From 1eaade12da9cc25d57f4939bf268f853c5705230 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Tue, 28 Nov 2023 19:46:01 -0700 Subject: [PATCH 1/3] add header prefix config field --- docs/Usage/ingests.md | 3 ++- pyproject.toml | 2 +- src/koza/cli_runner.py | 8 ++++++-- src/koza/io/reader/csv_reader.py | 6 +++++- src/koza/model/config/source_config.py | 4 +++- src/koza/model/source.py | 3 ++- 6 files changed, 19 insertions(+), 7 deletions(-) diff --git a/docs/Usage/ingests.md b/docs/Usage/ingests.md index c12dc0a..dfa8a32 100644 --- a/docs/Usage/ingests.md +++ b/docs/Usage/ingests.md @@ -49,8 +49,9 @@ Creating this ingest will require three things: | __Optional CSV Specific Properties__ | | | `columns` | List of columns to include in output (CSV only) | | `delimiter` | Delimiter for csv files | - | `header_delimiter` | Delimiter for header in csv files | | `header` | Header row index for csv files | + | `header_delimiter` | Delimiter for header in csv files | + | `header_prefix` | Prefix for header in csv files | | `comment_char` | Comment character for csv files | | `skip_blank_lines` | Skip blank lines in csv files | diff --git a/pyproject.toml b/pyproject.toml index 4050914..bf76482 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "koza" -version = "0.5.1" +version = "0.5.2" description = "Data transformation framework for LinkML data models" authors = [ "The Monarch Initiative ", diff --git a/src/koza/cli_runner.py b/src/koza/cli_runner.py index 053965d..f45cd2f 100644 --- a/src/koza/cli_runner.py +++ b/src/koza/cli_runner.py @@ -79,7 +79,9 @@ def transform_source( logger, ) - koza_app = _set_koza_app(koza_source, translation_table, output_dir, output_format, schema, node_type, edge_type, logger) + koza_app = _set_koza_app( + koza_source, translation_table, output_dir, output_format, schema, node_type, edge_type, logger + ) koza_app.process_maps() koza_app.process_sources() @@ -172,7 +174,9 @@ def _set_koza_app( ) -> KozaApp: """Create a KozaApp object for a given source""" - koza_apps[source.config.name] = KozaApp(source, translation_table, output_dir, output_format, schema, node_type, edge_type, logger) + koza_apps[source.config.name] = KozaApp( + source, translation_table, output_dir, output_format, schema, node_type, edge_type, logger + ) logger.debug(f"koza_apps entry created for {source.config.name}: {koza_apps[source.config.name]}") return koza_apps[source.config.name] diff --git a/src/koza/io/reader/csv_reader.py b/src/koza/io/reader/csv_reader.py index 6227511..a7d97f0 100644 --- a/src/koza/io/reader/csv_reader.py +++ b/src/koza/io/reader/csv_reader.py @@ -49,6 +49,7 @@ def __init__( delimiter: str = ",", header: Union[int, HeaderMode] = HeaderMode.infer, header_delimiter: str = None, + header_prefix: str = None, dialect: str = "excel", skip_blank_lines: bool = True, name: str = "csv file", @@ -69,6 +70,7 @@ def __init__( if field_type_map is None this will raise a ValueError :param header_delimiter: delimiter for the header row, default = self.delimiter + :param header_prefix: prefix for the header row, default = None :param dialect: csv dialect, default=excel :param skip_blank_lines: true to skip blank lines, false to insert NaN for blank lines, :param name: filename or alias @@ -82,6 +84,7 @@ def __init__( self.dialect = dialect self.header = header self.header_delimiter = header_delimiter if header_delimiter else delimiter + self.header_prefix = header_prefix self.skip_blank_lines = skip_blank_lines self.name = name self.comment_char = comment_char @@ -205,11 +208,12 @@ def _parse_header_line(self, skip_blank_or_commented_lines: bool = False) -> Lis Parse the header line and return a list of headers """ fieldnames = next(reader(self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect})) + if self.header_prefix and fieldnames[0].startswith(self.header_prefix): + fieldnames[0] = fieldnames[0].lstrip(self.header_prefix) if skip_blank_or_commented_lines: # there has to be a cleaner way to do this while not fieldnames or (self.comment_char is not None and fieldnames[0].startswith(self.comment_char)): fieldnames = next(reader(self.io_str, **{'delimiter': self.header_delimiter, 