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DataBiosphere / azul

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP
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Many unit tests fail if `AZUL_DSS_QUERY_PREFIX` is set #3321

Closed jessebrennan closed 3 years ago

jessebrennan commented 3 years ago

I started a test run with make test but the log was greater than my terminal history. Here is the end of it, along with a few other commands showing the branch/commit and variable set.

----------------------------------------------------------------------
Ran 342 tests in 1001.689s

FAILED (failures=123, errors=40, skipped=12)
make: *** [Makefile:159: test] Error 1
(.venv) jesse@vader ~/gi/azul.2 (default)$ git show HEAD
commit b8e4a508ab3344b4090eac6e70891a65a6d6afc7 (HEAD -> default, github/develop, github/HEAD, dev.dcp2.gitlab/develop)
Merge: b270c3d5 a252a29d
Author: Daniel Sotirhos <dsotirho@ucsc.edu>
Date:   Thu Aug 12 16:40:37 2021 -0700

    Can new prod bundles for matrix test cases (#3192, PR #3261)

(.venv) jesse@vader ~/gi/azul.2 (default)$ env | grep DSS_QUERY_PREFIX
AZUL_DSS_QUERY_PREFIX=42
azul_env_vars=AZUL_CATALOGS,AZUL_DEBUG,AZUL_DSS_DIRECT_ACCESS,AZUL_DOMAIN_NAME,AZUL_DRS_DOMAIN_NAME,AZUL_SUBDOMAIN_TEMPLATE,AZUL_RESOURCE_PREFIX,AZUL_ES_DOMAIN,AZUL_SHARE_ES_DOMAIN,AZUL_INDEX_PREFIX,AZUL_ES_INSTANCE_TYPE,AZUL_ES_VOLUME_SIZE,AZUL_ES_TIMEOUT,AZUL_VERSIONED_BUCKET,AZUL_DSS_WORKERS,AZUL_TDR_WORKERS,AZUL_SUBSCRIBE_TO_DSS,AZUL_DEPLOYMENT_INCARNATION,AZUL_GOOGLE_SERVICE_ACCOUNT,AZUL_GOOGLE_SERVICE_ACCOUNT_PUBLIC,AZUL_CONTRIBUTION_CONCURRENCY,AZUL_AGGREGATION_CONCURRENCY,AZUL_S3_BUCKET,AZUL_URL_REDIRECT_BASE_DOMAIN_NAME,AZUL_URL_REDIRECT_FULL_DOMAIN_NAME,AZUL_ENABLE_MONITORING,AZUL_DSS_QUERY_PREFIX,azul_terraform_component,azul_github_project,azul_github_access_token,PYTHONPATH,MYPYPATH,TF_DATA_DIR,XDG_CONFIG_HOME,AZUL_DEPLOYMENT_STAGE,AZUL_TDR_SOURCES,AZUL_TDR_DCP2EBI_SOURCES,AZUL_TDR_IT2EBI_SOURCES,AZUL_TDR_LUNGMAP_SOURCES,AZUL_TDR_IT3LUNGMAP_SOURCES,AZUL_TDR_SERVICE_URL,AZUL_SAM_SERVICE_URL,AZUL_ES_INSTANCE_COUNT,AZUL_OWNER,AZUL_AWS_ACCOUNT_ID,AWS_DEFAULT_REGION,GOOGLE_PROJECT,AZUL_GOOGLE_OAUTH2_CLIENT_ID,AWS_PROFILE,GOOGLE_APPLICATION_CREDENTIALS,project_root

For the record, I was in the process of running test when Hannes made his comment.

hannes-ucsc commented 3 years ago

@jessebrennan to provide evidence 1) that this occurs on develop and 2) on which commit.

jessebrennan commented 3 years ago

One of the less opaque failures:

