loqusdb 2.7.11__py3-none-any.whl → 2.7.12__py3-none-any.whl

loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.11"
+__version__ = "2.7.12"
 
 INDEXES = {
     "variant": [

loqusdb/commands/export.py

@@ -59,7 +59,10 @@ def export(ctx, outfile, variant_type, freq):
     head.add_meta_line("NrCases", nr_cases)
     if freq:
         head.add_info(
-            "Frq", "1", "Float", "Observation frequency of the variant (not allele frequency)"
+            "Frq",
+            "1",
+            "Float",
+            f"Observation frequency of the variant (not allele frequency) based on {nr_cases} cases",
         )
     head.add_info("Obs", "1", "Integer", "The number of observations for the variant")
     head.add_info("Hom", "1", "Integer", "The number of observed homozygotes")

{loqusdb-2.7.11.dist-info → loqusdb-2.7.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.11
+Version: 2.7.12
 Summary: A simple observation count database
 License: MIT
 Author: Your Name
@@ -9,6 +9,7 @@ Requires-Python: >=3.12,<4.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: PyYAML
 Requires-Dist: click
 Requires-Dist: coloredlogs

{loqusdb-2.7.11.dist-info → loqusdb-2.7.12.dist-info}/RECORD

@@ -1,5 +1,4 @@
-README.md,sha256=0-XD0EEYvCnenT07wkO0ZX6lJbzN8OC1cV3M9G47nps,4648
-loqusdb/__init__.py,sha256=tVCT5pNoMl8Zuqcc32Dbade0bG0SS7s05LMGyRM2gL0,1688
+loqusdb/__init__.py,sha256=8HkygPjhH1mlqoo1IXBaXPSGUkIRHyhkkz5f29Am25I,1688
 loqusdb/__main__.py,sha256=8FGKySAGaWSzAYMj6HRsxeyiME3V01Idt7HrmN7pSYY,397
 loqusdb/build_models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/build_models/case.py,sha256=AByutEYK2N3kS9JFvyZfPKNZdCpZHCSD0nNHAgaU1Cs,4127
@@ -9,7 +8,7 @@ loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,
 loqusdb/commands/annotate.py,sha256=748kImopE5WbaO1nuv3WUgIqezWFSsi7SBeWhOz26-s,1384
 loqusdb/commands/cli.py,sha256=wJD5S1BoCxtRTAobd1QtmQpzlngJg-mt1nsyD92fDD4,3176
 loqusdb/commands/delete.py,sha256=R6ysHKSMw1mmL4ZbktoUIKzdzDLQ3314YPYhIy1myic,1979
-loqusdb/commands/export.py,sha256=-9SHgvr0G8FlyW0FGSfe1dmNDnjx4HKAaa-xYzSkvNc,3238
+loqusdb/commands/export.py,sha256=DPcMo4QgTCA5fu8x_IWZ9YskRl4_ikKARXpnuFr1iow,3302
 loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
