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SQLite Utils: clean_like_nulls and More! #203

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merged 16 commits into from
Jun 9, 2022
Merged

SQLite Utils: clean_like_nulls and More! #203

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01f947f
add cyto_utils.sqlite; util for detecting conflicts in data
d33bs Jun 2, 2022
794ffdf
add update_columns_to_nullable and tests
d33bs Jun 3, 2022
72225ab
add update_columns_nan_to_null function; repurpose column loops
d33bs Jun 4, 2022
d93fd25
test collect_columns
d33bs Jun 5, 2022
b4c1b56
better test for collect_columns; some docs
d33bs Jun 6, 2022
aaeff28
add contains_str_like_null; expand update for like nulls
d33bs Jun 6, 2022
698074d
add clean_like_nulls
d33bs Jun 6, 2022
76f0400
rename to update_values_like_null_to_null for clarity
d33bs Jun 6, 2022
14e72a3
Update __init__.py
d33bs Jun 6, 2022
8673dfb
adjusting logging
d33bs Jun 6, 2022
7220f5b
avoid testing conflicts; version bump for sqlite3 backup capabilities
d33bs Jun 6, 2022
6d4e5cf
update to optional string types
d33bs Jun 6, 2022
e9295ec
various changes for cytomining/pycytominer#203
d33bs Jun 8, 2022
4cde8f1
various changes for cytomining/pycytominer#203
d33bs Jun 8, 2022
3a53ef9
run tests with PR to develop branch
d33bs Jun 9, 2022
6e9eab4
use sqlite_master instead of sqlite_schema for update_columns_to_null…
d33bs Jun 9, 2022
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9 changes: 9 additions & 0 deletions pycytominer/cyto_utils/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,3 +34,12 @@
aggregate_fields_count,
aggregate_image_features,
)
from .sqlite import (
clean_like_nulls,
collect_columns,
contains_conflicting_aff_strg_class,
contains_str_like_null,
engine_from_str,
update_columns_to_nullable,
update_values_like_null_to_null,
)
3 changes: 2 additions & 1 deletion pycytominer/cyto_utils/cells.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
extract_image_features,
aggregate_fields_count,
aggregate_image_features,
engine_from_str,
)

default_compartments = get_default_compartments()
Expand Down Expand Up @@ -148,7 +149,7 @@ def __init__(
self.set_subsample_n(self.subsample_n)

# Connect to sqlite engine
self.engine = create_engine(self.sql_file)
self.engine = engine_from_str(self.sql_file)
self.conn = self.engine.connect()

# Throw an error if both subsample_frac and subsample_n is set
Expand Down
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