idc-index-data 20.0.2__tar.gz → 21.0.0__tar.gz

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/PKG-INFO

@@ -1,27 +1,28 @@
 Metadata-Version: 2.1
 Name: idc-index-data
-Version: 20.0.2
+Version: 21.0.0
 Summary: ImagingDataCommons index to query and download data.
 Author-Email: Andrey Fedorov <andrey.fedorov@gmail.com>, Vamsi Thiriveedhi <vthiriveedhi@mgh.harvard.edu>, Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
 License: Copyright 2024 Andrey Fedorov
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy of
-        this software and associated documentation files (the "Software"), to deal in
-        the Software without restriction, including without limitation the rights to
-        use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
-        of the Software, and to permit persons to whom the Software is furnished to do
-        so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy of
+         this software and associated documentation files (the "Software"), to deal in
+         the Software without restriction, including without limitation the rights to
+         use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+         of the Software, and to permit persons to whom the Software is furnished to do
+         so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all
+         copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+         
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
@@ -38,19 +39,19 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Classifier: Typing :: Typed
 Project-URL: Homepage, https://github.com/ImagingDataCommons/idc-index-data
-Project-URL: Bug tracker, https://github.com/ImagingDataCommons/idc-index-data/issues
+Project-URL: Bug Tracker, https://github.com/ImagingDataCommons/idc-index-data/issues
 Project-URL: Discussions, https://discourse.canceridc.dev/
 Project-URL: Changelog, https://github.com/ImagingDataCommons/idc-index-data/releases
 Requires-Python: >=3.8
 Provides-Extra: test
-Provides-Extra: dev
-Provides-Extra: docs
 Requires-Dist: pandas; extra == "test"
 Requires-Dist: pyarrow; extra == "test"
 Requires-Dist: pytest>=6; extra == "test"
 Requires-Dist: pytest-cov>=3; extra == "test"
+Provides-Extra: dev
 Requires-Dist: pytest>=6; extra == "dev"
 Requires-Dist: pytest-cov>=3; extra == "dev"
+Provides-Extra: docs
 Requires-Dist: sphinx>=7.0; extra == "docs"
 Requires-Dist: myst_parser>=0.13; extra == "docs"
 Requires-Dist: sphinx_copybutton; extra == "docs"

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/assets/clinical_index.sql

@@ -6,6 +6,6 @@ SELECT
   column_label,
   `values`
 FROM
-  `bigquery-public-data.idc_v20_clinical.column_metadata`
+  `bigquery-public-data.idc_v21_clinical.column_metadata`
 ORDER BY
   collection_id, table_name

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/assets/sm_index.sql

@@ -31,7 +31,7 @@ WITH
 
 
   FROM
-    `bigquery-public-data.idc_v20.dicom_all` AS dicom_all
+    `bigquery-public-data.idc_v21.dicom_all` AS dicom_all
   GROUP BY
     SeriesInstanceUID
   ),
@@ -45,7 +45,7 @@ SpecimenPreparationSequence_unnested AS (
         concept_code_sequence.CodeMeaning AS ccs_cm,
         concept_code_sequence.CodingSchemeDesignator AS ccs_csd,
         concept_code_sequence.CodeValue AS ccs_val,
-      FROM `bigquery-public-data.idc_v20.dicom_all`,
+      FROM `bigquery-public-data.idc_v21.dicom_all`,
       UNNEST(SpecimenDescriptionSequence[SAFE_OFFSET(0)].SpecimenPreparationSequence) as preparation_unnest_step1,
       UNNEST(preparation_unnest_step1.SpecimenPreparationStepContentItemSequence) as preparation_unnest_step2,
       UNNEST(preparation_unnest_step2.ConceptNameCodeSequence) as concept_name_code_sequence,

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/assets/sm_instance_index.sql