 loqusdb/commands/load.py,sha256=sDGCOGbukdfebLn1iBGyWoI6t3tijLzywP1tg3WheQI,4431
 loqusdb/commands/load_profile.py,sha256=cflCbF9f77_HCH8xPnN8zSSocvIffRMnC2LPE0j7Xq8,3336
@@ -50,48 +49,8 @@ loqusdb/utils/profiling.py,sha256=3OizF7CpYvSl9kyl2g4KGJxbIRUqWfmfLxn3843XYDk,91
 loqusdb/utils/update.py,sha256=1edJG-u24FgOSxyXAQEiyTG4IyK-Uo3lSIl5qyzcXsI,4433
 loqusdb/utils/variant.py,sha256=U6nMZRUf5NDDQ74nG0HBCLMnFQVgFAT6eHll_F2uiwc,2087
 loqusdb/utils/vcf.py,sha256=ybmrTBEPYa0FbUXo8ttlwATk13RnKjX9eIDbRDwCiVE,5175
-tests/build_models/test_build_case.py,sha256=4CzykSmiBgAVZWlqzjLTjBmY9NafzmPol7LiEu4003U,4404
-tests/build_models/test_build_variant.py,sha256=-9ulYBNBIxAGt_FiyaADWLuTJ4bWwRVVfMbjzummMZA,537
-tests/build_models/test_is_greater.py,sha256=sAz_UB6oGr72Pqc7ZEbPTw6N07E0QR-Yvn8UCEi0yP8,1360
-tests/commands/test_export.py,sha256=Xdivbs_hDJzoJKNP60gnb6AgGfNdOqVTyk0lAkMFwPg,440
-tests/commands/test_identity.py,sha256=6yCD4m6ezGTsoW5lk7t7MQ5gxOi2u86ZcWtz-ghtsHk,564
-tests/commands/test_view.py,sha256=036iug8YB67ZYi_qtSU_VBBAIcJZEj_EolNDRsOaVCM,662
-tests/conftest.py,sha256=F7teEGvH3mD1zO5tqd_yEWneFrmW5U8d74-IDDSAXoI,10531
-tests/fixtures/643594.clinical.SV.vcf,sha256=e-RVC96kxwrohNmiZ7xHAHcTcnWI5-NSpOVMX2zGsXA,59626
-tests/fixtures/643594.clinical.vcf.gz,sha256=CuGqNRVLnkPDy8JM9i8JhYQZn28CDM1eGenECi2dD4E,413153
-tests/fixtures/double_variant.vcf,sha256=LlVy4mW1-HAw0dyJpWPJTbAGQm5LZOtOuD2uLkbJE7w,2165
-tests/fixtures/funny_trio.ped,sha256=t4Mroxg51i5zhLPnbbWSXaC2aKgETMvNcfQc-ArjFpk,130
-tests/fixtures/profile_snv.vcf,sha256=SdQA2CCzCLCrwYEEod2yuZsVt6--8dHppUVyaIKxan0,5420
-tests/fixtures/recessive_trio.ped,sha256=leXtMPWrwXeDQY557R_sL5QLcewu1uwHFsn8moOjMCY,148
-tests/fixtures/test.SV.vcf,sha256=OqNrkQQpgbXs2L1en7S6C8A0KFCKDn4w1czRRAU-lEY,59618
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-tests/fixtures/unsorted.vcf,sha256=NSsdgsVVJuJwd3udD__GBrZaregz4qa_egDg4OzBLF4,2049
-tests/functional/test_cli.py,sha256=XO7toMozpFU3MrqxSqsqKjUgeLSbeEmNtLSmGePWuXg,8095
-tests/plugins/mongo/test_case_operations.py,sha256=SJ9KHiDV7iHRtxu-4C9mp9uSKQ5wen3hoqK0W7JULGA,4271
-tests/plugins/mongo/test_connect.py,sha256=RsyDY5T9BkkgZANyOrMZ3-nXRZX8sjvBH7E1BD5noYU,199
-tests/plugins/mongo/test_flask_extension.py,sha256=UtvMJbRqVcVn82b9sGL-IQCK5GBW2KdnhckLuB9Dqkk,738
