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Merge branch 'dev' of github.com:broadinstitute/seqr-loading-pipelines
2 parents 9fdd172 + d093c22 commit d096722

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+20
-20
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-20
lines changed

‎v03_pipeline/lib/model/environment.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33

44
# NB: using os.environ.get inside the dataclass defaults gives a lint error.
55
HAIL_TMPDIR = os.environ.get('HAIL_TMPDIR', '/tmp') # noqa: S108
6-
HAIL_SEARCH_DATA = os.environ.get('HAIL_SEARCH_DATA', '/hail-search-data')
6+
HAIL_SEARCH_DATA = os.environ.get('HAIL_SEARCH_DATA', '/seqr/hail-search-data')
77
GRCH37_TO_GRCH38_LIFTOVER_REF_PATH = os.environ.get(
88
'GRCH37_TO_GRCH38_LIFTOVER_REF_PATH',
99
'gs://hail-common/references/grch37_to_grch38.over.chain.gz',
@@ -12,14 +12,14 @@
1212
'GRCH38_TO_GRCH37_LIFTOVER_REF_PATH',
1313
'gs://hail-common/references/grch38_to_grch37.over.chain.gz',
1414
)
15-
LOADING_DATASETS = os.environ.get('LOADING_DATASETS', '/seqr-loading-temp')
15+
LOADING_DATASETS = os.environ.get('LOADING_DATASETS', '/seqr/seqr-loading-temp')
1616
PRIVATE_REFERENCE_DATASETS = os.environ.get(
1717
'PRIVATE_REFERENCE_DATASETS',
18-
'/seqr-reference-data-private',
18+
'/seqr/seqr-reference-data-private',
1919
)
2020
REFERENCE_DATASETS = os.environ.get(
2121
'REFERENCE_DATASETS',
22-
'/seqr-reference-data',
22+
'/seqr/seqr-reference-data',
2323
)
2424
# Allele registry secrets :/
2525
ALLELE_REGISTRY_SECRET_NAME = os.environ.get('ALLELE_REGISTRY_SECRET_NAME', None)

‎v03_pipeline/lib/paths_test.py

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@ def test_cached_reference_dataset_query_path(self) -> None:
3636
DatasetType.SNV_INDEL,
3737
CachedReferenceDatasetQuery.CLINVAR_PATH_VARIANTS,
3838
),
39-
'/seqr-reference-data/v03/GRCh38/SNV_INDEL/cached_reference_dataset_queries/clinvar_path_variants.ht',
39+
'/seqr/seqr-reference-data/v03/GRCh38/SNV_INDEL/cached_reference_dataset_queries/clinvar_path_variants.ht',
4040
)
4141

4242
def test_family_table_path(self) -> None:
@@ -47,7 +47,7 @@ def test_family_table_path(self) -> None:
4747
SampleType.WES,
4848
'franklin',
4949
),
50-
'/hail-search-data/v3.1/GRCh37/SNV_INDEL/families/WES/franklin.ht',
50+
'/seqr/hail-search-data/v3.1/GRCh37/SNV_INDEL/families/WES/franklin.ht',
5151
)
5252
with patch('v03_pipeline.lib.paths.Env') as mock_env:
5353
mock_env.HAIL_SEARCH_DATA = 'gs://seqr-datasets/'
@@ -89,7 +89,7 @@ def test_project_table_path(self) -> None:
8989
SampleType.WES,
9090
'R0652_pipeline_test',
9191
),
92-
'/hail-search-data/v3.1/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht',
92+
'/seqr/hail-search-data/v3.1/GRCh38/MITO/projects/WES/R0652_pipeline_test.ht',
9393
)
9494

9595
def test_valid_reference_dataset_collection_path(self) -> None:
@@ -109,7 +109,7 @@ def test_valid_reference_dataset_collection_path(self) -> None:
109109
DatasetType.SNV_INDEL,
110110
ReferenceDatasetCollection.HGMD,
111111
),
112-
'/seqr-reference-data-private/v03/GRCh38/SNV_INDEL/reference_datasets/hgmd.ht',
112+
'/seqr/seqr-reference-data-private/v03/GRCh38/SNV_INDEL/reference_datasets/hgmd.ht',
113113
)
114114

115115
def test_lookup_table_path(self) -> None:
@@ -118,7 +118,7 @@ def test_lookup_table_path(self) -> None:
118118
ReferenceGenome.GRCh37,
119119
DatasetType.SV,
120120
),
121-
'/hail-search-data/v3.1/GRCh37/SV/lookup.ht',
121+
'/seqr/hail-search-data/v3.1/GRCh37/SV/lookup.ht',
122122
)
123123

124124
def test_sex_check_table_path(self) -> None:
@@ -128,7 +128,7 @@ def test_sex_check_table_path(self) -> None:
128128
DatasetType.SNV_INDEL,
129129
'gs://abc.efg/callset.vcf.gz',
130130
),
131-
'/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/sex_check/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.ht',
131+
'/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/sex_check/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.ht',
132132
)
133133