'dialect': self.dialect})) - fieldnames[0] = fieldnames[0].lstrip(self.comment_char) return [f.strip() for f in fieldnames] diff --git a/src/koza/model/config/source_config.py b/src/koza/model/config/source_config.py index 74a3eb6..a8dc2e8 100644 --- a/src/koza/model/config/source_config.py +++ b/src/koza/model/config/source_config.py @@ -147,8 +147,9 @@ class SourceConfig: columns: List[str] (optional) - list of columns to include required_properties: List[str] (optional) - list of properties which must be in json data files delimiter: str (optional) - delimiter for csv files - header_delimiter: str (optional) - delimiter for header in csv files header: int (optional) - header row index + header_delimiter: str (optional) - delimiter for header in csv files + header_prefix: str (optional) - prefix for header in csv files comment_char: str (optional) - comment character for csv files skip_blank_lines: bool (optional) - skip blank lines in csv files filters: List[ColumnFilter] (optional) - list of filters to apply @@ -171,6 +172,7 @@ class SourceConfig: delimiter: Optional[str] = None header: Union[int, HeaderMode] = HeaderMode.infer header_delimiter: Optional[str] = None + header_prefix: Optional[str] = None comment_char: str = "#" skip_blank_lines: bool = True filters: List[ColumnFilter] = field(default_factory=list) diff --git a/src/koza/model/source.py b/src/koza/model/source.py index 2fa50b9..294c643 100644 --- a/src/koza/model/source.py +++ b/src/koza/model/source.py @@ -40,8 +40,9 @@ def __init__(self, config: Union[PrimaryFileConfig, MapFileConfig], row_limit: O name=config.name, field_type_map=config.field_type_map, delimiter=config.delimiter, - header_delimiter=config.header_delimiter, header=config.header, + header_delimiter=config.header_delimiter, + header_prefix=config.header_prefix, comment_char=self.config.comment_char, row_limit=self.row_limit, ) From 49ae98430c9eaa413e56e251b22ec26816efbbee Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 29 Nov 2023 10:17:13 -0700 Subject: [PATCH 2/3] stop printing field type map --- src/koza/model/config/source_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/koza/model/config/source_config.py b/src/koza/model/config/source_config.py index a8dc2e8..39aa016 100644 --- a/src/koza/model/config/source_config.py +++ b/src/koza/model/config/source_config.py @@ -292,7 +292,7 @@ def __post_init__(self): raise ValueError("Field type map contains more than one key") for key, val in field.items(): field_type_map[key] = val - print(f"FIELD TYPE MAP: {field_type_map}") + # print(f"FIELD TYPE MAP: {field_type_map}") self.field_type_map = field_type_map From 4da41e77c3e7ba7e151a4d91486fee890993b978 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Thu, 30 Nov 2023 16:03:45 -0700 Subject: [PATCH 3/3] update biolink model to 3.6 --- poetry.lock | 511 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 247 insertions(+), 266 deletions(-) diff --git a/poetry.lock b/poetry.lock index b47c2ad..d68a42d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -95,25 +95,19 @@ lxml = ["lxml"] [[package]] name = "biolink-model" -version = "3.3.3.post25.dev0+93c02412c" -description = "Entity and association taxonomy and datamodel for life-sciences data" +version = "3.6.0" +description = "'A high level datamodel of biological entities and associations'" optional = false -python-versions = "^3.9" -files = [] -develop = false +python-versions = ">=3.9" +files = [ + {file = "biolink-model-3.6.0.tar.gz", hash = "sha256:8fd3dc3d3364fa9714775e73857aff97cc72a3809ecd2916826d6c39c5a70ee4"}, + {file = "biolink_model-3.6.0-py3-none-any.whl", hash = "sha256:78cc0827bb6657ea4712d5be439dddd4307daddb51d38b03e6b53f884417d60f"}, +] [package.dependencies] -bs4 = "^0.0.1" -curies = "^0.7.4" -linkml = ">=1.6.3" -prefixmaps = "^0.2.0" -pytest = "^7.3.1" - 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b/pyproject.toml @@ -30,7 +30,7 @@ sssom = "^0.3.41" black = "^23.10.0" ruff = "*" pytest = ">=6.0.0" -biolink-model = { git = "https://github.com/glass-ships/biolink-model.git", branch = "dependencies" } # ">=3.5.5" +biolink-model = ">=3.6" dask = ">=2022.5.2" mkdocs = ">=1.4.2" mkdocs-material = ">=9.1.16"