-tests/plugins/mongo/test_get_sv.py,sha256=9LBnCv7zLjKuioNMhSBMo0zJ3Md3wpEUa395Gz_18ms,1029
-tests/plugins/mongo/test_load_svs.py,sha256=zkDiowbG2p6uiUC5nzajDp_QDky5lyKAnyr_sir8Pic,2670
-tests/plugins/mongo/test_variant_operations.py,sha256=Th42H-rHuN8oa-e8Sug29-_8tJtezevjmD4rM3543kM,9687
-tests/utils/test_case.py,sha256=DTbdiTn5myeE1K91wXtJwiDeLfmYOU8uqooSAq_B56o,1317
-tests/utils/test_delete.py,sha256=Gzatf_WpqdtRhkELEt2WgVuKF-UwiPUuycS7cjtKcgg,1872
-tests/utils/test_delete_family.py,sha256=ym0ffeCf8IvNy9-AUL2ix1BWBapxZo4P4ZuLtQfQNtQ,845
-tests/utils/test_delete_variant.py,sha256=bRNFmV9OvQJ-Ao6eq2yKIhjz3-FOH75OCqclKTu9c8A,2171
-tests/utils/test_get_family.py,sha256=WLIqNHCfmHbZoL-TMLf6wFGxf_vBeEBE9ndWOE2iHTQ,329
-tests/utils/test_load_database.py,sha256=gZOLSTrRYsTq8q3in0gazmZJxZVreoFN1_o9EzXD_1s,1473
-tests/utils/test_load_family.py,sha256=DWDqC9UCMVMwVKoYToL_KGc0kpsn9DVFFZovD3zOCMc,2376
-tests/utils/test_load_variants.py,sha256=CAo8oDw9mz8oTszscIS38yl7jKUPVapJIH_Y4MUBZHs,6278
-tests/utils/test_migrate.py,sha256=DM4RC_sY6C3aCbE0-Rzg5Yi5pp0BgKNefP1OCaviPSw,1177
-tests/utils/test_profiling.py,sha256=tehPKrE0tNbaz26On8lp4MeDTMwTpw_iyQdW1cW5iMo,2658
-tests/vcf_tools/test_check_par.py,sha256=zmG3HKWy6omyofqK4WjzmcbkVEvkncUm26GeMtnxHiI,1155
-tests/vcf_tools/test_check_vcf.py,sha256=bTZQOSbhXthRDwTmcfvf4sW-DMUdlpM7bBSDsmXSDrU,1966
-tests/vcf_tools/test_format_sv_variant.py,sha256=eeQ6XI6X2lNpsVaWecu5lfdRHrDh1XZvcz9UhL7j3qo,4375
-tests/vcf_tools/test_format_variant.py,sha256=CfgCnrS5OvuIcUOCTUGCiDRUelk3fZgT7YQAytNPvvM,4176
-tests/vcf_tools/test_vcf.py,sha256=Fc9tO1IgKFo_DCfj_GrsXGx9t_69xkWhn1ZCL7IXqLU,1563
-loqusdb-2.7.11.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.11.dist-info/METADATA,sha256=Kcjp_pYPIFrSDYb5sQYxHfTJY5z1ql99WYlGQSWB0SY,5270
-loqusdb-2.7.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-loqusdb-2.7.11.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
-loqusdb-2.7.11.dist-info/RECORD,,
+loqusdb-2.7.12.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.12.dist-info/METADATA,sha256=xuej6Yy1Xc1YBsrc1YxlnTO6MkMr80_HoDAYqVcqzKs,5321
+loqusdb-2.7.12.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
+loqusdb-2.7.12.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
+loqusdb-2.7.12.dist-info/RECORD,,