======================================================================
FAIL: test_indexing (indexer.test_hca_indexer.TestHCAIndexer)
Index a bundle and assert the index contents verbatim
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/jesse/gi/azul.2/test/indexer/test_hca_indexer.py", line 161, in test_indexing
    self.assertElasticsearchResultsEqual(expected_hits, hits)
  File "/home/jesse/gi/azul.2/test/es_test_case.py", line 74, in assertElasticsearchResultsEqual
    self.assertEqual(sort_frozen(freeze(first)), sort_frozen(freeze(second)))
AssertionError: Tuples differ: ((('_[4395 chars]test:')),)), ('total_estimated_cells', 1))), ([95851 chars]c'))) != ((('_[4395 chars]test:42')),)), ('total_estimated_cells', 1))),[95875 chars]c')))

First differing element 0:
(('_i[4394 chars]test:')),)), ('total_estimated_cells', 1))), ('_type', 'doc'))
(('_i[4394 chars]test:42')),)), ('total_estimated_cells', 1))),[13 chars]oc'))

  ((('_id', '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb'),
    ('_index', 'azul_v2_dev_test_files_aggregate'),
    ('_score', 1.0),
    ('_source',
     (('bundles',
       ((('uuid', 'aaa96233-bf27-44c7-82df-b4dc15ad4d9d'),
         ('version', '2018-11-02T113344.698028Z')),)),
      ('contents',
       (('analysis_protocols', ()),
        ('cell_lines', ()),
        ('cell_suspensions',
         ((('biomaterial_id', ('GSM2172585 1',)),
           ('document_id', ('412898c5-5b9b-4907-b07c-e9b89666e204',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('selected_cell_type', ('~null',)),
           ('total_estimated_cells', 1),
           ('total_estimated_cells_', 1)),)),
        ('donors',
         ((('biological_sex', ('female',)),
           ('biomaterial_id', ('DID_scRSq06',)),
           ('development_stage', ('~null',)),
           ('diseases', ('normal',)),
           ('document_id', ('7b07b9d0-cc0e-4098-9f64-f4a569f7d746',)),
           ('donor_count', 1),
           ('donor_count_', 1),
           ('genus_species', ('Australopithecus',)),
           ('organism_age', ('38 year',)),
           ('organism_age_range',
            ((('gte', 1198368000.0), ('lte', 1198368000.0)),)),
           ('organism_age_unit', ('year',)),
           ('organism_age_value', ('38',))),)),
        ('files',
         ((('_type', 'file'),
           ('content-type', 'application/gzip; dcp-type=data'),
           ('content_description', ('~null',)),
           ('crc32c', '1d998e49'),
           ('document_id', '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb'),
           ('drs_path',
            '7b07f99e-4a8a-4ad0-bd4f-db0d7a00c7bb?version=2018-11-02T113344.698028Z'),
           ('file_format', 'fastq.gz'),
           ('file_type', 'sequence_file'),
           ('indexed', 0),
           ('is_intermediate', 9223372036854774784),
           ('lane_index', 9223372036854774784),
           ('lane_index_', None),
           ('name', 'SRR3562915_1.fastq.gz'),
           ('read_index', 'read1'),
           ('related_files', ()),
           ('sha256',
            '77337cb51b2e584b5ae1b99db6c163b988cbc5b894dda2f5d22424978c3bfc7a'),
           ('size', 195142097),
           ('size_', 195142097),
           ('source', '~null'),
