idc-index-data 22.1.5__tar.gz → 23.0.1__tar.gz

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: idc-index-data
-Version: 22.1.5
+Version: 23.0.1
 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

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/assets/clinical_index.sql

@@ -25,6 +25,6 @@ SELECT
   # values encountered in the column
   `values`
 FROM
-  `bigquery-public-data.idc_v22_clinical.column_metadata`
+  `bigquery-public-data.idc_v23_clinical.column_metadata`
 ORDER BY
   collection_id, table_name

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/assets/sm_index.sql

@@ -37,7 +37,7 @@ WITH
 
 
   FROM
-    `bigquery-public-data.idc_v22.dicom_all` AS dicom_all
+    `bigquery-public-data.idc_v23.dicom_all` AS dicom_all
   GROUP BY
     SeriesInstanceUID
   ),
@@ -51,7 +51,7 @@ 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_v22.dicom_all`,
+      FROM `bigquery-public-data.idc_v23.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,
@@ -86,6 +86,8 @@ SpecimenPreparationSequence_unnested AS (
     )
 
 SELECT
+  # description:
+  # DICOM SeriesInstanceUID identifier of the series
   temp_table.SeriesInstanceUID,
   -- Embedding Medium
   # description:

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/assets/sm_instance_index.sql

@@ -16,7 +16,7 @@ WITH
     concept_code_sequence.CodingSchemeDesignator AS ccs_csd,
     concept_code_sequence.CodeValue AS ccs_val,
   FROM
-    `bigquery-public-data.idc_v22.dicom_all`,
+    `bigquery-public-data.idc_v23.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,
@@ -144,7 +144,7 @@ SELECT
   # unique identifier of the instance within the IDC
   dicom_all.crdc_instance_uuid AS crdc_instance_uuid
 FROM
-  `bigquery-public-data.idc_v22.dicom_all` AS dicom_all
+  `bigquery-public-data.idc_v23.dicom_all` AS dicom_all
 LEFT JOIN
   slide_embedding
 ON

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/pyproject.toml

@@ -13,7 +13,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "idc-index-data"
-version = "22.1.5"
+version = "23.0.1"
 authors = [
   { name = "Andrey Fedorov", email = "andrey.fedorov@gmail.com" },
   { name = "Vamsi Thiriveedhi", email = "vthiriveedhi@mgh.harvard.edu" },

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/scripts/python/idc_index_data_manager.py

@@ -423,7 +423,7 @@ class IDCIndexDataManager:
         SELECT
             MAX(idc_version) AS latest_idc_release_version
         FROM
-            `bigquery-public-data.idc_current.version_metadata`
+            `bigquery-public-data.idc_v23.version_metadata`
         """
         query_job = self.client.query(query)
         result = query_job.result()

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/scripts/sql/analysis_results_index.sql

@@ -43,4 +43,4 @@ SELECT
   # citation for the analysis results collection that should be used for acknowledgment
   Citation
 FROM
-  `bigquery-public-data.idc_v22.analysis_results_metadata`
+  `bigquery-public-data.idc_v23.analysis_results_metadata`

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/scripts/sql/collections_index.sql

@@ -40,4 +40,4 @@ SELECT
   # detailed information about the collection
   Description
 FROM
-  `bigquery-public-data.idc_v22.original_collections_metadata`
+  `bigquery-public-data.idc_v23.original_collections_metadata`

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/scripts/sql/idc_index.sql

@@ -1,3 +1,7 @@
+# table-description:
+# This is the main metadata table provided by idc-index. Each row corresponds to a DICOM series, and contains
+# attributes at the collection, patient, study, and series levels. The table also contains download-related
+# attributes, such as the AWS S3 bucket and URL to download the series.
 SELECT
   # collection level attributes
   # description:
@@ -22,7 +26,7 @@ SELECT
   # series; follow this DOI to learn more about the activity that produced
   # this series
   ANY_VALUE(source_DOI) AS source_DOI,
-  # patient level attributes
+  # patient level attributes:
   # description:
   # age of the subject at the time of imaging (DICOM attribute)
   ANY_VALUE(PatientAge) AS PatientAge,
@@ -79,9 +83,9 @@ SELECT
   # total size of the series in megabytes
   ROUND(SUM(SAFE_CAST(instance_size AS float64))/1000000, 2) AS series_size_MB,
 FROM
-  `bigquery-public-data.idc_v22.dicom_all` AS dicom_all
+  `bigquery-public-data.idc_v23.dicom_all` AS dicom_all
 JOIN
-  `bigquery-public-data.idc_v22.dicom_metadata_curated` AS dicom_curated
+  `bigquery-public-data.idc_v23.dicom_metadata_curated` AS dicom_curated
 ON
   dicom_all.SOPInstanceUID = dicom_curated.SOPInstanceUID
 GROUP BY

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/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 22;
+DECLARE latest_idc_version INT64 DEFAULT 23;
 DECLARE union_all_query STRING;
 
 --Step 2

{idc_index_data-22.1.5 → idc_index_data-23.0.1}/tests/test_package.py

@@ -7,7 +7,7 @@ from packaging.version import Version
 
 import idc_index_data as m
 
-EXPECTED_IDC_INDEX_VERSION = 22
+EXPECTED_IDC_INDEX_VERSION = 23
 
 
 def test_version():