study_id,
Expand All @@ -527,9 +519,7 @@ def _build_protocol_ref_and_name(
name = line[self.name_header.col_no]
name_type = self.name_header.column_type
if name:
unique_name = "{}{}-{}-{}".format(
self.study_id, assay_id, name, self.name_header.col_no + 1
)
unique_name = f"{self.study_id}{assay_id}-{name}-{self.name_header.col_no + 1}"
else:
name_val = "{}{}-{}-{}-{}".format(
self.study_id,
Expand All @@ -544,7 +534,7 @@ def _build_protocol_ref_and_name(
tpl = "Missing protocol reference in column {} of file {} "
msg = tpl.format(self.protocol_ref_header.col_no + 1, self.filename)
else:
msg = "Missing protocol reference in file {}".format(self.filename)
msg = f"Missing protocol reference in file {self.filename}"
raise ParseIsatabException(msg)
return protocol_ref, unique_name, name, name_type

Expand Down Expand Up @@ -596,16 +586,16 @@ def _intercept_duplicates(self, start, end):
]
header = [h for h in self.header[start:end] if h.column_type in column_types_to_check]
names = [
"{}[{}]".format(h.column_type, h.label)
if isinstance(h, LabeledColumnHeader)
else h.column_type
f"{h.column_type}[{h.label}]" if isinstance(h, LabeledColumnHeader) else h.column_type
for h in header
]
duplicates = set([c for c in names if names.count(c) > 1])
if duplicates:
assay = " assay {}".format(self.assay_id) if self.assay_id else ""
tpl = "Found duplicated column types in header of study {}{}: {}"
msg = tpl.format(self.study_id, assay, ", ".join(duplicates))
assay = f" assay {self.assay_id}" if self.assay_id else ""
msg = (
"Found duplicated column types in header of study "
f"{self.study_id}{assay}: {', '.join(duplicates)}"
)
raise ParseIsatabException(msg)

def _make_breaks(self):
Expand Down Expand Up @@ -768,23 +758,23 @@ def _construct(self, rows):
if (
entry.unique_name in processes and entry != processes[entry.unique_name]
): # pragma: no cover
tpl = (
msg = (
"Found processes with same name but different "
"annotation:\nprocess 1: {}\nprocess 2: {}"
f"annotation:\nprocess 1: {entry}\n"
f"process 2: {processes[entry.unique_name]}"
)
msg = tpl.format(entry, processes[entry.unique_name])
raise ParseIsatabException(msg)
processes[entry.unique_name] = entry
else:
assert isinstance(entry, models.Material)
if (
entry.unique_name in materials and entry != materials[entry.unique_name]
): # pragma: no cover
tpl = (
msg = (
"Found materials with same name but different "
"annotation:\nmaterial 1: {}\nmaterial 2: {}"
f"annotation:\nmaterial 1: {entry}\n"
f"material 2: {materials[entry.unique_name]}"
)
msg = tpl.format(entry, materials[entry.unique_name])
raise ParseIsatabException(msg)
materials[entry.unique_name] = entry
# Collect arc
Expand Down
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