           ('uuid', '7b07f99e-4a8a-4ad0-bd4f-db0d7a00c7bb'),
           ('version', '2018-11-02T113344.698028Z')),)),
        ('imaging_protocols', ()),
        ('library_preparation_protocols',
         ((('library_construction_approach', ('Smart-seq2',)),
           ('nucleic_acid_source', ('single cell',))),)),
        ('organoids', ()),
        ('projects',
         ((('_type', ('project',)),
           ('array_express_accessions', ('~null',)),
           ('document_id', ('e8642221-4c2c-4fd7-b926-a68bce363c88',)),
           ('geo_series_accessions', ('~null',)),
           ('insdc_project_accessions', ('~null',)),
           ('insdc_study_accessions', ('~null',)),
           ('institutions', ('Farmers Trucks', 'University')),
           ('laboratory', ('John Dear',)),
           ('project_short_name', ('Single of human pancreas',)),
           ('project_title', ('Single cell transcriptome patterns.',)),
           ('publication_titles',
            ('Single-Cell Analysis of Human Pancreas Reveals Transcriptional '
             'Signatures of Aging and Somatic Mutation Patterns.',)),
           ('supplementary_links',
            ('https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/Results',))),)),
        ('sample_specimens',
         ((('_source', ('specimen_from_organism',)),
           ('_type', ('specimen',)),
           ('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('disease', ('normal',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('has_input_biomaterial', ('~null',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('preservation_method', ('~null',)),
           ('storage_method', ('~null',))),)),
        ('samples',
         ((('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('effective_organ', ('pancreas',)),
           ('entity_type', ('specimens',)),
           ('model_organ', ('~null',)),
           ('model_organ_part', ('~null',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',))),)),
        ('sequencing_inputs',
         ((('biomaterial_id', ('GSM2172585 1',)),
           ('document_id', ('412898c5-5b9b-4907-b07c-e9b89666e204',)),
           ('sequencing_input_type', ('cell_suspension',))),)),
        ('sequencing_processes',
         ((('document_id', ('771ddaf6-3a4f-4314-97fe-6294ff8e25a4',)),),)),
        ('sequencing_protocols',
         ((('instrument_manufacturer_model', ('Illumina NextSeq 500',)),
           ('paired_end', (1,))),)),
        ('specimens',
         ((('_source', ('specimen_from_organism',)),
           ('_type', ('specimen',)),
           ('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('disease', ('normal',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('has_input_biomaterial', ('~null',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('preservation_method', ('~null',)),
           ('storage_method', ('~null',))),)))),
      ('entity_id', '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb'),
      ('num_contributions', 1),
      ('sources',
-      ((('id', '4b737739-4dc9-5d4b-9989-a4942047c91c'), ('spec', 'test:')),)),
+      ((('id', '4b737739-4dc9-5d4b-9989-a4942047c91c'), ('spec', 'test:42')),)),
?                                                                       ++