@@ -9,7 +9,7 @@ WITH
     concept_code_sequence.CodingSchemeDesignator AS ccs_csd,
     concept_code_sequence.CodeValue AS ccs_val,
   FROM
-    `bigquery-public-data.idc_v20.dicom_all`,
+    `bigquery-public-data.idc_v21.dicom_all`,
     UNNEST(SpecimenDescriptionSequence[SAFE_OFFSET(0)].SpecimenPreparationSequence) AS preparation_unnest_step1,
     UNNEST(preparation_unnest_step1.SpecimenPreparationStepContentItemSequence) AS preparation_unnest_step2,
     UNNEST(preparation_unnest_step2.ConceptNameCodeSequence) AS concept_name_code_sequence,
@@ -107,7 +107,7 @@ SELECT
   -- attributes needed to retrieve the selected instances/files
   dicom_all.crdc_instance_uuid
 FROM
-  `bigquery-public-data.idc_v20.dicom_all` AS dicom_all
+  `bigquery-public-data.idc_v21.dicom_all` AS dicom_all
 LEFT JOIN
   slide_embedding
 ON

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/pyproject.toml

@@ -13,7 +13,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "idc-index-data"
-version = "20.0.2"
+version = "21.0.0"
 authors = [
   { name = "Andrey Fedorov", email = "andrey.fedorov@gmail.com" },
   { name = "Vamsi Thiriveedhi", email = "vthiriveedhi@mgh.harvard.edu" },

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/scripts/sql/idc_index.sql

@@ -23,12 +23,15 @@ SELECT
   COUNT(dicom_all.SOPInstanceUID) AS instanceCount,
   ANY_VALUE(license_short_name) as license_short_name,
   # download related attributes
+  ANY_VALUE(aws_bucket)  AS aws_bucket,
+  ANY_VALUE(crdc_series_uuid) AS crdc_series_uuid,
+  # series_aws_url will be phased out in favor of constructing URL from bucket+UUID
   ANY_VALUE(CONCAT(series_aws_url,"*")) AS series_aws_url,
   ROUND(SUM(SAFE_CAST(instance_size AS float64))/1000000, 2) AS series_size_MB,
 FROM
-  `bigquery-public-data.idc_v20.dicom_all` AS dicom_all
+  `bigquery-public-data.idc_v21.dicom_all` AS dicom_all
 JOIN
-  `bigquery-public-data.idc_v20.dicom_metadata_curated` AS dicom_curated
+  `bigquery-public-data.idc_v21.dicom_metadata_curated` AS dicom_curated
 ON
   dicom_all.SOPInstanceUID = dicom_curated.SOPInstanceUID
 GROUP BY

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/scripts/sql/prior_versions_index.sql

@@ -3,7 +3,7 @@
 --
 -- Step 1: Declare variables
 DECLARE idc_versions ARRAY<INT64>;
-DECLARE latest_idc_version INT64 DEFAULT 20;
+DECLARE latest_idc_version INT64 DEFAULT 21;
 DECLARE union_all_query STRING;
 
 --Step 2
@@ -72,6 +72,17 @@ SELECT
   WHEN gcs_bucket='idc-open-idc1' THEN CONCAT('s3://','idc-open-data-two/',crdc_series_uuid, '/*')
   WHEN gcs_bucket='idc-open-cr' THEN CONCAT('s3://','idc-open-data-cr/',crdc_series_uuid, '/*')
     END AS series_aws_url,
+
+  gcs_bucket,
+  CASE
+
+  # map GCS bucket to AWS bucket, since for idc-index we prefer AWS
+  # if new buckets are included in IDC, this will need to be updated!
+
+  WHEN gcs_bucket='public-datasets-idc' THEN 'idc-open-data'
+  WHEN gcs_bucket='idc-open-idc1' THEN 'idc-open-data-two'
+  WHEN gcs_bucket='idc-open-cr' THEN 'idc-open-data-cr'
+    END AS aws_bucket,
   MIN(idc_version) AS min_idc_version,
   MAX(idc_version) AS max_idc_version
 FROM all_versions

{idc_index_data-20.0.2 → idc_index_data-21.0.0}/tests/test_package.py

@@ -7,7 +7,7 @@ from packaging.version import Version
 
 import idc_index_data as m
 
-EXPECTED_IDC_INDEX_VERSION = 20
+EXPECTED_IDC_INDEX_VERSION = 21
 
 
 def test_version():