134134
def test_relatedness_check_table_path(self) -> None:
@@ -138,7 +138,7 @@ def test_relatedness_check_table_path(self) -> None:
138138
DatasetType.SNV_INDEL,
139139
'gs://abc.efg/callset.vcf.gz',
140140
),
141-
'/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.ht',
141+
'/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.ht',
142142
)
143143

144144
def test_metadata_for_run_path(self) -> None:
@@ -148,7 +148,7 @@ def test_metadata_for_run_path(self) -> None:
148148
DatasetType.SNV_INDEL,
149149
'manual__2023-06-26T18:30:09.349671+00:00',
150150
),
151-
'/hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json',
151+
'/seqr/hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/metadata.json',
152152
)
153153

154154
def test_variant_annotations_table_path(self) -> None:
@@ -157,7 +157,7 @@ def test_variant_annotations_table_path(self) -> None:
157157
ReferenceGenome.GRCh38,
158158
DatasetType.GCNV,
159159
),
160-
'/hail-search-data/v3.1/GRCh38/GCNV/annotations.ht',
160+
'/seqr/hail-search-data/v3.1/GRCh38/GCNV/annotations.ht',
161161
)
162162

163163
def test_remapped_and_subsetted_callset_path(self) -> None:
@@ -168,7 +168,7 @@ def test_remapped_and_subsetted_callset_path(self) -> None:
168168
'gs://abc.efg/callset.vcf.gz',
169169
'R0111_tgg_bblanken_wes',
170170
),
171-
'/seqr-loading-temp/v3.1/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.mt',
171+
'/seqr/seqr-loading-temp/v3.1/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.mt',
172172
)
173173
self.assertEqual(
174174
remapped_and_subsetted_callset_path(
@@ -177,7 +177,7 @@ def test_remapped_and_subsetted_callset_path(self) -> None:
177177
'gs://abc.efg/callset/*.vcf.gz',
178178
'R0111_tgg_bblanken_wes',
179179
),
180-
'/seqr-loading-temp/v3.1/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/bce53ccdb49a5ed2513044e1d0c6224e3ffcc323f770dc807d9175fd3c70a050.mt',
180+
'/seqr/seqr-loading-temp/v3.1/GRCh38/GCNV/remapped_and_subsetted_callsets/R0111_tgg_bblanken_wes/bce53ccdb49a5ed2513044e1d0c6224e3ffcc323f770dc807d9175fd3c70a050.mt',
181181
)
182182

183183
def test_imported_callset_path(self) -> None:
@@ -187,7 +187,7 @@ def test_imported_callset_path(self) -> None:
187187
DatasetType.SNV_INDEL,
188188
'gs://abc.efg/callset.vcf.gz',
189189
),
190-
'/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/imported_callsets/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.mt',
190+
'/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/imported_callsets/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.mt',
191191
)
192192

193193
def test_imputed_sex_path(self) -> None:
@@ -197,7 +197,7 @@ def test_imputed_sex_path(self) -> None:
197197
DatasetType.SNV_INDEL,
198198
'gs://abc.efg/callset.vcf.gz',
199199
),
200-
'/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/imputed_sex/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.tsv',
200+
'/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/imputed_sex/ead56bb177a5de24178e1e622ce1d8beb3f8892bdae1c925d22ca0af4013d6dd.tsv',
201201
)
202202

203203
def test_new_variants_table_path(self) -> None:
@@ -207,7 +207,7 @@ def test_new_variants_table_path(self) -> None:
207207
DatasetType.SNV_INDEL,
208208
'manual__2023-06-26T18:30:09.349671+00:00',
209209
),
210-
'/hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht',
210+
'/seqr/hail-search-data/v3.1/GRCh38/SNV_INDEL/runs/manual__2023-06-26T18:30:09.349671+00:00/new_variants.ht',
211211
)
212212

213213
def test_project_remap_path(self) -> None:
@@ -218,7 +218,7 @@ def test_project_remap_path(self) -> None:
218218
SampleType.WGS,
219219
'R0652_pipeline_test',
220220
),
221-
'/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/remaps/WGS/R0652_pipeline_test.ht',
221+
'/seqr/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/remaps/WGS/R0652_pipeline_test.ht',
222222
)
223223

224224
def test_project_pedigree_path(self) -> None:
@@ -229,5 +229,5 @@ def test_project_pedigree_path(self) -> None:
229229
SampleType.WES,
230230
'R0652_pipeline_test',
231231
),
232-
'/seqr-loading-temp/v3.1/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test.ht',
232+
'/seqr/seqr-loading-temp/v3.1/GRCh38/GCNV/pedigrees/WES/R0652_pipeline_test.ht',
233233
)

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