      ('total_estimated_cells', 1))),
    ('_type', 'doc')),
   (('_id',
     '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb_aaa96233-bf27-44c7-82df-b4dc15ad4d9d_2018-11-02T113344.698028Z_exists'),
    ('_index', 'azul_v2_dev_test_files'),
    ('_score', 1.0),
    ('_source',
     (('bundle_deleted', False),
      ('bundle_uuid', 'aaa96233-bf27-44c7-82df-b4dc15ad4d9d'),
      ('bundle_version', '2018-11-02T113344.698028Z'),
      ('contents',
       (('analysis_protocols', ()),
        ('cell_lines', ()),
        ('cell_suspensions',
         ((('biomaterial_id', 'GSM2172585 1'),
           ('document_id', '412898c5-5b9b-4907-b07c-e9b89666e204'),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('selected_cell_type', ('~null',)),
           ('total_estimated_cells', 1),
           ('total_estimated_cells_', 1)),)),
        ('donors',
         ((('biological_sex', 'female'),
           ('biomaterial_id', 'DID_scRSq06'),
           ('development_stage', '~null'),
           ('diseases', ('normal',)),
           ('document_id', '7b07b9d0-cc0e-4098-9f64-f4a569f7d746'),
           ('genus_species', ('Australopithecus',)),
           ('organism_age', '38 year'),
           ('organism_age_range', (('gte', 1198368000.0), ('lte', 1198368000.0))),
           ('organism_age_unit', 'year'),
           ('organism_age_value', '38')),)),
        ('files',
         ((('_type', 'file'),
           ('content-type', 'application/gzip; dcp-type=data'),
           ('content_description', ('~null',)),
           ('crc32c', '1d998e49'),
           ('document_id', '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb'),
           ('drs_path',
            '7b07f99e-4a8a-4ad0-bd4f-db0d7a00c7bb?version=2018-11-02T113344.698028Z'),
           ('file_format', 'fastq.gz'),
           ('file_type', 'sequence_file'),
           ('indexed', 0),
           ('is_intermediate', 9223372036854774784),
           ('lane_index', 9223372036854774784),
           ('lane_index_', None),
           ('name', 'SRR3562915_1.fastq.gz'),
           ('read_index', 'read1'),
           ('related_files', ()),
           ('sha256',
            '77337cb51b2e584b5ae1b99db6c163b988cbc5b894dda2f5d22424978c3bfc7a'),
           ('size', 195142097),
           ('size_', 195142097),
           ('source', '~null'),
           ('uuid', '7b07f99e-4a8a-4ad0-bd4f-db0d7a00c7bb'),
           ('version', '2018-11-02T113344.698028Z')),)),
        ('imaging_protocols', ()),
        ('library_preparation_protocols',
         ((('document_id', '9c32cf70-3ed7-4720-badc-5ee71e8a38af'),
           ('library_construction_approach', 'Smart-seq2'),
           ('nucleic_acid_source', 'single cell')),)),
        ('organoids', ()),
        ('projects',
         ((('_type', 'project'),
           ('array_express_accessions', ('~null',)),
           ('contact_names', ('Laura,,Huerta', 'Martin, Enge', 'Matthew,,Green')),
           ('contributors',
            ((('contact_name', 'Laura,,Huerta'),
              ('corresponding_contributor', 0),
              ('email', 'lauhuema@ebi.ac.uk'),
              ('institution', 'Farmers Trucks'),
              ('laboratory', 'John Dear'),
              ('project_role', 'external curator')),
             (('contact_name', 'Martin, Enge'),
              ('corresponding_contributor', 9223372036854774784),
              ('email', 'martin.enge@gmail.com'),
              ('institution', 'University'),
              ('laboratory', '~null'),
              ('project_role', '~null')),
             (('contact_name', 'Matthew,,Green'),
              ('corresponding_contributor', 0),
              ('email', 'hewgreen@ebi.ac.uk'),
              ('institution', 'Farmers Trucks'),
              ('laboratory', 'John Dear'),
              ('project_role', 'Human Cell Atlas wrangler')))),
           ('document_id', 'e8642221-4c2c-4fd7-b926-a68bce363c88'),
           ('geo_series_accessions', ('~null',)),
           ('insdc_project_accessions', ('~null',)),
           ('insdc_study_accessions', ('~null',)),
           ('institutions', ('Farmers Trucks', 'University')),
           ('laboratory', ('John Dear',)),
           ('project_description',
            'As organisms age, cells accumulate genetic and epigenetic changes '
            'that eventually lead to impaired organ function or catastrophic '
            'failure such as cancer. Here we describe a single-cell '
            'transcriptome analysis of 2544 human pancreas cells from donors, '
            'spanning six decades of life. We find that islet cells from older '
            'donors have increased levels of disorder as measured both by noise '
