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fix: Handle missing section headers at EOF
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@sellth
sellth committed Nov 2, 2023
1 parent 1009797 commit 18de981
Showing 1 changed file with 21 additions and 11 deletions.
32 changes: 21 additions & 11 deletions altamisa/isatab/parse_investigation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,9 @@ def _read_single_column_section(self, prefix, ref_keys, section_name):
def _read_ontology_source_reference(self) -> Iterator[models.OntologyRef]:
# Read ONTOLOGY SOURCE REFERENCE header
line = self._read_next_line()
if not line[0] == investigation_headers.ONTOLOGY_SOURCE_REFERENCE: # pragma: no cover
if (
line is None or not line[0] == investigation_headers.ONTOLOGY_SOURCE_REFERENCE
): # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.ONTOLOGY_SOURCE_REFERENCE, line)
raise ParseIsatabException(msg)
Expand All @@ -259,7 +261,7 @@ def _read_ontology_source_reference(self) -> Iterator[models.OntologyRef]:
def _read_basic_info(self) -> models.BasicInfo:
# Read INVESTIGATION header
line = self._read_next_line()
if not line[0] == investigation_headers.INVESTIGATION: # pragma: no cover
if line is None or not line[0] == investigation_headers.INVESTIGATION: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.INVESTIGATION, line)
raise ParseIsatabException(msg)
Expand All @@ -286,7 +288,9 @@ def _read_basic_info(self) -> models.BasicInfo:
def _read_publications(self) -> Iterator[models.PublicationInfo]:
# Read INVESTIGATION PUBLICATIONS header
line = self._read_next_line()
if not line[0] == investigation_headers.INVESTIGATION_PUBLICATIONS: # pragma: no cover
if (
line is None or not line[0] == investigation_headers.INVESTIGATION_PUBLICATIONS
): # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.INVESTIGATION_PUBLICATIONS, line)
raise ParseIsatabException(msg)
Expand All @@ -311,7 +315,9 @@ def _read_publications(self) -> Iterator[models.PublicationInfo]:
def _read_contacts(self) -> Iterator[models.ContactInfo]:
# Read INVESTIGATION CONTACTS header
line = self._read_next_line()
if not line[0] == investigation_headers.INVESTIGATION_CONTACTS: # pragma: no cover
if (
line is None or not line[0] == investigation_headers.INVESTIGATION_CONTACTS
): # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.INVESTIGATION_CONTACTS, line)
raise ParseIsatabException(msg)
Expand Down Expand Up @@ -359,7 +365,7 @@ def _read_studies(self) -> Iterator[models.StudyInfo]:
while self._line:
# Read STUDY header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY: # pragma: no cover
if line is None or not line[0] == investigation_headers.STUDY: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.INVESTIGATION, line)
raise ParseIsatabException(msg)
Expand Down Expand Up @@ -399,7 +405,9 @@ def _read_studies(self) -> Iterator[models.StudyInfo]:
def _read_study_design_descriptors(self) -> Iterator[models.FreeTextOrTermRef]:
# Read STUDY DESIGN DESCRIPTORS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_DESIGN_DESCRIPTORS: # pragma: no cover
if (
line is None or not line[0] == investigation_headers.STUDY_DESIGN_DESCRIPTORS
): # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_DESIGN_DESCRIPTORS, line)
raise ParseIsatabException(msg)
Expand All @@ -419,7 +427,9 @@ def _read_study_design_descriptors(self) -> Iterator[models.FreeTextOrTermRef]:
def _read_study_publications(self) -> Iterator[models.PublicationInfo]:
# Read STUDY PUBLICATIONS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_PUBLICATIONS: # pragma: no cover
if (
line is None or not line[0] == investigation_headers.STUDY_PUBLICATIONS
): # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_PUBLICATIONS, line)
raise ParseIsatabException(msg)
Expand All @@ -444,7 +454,7 @@ def _read_study_publications(self) -> Iterator[models.PublicationInfo]:
def _read_study_factors(self) -> Iterator[models.FactorInfo]:
# Read STUDY FACTORS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_FACTORS: # pragma: no cover
if line is None or not line[0] == investigation_headers.STUDY_FACTORS: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_FACTORS, line)
raise ParseIsatabException(msg)
Expand All @@ -464,7 +474,7 @@ def _read_study_factors(self) -> Iterator[models.FactorInfo]:
def _read_study_assays(self) -> Iterator[models.AssayInfo]:
# Read STUDY ASSAYS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_ASSAYS: # pragma: no cover
if line is None or not line[0] == investigation_headers.STUDY_ASSAYS: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_ASSAYS, line)
raise ParseIsatabException(msg)
Expand Down Expand Up @@ -517,7 +527,7 @@ def _read_study_assays(self) -> Iterator[models.AssayInfo]:
def _read_study_protocols(self) -> Iterator[models.ProtocolInfo]:
# Read STUDY PROTOCOLS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_PROTOCOLS: # pragma: no cover
if line is None or not line[0] == investigation_headers.STUDY_PROTOCOLS: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_PROTOCOLS, line)
raise ParseIsatabException(msg)
Expand Down Expand Up @@ -581,7 +591,7 @@ def _read_study_protocols(self) -> Iterator[models.ProtocolInfo]:
def _read_study_contacts(self) -> Iterator[models.ContactInfo]:
# Read STUDY CONTACTS header
line = self._read_next_line()
if not line[0] == investigation_headers.STUDY_CONTACTS: # pragma: no cover
if line is None or not line[0] == investigation_headers.STUDY_CONTACTS: # pragma: no cover
tpl = "Expected {} but got {}"
msg = tpl.format(investigation_headers.STUDY_CONTACTS, line)
raise ParseIsatabException(msg)
Expand Down

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