Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat!: Support semicolon-separated lists in Performer fields #141

Merged
merged 3 commits into from
Feb 5, 2024
Merged

feat!: Support semicolon-separated lists in Performer fields #141

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e007d64
feat: Add list processing for Performer fields
sellth Jan 31, 2024
b15af8e
adapt writer & tests
sellth Feb 1, 2024
643ecfe
note extension in documentation
sellth Feb 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion altamisa/isatab/models.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -460,7 +460,7 @@ class Process:
#: Process date
date: Optional[Union[datetime.date, Literal[""]]]
#: Performer of process
performer: Optional[str]
performer: Optional[Tuple[str, ...]]
#: Tuple of parameters values
parameter_values: Tuple[ParameterValue, ...]
#: Tuple of process comments
Expand Down
2 changes: 1 addition & 1 deletion altamisa/isatab/parse_assay_study.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -442,7 +442,7 @@ def build(self, line: List[str]) -> models.Process:
else:
date = None
if self.performer_header:
performer = line[self.performer_header.col_no]
performer = tuple(self._token_with_escape(line[self.performer_header.col_no]))
else:
performer = None
comments = tuple(
Expand Down
4 changes: 3 additions & 1 deletion altamisa/isatab/write_assay_study.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -411,7 +411,9 @@ def _extract_process(self, node: Process) -> dict:
if node.protocol_ref != TOKEN_UNKNOWN:
attributes[table_headers.PROTOCOL_REF] = node.protocol_ref
if node.performer is not None:
attributes[table_headers.PERFORMER] = node.performer
attributes[table_headers.PERFORMER] = ";".join(
[p.replace(";", "\\;") if p else "" for p in node.performer]
)
if node.date is not None:
attributes[table_headers.DATE] = node.date
for parameter in node.parameter_values:
Expand Down
8 changes: 4 additions & 4 deletions docs/index.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,10 +53,10 @@ Special Extensions
In addition to the original ISA-Tab format specifications, AltamISA supports
the following special modifications to improve specific use cases:

- **List of values** in ``Characterics``, ``Parameter Value``, or ``Factor Value`` fields by using
semicolon-separators (";"). Note, for ontology terms the same number of
splits is expected in the associated field ``Term Source REF`` and
``Term Accession Number``.
- **List of values** in ``Characterics``, ``Parameter Value``, ``Factor Value``,
and ``Performer`` fields by using semicolon-separators (";"). Note: For
ontology terms the same number of splits is expected in the associated field
``Term Source REF`` and ``Term Accession Number``.
- **Material name** ``Library Name`` for improved library
annotation in nucleotide sequencing assays.

Expand Down
10 changes: 5 additions & 5 deletions tests/test_parse_study.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,7 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
None,
None,
date(2018, 2, 2),
"John Doe",
("John Doe",),
(models.ParameterValue("instrument", ["scalpel"], None),),
(),
None,
Expand Down Expand Up @@ -298,7 +298,7 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
None,
None,
date(2018, 2, 2),
"John Doe",
("John Doe",),
(models.ParameterValue("instrument", ["scalpel type A", "scalpel type B"], None),),
(),
None,
Expand Down Expand Up @@ -507,7 +507,7 @@ def test_study_reader_small_study(
None,
None,
date(2018, 2, 2),
"John Doe",
("John Doe",),
(models.ParameterValue("instrument", ["scalpel"], None),),
(),
None,
Expand All @@ -522,7 +522,7 @@ def test_study_reader_small_study(
None,
None,
date(2018, 2, 2),
"John Doe",
("John Doe",),
(models.ParameterValue("instrument", ["scalpel type A", "scalpel type B"], None),),
(),
None,
Expand All @@ -537,7 +537,7 @@ def test_study_reader_small_study(
None,
None,
date(2018, 2, 2),
"John Doe",
("John Doe",),
(models.ParameterValue("instrument", ["scalpel"], None),),
(),
None,
Expand Down
Loading