            'in the transcriptome and by the number of cells which display '
            'inappropriate hormone expression, revealing a transcriptional '
            'instability associated with aging. By analyzing the spectrum of '
            'somatic mutations in single cells from previously-healthy donors, '
            'we find a specific age-dependent mutational signature characterized '
            'by C to A and C to G transversions, indicators of oxidative stress, '
            'which is absent in single cells from human brain tissue or in a '
            'tumor cell line. Cells carrying a high load of such mutations also '
            'express higher levels of stress and senescence markers, including '
            'FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers '
            'previously linked to pancreatic diseases with substantial '
            'age-dependent risk, such as type 2 diabetes mellitus and '
            'adenocarcinoma. Thus, our single-cell approach unveils gene '
            'expression changes and somatic mutations acquired in aging human '
            'tissue, and identifies molecular pathways induced by these genetic '
            'changes that could influence human disease. Also, our results '
            'demonstrate the feasibility of using single-cell RNA-seq data from '
            'primary cells to derive meaningful insights into the genetic '
            'processes that operate on aging human tissue and to determine which '
            'molecular mechanisms are coordinated with these processes. '
            'Examination of single cells from primary human pancreas tissue'),
           ('project_short_name', 'Single of human pancreas'),
           ('project_title', 'Single cell transcriptome patterns.'),
           ('publication_titles',
            ('Single-Cell Analysis of Human Pancreas Reveals Transcriptional '
             'Signatures of Aging and Somatic Mutation Patterns.',)),
           ('publications',
            ((('publication_title',
               'Single-Cell Analysis of Human Pancreas Reveals Transcriptional '
               'Signatures of Aging and Somatic Mutation Patterns.'),
              ('publication_url',
               'https://www.ncbi.nlm.nih.gov/pubmed/28965763')),)),
           ('supplementary_links',
            ('https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/Results',))),)),
        ('sample_specimens',
         ((('_source', 'specimen_from_organism'),
           ('_type', 'specimen'),
           ('biomaterial_id', 'DID_scRSq06_pancreas'),
           ('disease', ('normal',)),
           ('document_id', 'a21dc760-a500-4236-bcff-da34a0e873d2'),
           ('has_input_biomaterial', '~null'),
           ('organ', 'pancreas'),
           ('organ_part', ('islet of Langerhans',)),
           ('preservation_method', '~null'),
           ('storage_method', '~null')),)),
        ('samples',
         ((('biomaterial_id', 'DID_scRSq06_pancreas'),
           ('document_id', 'a21dc760-a500-4236-bcff-da34a0e873d2'),
           ('effective_organ', 'pancreas'),
           ('entity_type', 'specimens'),
           ('model_organ', '~null'),
           ('model_organ_part', '~null'),
           ('organ', 'pancreas'),
           ('organ_part', ('islet of Langerhans',))),)),
        ('sequencing_inputs',
         ((('biomaterial_id', 'GSM2172585 1'),
           ('document_id', '412898c5-5b9b-4907-b07c-e9b89666e204'),
           ('sequencing_input_type', 'cell_suspension')),)),
        ('sequencing_processes',
         ((('document_id', '771ddaf6-3a4f-4314-97fe-6294ff8e25a4'),),)),
        ('sequencing_protocols',
         ((('document_id', '61e629ed-0135-4492-ac8a-5c4ab3ccca8a'),
           ('instrument_manufacturer_model', 'Illumina NextSeq 500'),
           ('paired_end', 1)),)),
        ('specimens',
         ((('_source', 'specimen_from_organism'),
           ('_type', 'specimen'),
           ('biomaterial_id', 'DID_scRSq06_pancreas'),
           ('disease', ('normal',)),
           ('document_id', 'a21dc760-a500-4236-bcff-da34a0e873d2'),
           ('has_input_biomaterial', '~null'),
           ('organ', 'pancreas'),
           ('organ_part', ('islet of Langerhans',)),
           ('preservation_method', '~null'),
           ('storage_method', '~null')),)))),
      ('entity_id', '0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb'),
      ('source',
-      (('id', '4b737739-4dc9-5d4b-9989-a4942047c91c'), ('spec', 'test:'))))),
+      (('id', '4b737739-4dc9-5d4b-9989-a4942047c91c'), ('spec', 'test:42'))))),
?                                                                      ++

