nci-cidc-api-modules 1.2.16__py3-none-any.whl → 1.2.25__py3-none-any.whl

cidc_api/shared/file_handling.py

@@ -1,14 +1,15 @@
 from pathlib import Path
 
+from pandas import Series, DataFrame
+from sqlalchemy.orm.session import Session
 from werkzeug.datastructures import FileStorage
 from werkzeug.exceptions import BadRequest, InternalServerError
 
 from ..config.logging import get_logger
 from ..config.settings import GOOGLE_CLINICAL_DATA_BUCKET
-from ..models import PreprocessedFiles
+from ..models import PreprocessedFiles, TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER
 from ..shared.auth import get_current_user
 from ..shared.gcloud_client import upload_file_to_gcs, move_gcs_file
-from sqlalchemy.orm.session import Session
 
 logger = get_logger(__name__)
 
@@ -104,3 +105,37 @@ def strip_filename_and_pending_folder(path_str):
     if path.parent.name != "pending":
         raise ValueError("Expected 'pending' folder above file")
     return str(path.parent.parent)
+
+
+def get_row_at_condition(df: DataFrame, condition):
+    condition_met_index = df[condition].index[0]
+    row_at_condition_series = df.iloc[condition_met_index]
+
+    return row_at_condition_series
+
+
+def get_column(header_row_series: Series, header_name: str, use_raw_header_val: bool = False):
+    for idx, raw_header in enumerate(header_row_series):
+        if str(raw_header).lower() == header_name.lower():
+            return raw_header if use_raw_header_val else header_row_series.index[idx]
+    return None
+
+
+def get_column_from_appendix_a(appendix_a_df: DataFrame, header_name: str):
+    category_column = appendix_a_df.columns[0]
+    aa_header_condition = appendix_a_df[category_column] == TRIAL_APPENDIX_A_CELL_THAT_ENDS_THE_HEADER
+    header_row_series = get_row_at_condition(appendix_a_df, aa_header_condition)
+    return get_column(header_row_series, header_name)
+
+
+def get_column_from_first_row(df: DataFrame, header_name: str):
+    use_raw_header_val = False
+    if df.columns.inferred_type == "integer":
+        # If columns are integers (i.e. file was read without headers), treat the first row as header values.
+        header_row_series = df.iloc[0]
+    else:
+        # Otherwise columns already are headers
+        header_row_series = Series(df.columns)
+        use_raw_header_val = True
+
+    return get_column(header_row_series, header_name, use_raw_header_val=use_raw_header_val)

cidc_api/shared/utils.py

@@ -5,4 +5,7 @@ def strip_whitespaces(df):
         else:
             return x
 
-    return df.map(stripper)
+    df.rename(columns=stripper, inplace=True)
+    df = df.map(stripper)
+
+    return df

{nci_cidc_api_modules-1.2.16.dist-info → nci_cidc_api_modules-1.2.25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.2.16
+Version: 1.2.25
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license
@@ -28,8 +28,9 @@ Requires-Dist: pyarrow>=22.0.0
 Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: requests>=2.32.5
 Requires-Dist: sqlalchemy>=2.0.44
+Requires-Dist: sqlalchemy-mixins~=2.0.5
 Requires-Dist: werkzeug>=3.1.3
-Requires-Dist: nci-cidc-schemas==0.28.8
+Requires-Dist: nci-cidc-schemas==0.28.10
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
@@ -217,13 +218,14 @@ gcloud auth application-default login
 In your .env file, comment out `POSTGRES_URI` and uncommment
 `CLOUD_SQL_INSTANCE_NAME CLOUD_SQL_DB_USER CLOUD_SQL_DB_NAME` Replace `CLOUD_SQL_DB_USER` with your NIH email.
 
-### Running database migrations
+### Creating/Running database migrations
 
 This project uses [`Flask Migrate`](https://flask-migrate.readthedocs.io/en/latest/) for managing database migrations. To create a new migration and upgrade the database specified in your `.env` config:
 
 ```bash
 export FLASK_APP=cidc_api/app.py
-# Generate the migration script
+# First, make your changes to the model(s)
+# Then, let flask automatically generate the db change. Double check the migration script!
 flask db migrate -m "<a message describing the changes in this migration>"
 # Apply changes to the database
 flask db upgrade

nci_cidc_api_modules-1.2.25.dist-info/RECORD

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+cidc_api/config/db.py,sha256=CRgpyw7uVP9v7CTAa7_1dcXURqrfjRcLNjGgZC7iPQE,1627
+cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
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+cidc_api/models/migrations.py,sha256=UlS5How3J4ryaRuZT6F5VQtAKikkl0LTv9MgMO_ltiQ,11161
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nci_cidc_api_modules-1.2.16.dist-info/RECORD

@@ -1,26 +0,0 @@
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-cidc_api/config/db.py,sha256=eFCkJDeykRIJZ25kePVjRNrZcrcKTc1s2K0yErr46LI,1683
-cidc_api/config/logging.py,sha256=abhVYtn8lfhIt0tyV2WHFgSmp_s2eeJh7kodB6LH4J0,1149
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