Merge pull request #40 from PGScatalog/bugfix_schema

Fix assertion errors
PGScatalog · Jan 27, 2023 · 6735566 · 6735566
2 parents e220f14 + 4166333
commit 6735566
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Showing 4 changed files with 4 additions and 3 deletions.
diff --git a/pgscatalog_utils/__init__.py b/pgscatalog_utils/__init__.py
@@ -1 +1 @@
-__version__ = '0.3.0'
+__version__ = '0.3.1'
diff --git a/pgscatalog_utils/match/read.py b/pgscatalog_utils/match/read.py
@@ -28,6 +28,7 @@ def read_scorefile(path: str, chrom: typing.Union[str, None]) -> pl.LazyFrame:
               'chr_position': pl.UInt64,
               'effect_allele': pl.Utf8,  # str functions required to complement
               'other_allele': pl.Utf8,
+              'effect_weight': pl.Float64,
               'effect_type': pl.Categorical,
               'accession': pl.Categorical}
 

diff --git a/pgscatalog_utils/match/write.py b/pgscatalog_utils/match/write.py
@@ -68,7 +68,7 @@ def _check_column_types(matches: pl.LazyFrame):
                       'matched_effect_allele': pl.Categorical, 'effect_weight': pl.Float64,
                       'effect_type': pl.Categorical, 'accession': pl.Categorical}
     col_types = {x: matches.schema.get(x) for x in list((matches.schema.keys() & correct_schema.keys()))}
-    assert col_types == correct_schema
+    assert col_types == correct_schema, "MISMATCHED SCHEMA\nCurrent columns: {}\nCorrect schema:{}".format(col_types, correct_schema)
 
 
 def _write_split(deduplicated: dict[str: tuple[int, pl.LazyFrame]], chrom: str, dataset: str):

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pgscatalog_utils"
-version = "0.3.0"
+version = "0.3.1"
 description = "Utilities for working with PGS Catalog API and scoring files"
 homepage = "https://github.com/PGScatalog/pgscatalog_utils"
 authors = ["Benjamin Wingfield <[email protected]>", "Samuel Lambert <[email protected]>", "Laurent Gil <[email protected]>"]