    ('_type', 'doc')),
   (('_id', '412898c5-5b9b-4907-b07c-e9b89666e204'),
    ('_index', 'azul_v2_dev_test_cell_suspensions_aggregate'),
    ('_score', 1.0),
    ('_source',
     (('bundles',
       ((('uuid', 'aaa96233-bf27-44c7-82df-b4dc15ad4d9d'),
         ('version', '2018-11-02T113344.698028Z')),)),
      ('contents',
       (('analysis_protocols', ()),
        ('cell_lines', ()),
        ('cell_suspensions',
         ((('biomaterial_id', 'GSM2172585 1'),
           ('document_id', '412898c5-5b9b-4907-b07c-e9b89666e204'),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('selected_cell_type', ('~null',)),
           ('total_estimated_cells', 1),
           ('total_estimated_cells_', 1)),)),
        ('donors',
         ((('biological_sex', ('female',)),
           ('biomaterial_id', ('DID_scRSq06',)),
           ('development_stage', ('~null',)),
           ('diseases', ('normal',)),
           ('document_id', ('7b07b9d0-cc0e-4098-9f64-f4a569f7d746',)),
           ('donor_count', 1),
           ('donor_count_', 1),
           ('genus_species', ('Australopithecus',)),
           ('organism_age', ('38 year',)),
           ('organism_age_range',
            ((('gte', 1198368000.0), ('lte', 1198368000.0)),)),
           ('organism_age_unit', ('year',)),
           ('organism_age_value', ('38',))),)),
        ('files',
         ((('content_description', ('~null',)),
           ('count', 2),
           ('file_format', 'fastq.gz'),
           ('is_intermediate', 9223372036854774784),
           ('matrix_cell_count', 9223372036854774784),
           ('matrix_cell_count_', None),
           ('size', 385472253),
           ('size_', 385472253),
           ('source', ('~null',))),)),
        ('imaging_protocols', ()),
        ('library_preparation_protocols',
         ((('library_construction_approach', ('Smart-seq2',)),
           ('nucleic_acid_source', ('single cell',))),)),
        ('organoids', ()),
        ('projects',
         ((('_type', ('project',)),
           ('array_express_accessions', ('~null',)),
           ('document_id', ('e8642221-4c2c-4fd7-b926-a68bce363c88',)),
           ('geo_series_accessions', ('~null',)),
           ('insdc_project_accessions', ('~null',)),
           ('insdc_study_accessions', ('~null',)),
           ('institutions', ('Farmers Trucks', 'University')),
           ('laboratory', ('John Dear',)),
           ('project_short_name', ('Single of human pancreas',)),
           ('project_title', ('Single cell transcriptome patterns.',)),
           ('publication_titles',
            ('Single-Cell Analysis of Human Pancreas Reveals Transcriptional '
             'Signatures of Aging and Somatic Mutation Patterns.',)),
           ('supplementary_links',
            ('https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/Results',))),)),
        ('sample_specimens',
         ((('_source', ('specimen_from_organism',)),
           ('_type', ('specimen',)),
           ('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('disease', ('normal',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('has_input_biomaterial', ('~null',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',)),
           ('preservation_method', ('~null',)),
           ('storage_method', ('~null',))),)),
        ('samples',
         ((('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('effective_organ', ('pancreas',)),
           ('entity_type', ('specimens',)),
           ('model_organ', ('~null',)),
           ('model_organ_part', ('~null',)),
           ('organ', ('pancreas',)),
           ('organ_part', ('islet of Langerhans',))),)),
        ('sequencing_inputs',
         ((('biomaterial_id', ('GSM2172585 1',)),
           ('document_id', ('412898c5-5b9b-4907-b07c-e9b89666e204',)),
           ('sequencing_input_type', ('cell_suspension',))),)),
        ('sequencing_processes',
         ((('document_id', ('771ddaf6-3a4f-4314-97fe-6294ff8e25a4',)),),)),
        ('sequencing_protocols',
         ((('instrument_manufacturer_model', ('Illumina NextSeq 500',)),
           ('paired_end', (1,))),)),
        ('specimens',
         ((('_source', ('specimen_from_organism',)),
           ('_type', ('specimen',)),
           ('biomaterial_id', ('DID_scRSq06_pancreas',)),
           ('disease', ('normal',)),
           ('document_id', ('a21dc760-a500-4236-bcff-da34a0e873d2',)),
           ('has_input_biomaterial', ('~null',)),
           ('organ', ('pancreas',)),
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?                                                                       ++

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            'FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers '
            'previously linked to pancreatic diseases with substantial '
            'age-dependent risk, such as type 2 diabetes mellitus and '
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            'tissue, and identifies molecular pathways induced by these genetic '
            'changes that could influence human disease. Also, our results '
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            'processes that operate on aging human tissue and to determine which '
            'molecular mechanisms are coordinated with these processes. '
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?                                                                      ++

    ('_type', 'doc')))

======================================================================
hannes-ucsc commented 3 years ago

The drop commit on the PR branch makes demoing this unnecessary.

image