✅ Update tests to use URL_LIST

kids-first · May 28, 2019 · 71bd0db · 71bd0db
1 parent 433ee40
commit 71bd0db
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/...data/test_boyd_study/extract_configs/s3_files_kf-seq-data-hudsonalpha_haib17SB5136_map.py b/...data/test_boyd_study/extract_configs/s3_files_kf-seq-data-hudsonalpha_haib17SB5136_map.py
@@ -26,7 +26,7 @@
     ),
     keep_map(
         in_col='file_path',
-        out_col=CONCEPT.GENOMIC_FILE.FILE_PATH
+        out_col=CONCEPT.GENOMIC_FILE.URL_LIST
     ),
     keep_map(
         in_col='file_path',

diff --git a/tests/data/test_study/extract_configs/simple_tsv_example2.py b/tests/data/test_study/extract_configs/simple_tsv_example2.py
@@ -34,10 +34,10 @@
     ),
     row_map(
         m=lambda row: row['storage_dir'] + '/' + row['bam_file_name'],
-        out_col=CONCEPT.GENOMIC_FILE.FILE_PATH
+        out_col=CONCEPT.GENOMIC_FILE.URL_LIST
     ),
     row_map(
         m=lambda row: row['storage_dir'] + '/' + row['cram_file_name'],
-        out_col=CONCEPT.GENOMIC_FILE.FILE_PATH
+        out_col=CONCEPT.GENOMIC_FILE.URL_LIST
     )
 ]
diff --git a/tests/data/test_study/extract_configs/unsimple_xlsx_example1.py b/tests/data/test_study/extract_configs/unsimple_xlsx_example1.py
@@ -34,7 +34,7 @@
     value_map(
         in_col='s3_path',
         m=lambda x: 's3://' + x,
-        out_col=CONCEPT.GENOMIC_FILE.FILE_PATH
+        out_col=CONCEPT.GENOMIC_FILE.URL_LIST
     ),
     value_map(
         in_col='DNA/RNA',

diff --git a/tests/data/test_study/extract_outputs/simple_tsv_example2_output.tsv b/tests/data/test_study/extract_outputs/simple_tsv_example2_output.tsv
@@ -1,4 +1,4 @@
-index	BIOSPECIMEN|ALIQUOT_ID	GENOMIC_FILE|FILE_PATH	GENOMIC_FILE|FILE_NAME	BIOSPECIMEN|ID
+index	BIOSPECIMEN|ALIQUOT_ID	GENOMIC_FILE|URL_LIST	GENOMIC_FILE|FILE_NAME	BIOSPECIMEN|ID
 0	4	FLDR0/2.bam	2.bam	4
 1	5	FLDR0/3.bam	3.bam	5
 2	6	FLDR0/4.bam	4.bam	6

diff --git a/tests/data/test_study/extract_outputs/unsimple_xlsx_example1_output.tsv b/tests/data/test_study/extract_outputs/unsimple_xlsx_example1_output.tsv
@@ -1,4 +1,4 @@
-index	BIOSPECIMEN|ALIQUOT_ID	BIOSPECIMEN|ID	GENOMIC_FILE|FILE_PATH	BIOSPECIMEN|ANALYTE
+index	BIOSPECIMEN|ALIQUOT_ID	BIOSPECIMEN|ID	GENOMIC_FILE|URL_LIST	BIOSPECIMEN|ANALYTE
 0	4	4	s3://foo/bar/vgrnqzhvrudvz3z/mn0ql.bam	DNA
 1	5	5	s3://foo/bar/bciz5579cez770wnaani.bam	DNA
 2	6	6	s3://foo/bar/35bevuz0hw5qu7ph0tis.bam	DNA