{loqusdb-2.7.11.dist-info → loqusdb-2.7.12.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 2.0.0
 Root-Is-Purelib: true
 Tag: py3-none-any

README.md

@@ -1,148 +0,0 @@
-# loqusdb
-[![Publish to PyPI](https://github.com/moonso/loqusdb/actions/workflows/build_and_publish.yml/badge.svg)](https://github.com/moonso/loqusdb/actions/workflows/build_and_publish.yml)
-[![Coverage Status](https://coveralls.io/repos/github/moonso/loqusdb/badge.svg?branch=master)](https://coveralls.io/github/moonso/loqusdb?branch=master)
-[![PyPI Version][pypi-img]][pypi-url]
-
-Small tool to set up a local variant database.
-If you find Loqusdb useful in your work, please cite the [article][publication].
-
-Right now **Locusdb** uses [mongodb][mongodb] as backend for
-storing variants, but there should not be a huge difference to use another
-database manager.
-
-## Installation ##
-
-
-`poetry install`
-
-or
-
-```
-$git clone https://github.com/moonso/loqusdb
-$cd loqusdb
-$poetry install
-```
-
-## Idea ##
-
-Tool to keep track of what variants that have been seen and in what families they have been observed.
-This is **NOT** a tool to create a true frequency database.
-It will basically count the number of times we have seen a variant in any individual.
-We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
-
-Variants are stored by providing a VCF file and a (ped or ped like) family file.
-
-Loqusdb will first check if the VCF file adheres to the VCF format.
-
-The tool will then check all variants if they have been observed in any of the individuals in the family.
-
-When the variants are added:
-
-- Either the variant exists, in this case we increase the number of observations with one
-- Or this variant has not been seen before, then the variant is added to the database
-
-
-## Command Line Interface ##
-
-```
-$ loqusdb
-Usage: loqusdb [OPTIONS] COMMAND [ARGS]...
-
-  loqusdb: manage a local variant count database.
-
-Options:
-  -db, --database TEXT            Defaults to 'loqusdb' if not specified
-  -u, --username TEXT
-  -p, --password TEXT
-  -a, --authdb TEXT               If authentication should be done against
-                                  another database than --database
-
-  -port, --port INTEGER           Specify the port where to look for the mongo
-                                  database.  [default: 27017]
-
-  -h, --host TEXT                 Specify the host where to look for the mongo
-                                  database.  [default: localhost]
-
-  --uri TEXT                      Specify a mongodb uri
-  -c, --config FILENAME           Use a config with db information
-  -t, --test                      Used for testing. This will use a mongomock
-                                  database.
-
-  -g, --genome-build [GRCh37|GRCh38]
-                                  Specify what genome build to use
-  -v, --verbose
-  --version                       Show the version and exit.
-  --help                          Show this message and exit.
-
-Commands:
-  annotate  Annotate a VCF with observations
-  cases     Display cases in database
-  delete    Delete the variants of a family
-  dump      Dump the database
-  export    Export variants to VCF format
-  identity  Search identity collection
-  index     Add indexes to database
-  load      Load the variants of a family
-  migrate   Migrate an old loqusdb instance
-  profile   Loads variants to be used in profiling
-  restore   Restore database from dump
-  update    Update an existing case with a new type of variants
-  variants  Display variants in database
-  wipe      Wipe a loqusdb instance
-```
-
-
-## Database ##
-
-### Connecting ###
-
-Connection can be specified on command line with `--database`, `--username`, `--password`, `--port`, `--host` and/or `--uri`. Or these options can be sent with a config file that can take the same options:
-
-```yaml
-uri: mongodb://loqusdb-username:loqusdb-pwd@localhost:27030/loqusdb-rd?authSource=admin
-db_name: loqusdb_test
-```
-or
-```yaml
-host: localhost
-port: 27030
-username: loqusdb-username
-password: loqusdb-pwd
-authdb: admin
-db_name: loqusdb_test
-```
-
-### Mongo ###
-
-The collections are defined as follows:
-
-**Case**
-
-```python
-{
-    'case_id': 'case_id',
-    'vcf_path': 'path_to_vcf'
-}
-```
-
-**Variant**
-
-```python
-{
-    '_id': 'variant_id',
-    'chrom': 'CHROM',
-    'start': postition,
-    'end': end postition,
-    'ref': reference base(s),
-    'alt': alternative base(s),
-    'homozygote': number_of_homozygotes,
-    'hemizygote': number_of_hemizygotes,
-    'observations': number_of_observations,
-    'families': ['family_id', ...]
-}
-```
-
-[mongodb]: https://www.mongodb.org
-[publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
-[pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square
-[pypi-url]: https://pypi.python.org/pypi/loqusdb/

tests/build_models/test_build_case.py

@@ -1,150 +0,0 @@
-import pytest
-
-from loqusdb.build_models.case import build_case, get_individual_positions
-from loqusdb.exceptions import CaseError
-
-
-def test_get_individual_positions():
-    ## GIVEN a list with ids
-    inds = ["1", "2", "3"]
-    ## WHEN getting the individual positions
-    ind_pos = get_individual_positions(inds)
-    ## THEN assert they where given the correct position
-    assert ind_pos["1"] == 0
-    assert ind_pos["2"] == 1
-    assert ind_pos["3"] == 2
-
-
-def test_get_individual_positions_no_inds():
-    ## GIVEN a list with ids
-    inds = None
-    ## WHEN getting the individual positions
-    ind_pos = get_individual_positions(inds)
-    ## THEN assert an empty dict is returned
-    assert ind_pos == {}
-
-
-def test_build_case_no_ped():
-    ## GIVEN some vcf individuals
-
-    vcf_individuals = ["mother", "proband"]
-    case_id = "test"
-
-    ## WHEN building a case object
-    case_obj = build_case(
-        case=None,
-        vcf_individuals=vcf_individuals,
-        case_id=case_id,
-    )
-
-    ## THEN assert that the case got the right ID
-    assert case_obj["case_id"] == case_id
-    for ind_obj in case_obj["individuals"]:
-        assert ind_obj["name"] in vcf_individuals
-        assert ind_obj["ind_id"] in vcf_individuals
-
-
-def test_build_case_no_ped_no_case_id():
-    ## WHEN building a case object
-
-    ## THEN assert a CaseError is raised
-    with pytest.raises(CaseError):
-        ## GIVEN some vcf individuals
-
-        vcf_individuals = ["mother", "proband"]
-
-        case_obj = build_case(
-            case=None,
-            vcf_individuals=vcf_individuals,
-        )
-
-
-def test_build_case_ped(family_obj, vcf_path):
-    ## GIVEN a ped parser family_obj
-    vcf_inds = [ind_id for ind_id in family_obj.individuals]
-    nr_variants = 10
-
-    ## WHEN building a case object
-    case_obj = build_case(
-        case=family_obj,
-        vcf_individuals=vcf_inds,
-        vcf_path=vcf_path,
-        nr_variants=nr_variants,
-    )
-
-    ## THEN assert that the case has the correct id
-    assert case_obj["case_id"] == family_obj.family_id
-
-    for ind_obj in case_obj["individuals"]:
-        assert ind_obj["ind_id"] in vcf_inds
-
-    ## THEN assert that the vcf_path was added
-    assert case_obj["vcf_path"] == vcf_path
-
-    ## THEN assert that the nr variants is correct
-    assert case_obj["nr_variants"] == nr_variants
-
-
-def test_build_case_ped_sv(family_obj, sv_vcf_path):
-    ## GIVEN a ped parser family_obj
-    vcf_inds = [ind_id for ind_id in family_obj.individuals]
-    nr_sv_variants = 10
-
-    ## WHEN building a case object
-    case_obj = build_case(
-        case=family_obj,
-        sv_individuals=vcf_inds,
-        vcf_sv_path=sv_vcf_path,
-        nr_sv_variants=nr_sv_variants,
-    )
-
-    ## THEN assert that the case has the correct id
-    assert case_obj["case_id"] == family_obj.family_id
-
-    case_obj["individuals"] == []
-    for ind_obj in case_obj["sv_individuals"]:
-        assert ind_obj["ind_id"] in vcf_inds
-
-    ## THEN assert that the vcf_path was added
-    assert case_obj["vcf_path"] is None
-    assert case_obj["vcf_sv_path"] == sv_vcf_path
-
-    ## THEN assert that the nr variants is correct
-    assert case_obj["nr_variants"] is None
-    assert case_obj["nr_sv_variants"] == nr_sv_variants
-
-
-def test_build_case_ped_sv_and_snv(family_obj, sv_vcf_path, vcf_path):
-    ## GIVEN a ped parser family_obj
-    vcf_inds = [ind_id for ind_id in family_obj.individuals]
-    sv_vcf_inds = [ind_id for ind_id in family_obj.individuals]
-    nr_sv_variants = 10
-    nr_variants = 20
-
-    ## WHEN building a case object
-    case_obj = build_case(
-        case=family_obj,
-        sv_individuals=vcf_inds,
-        vcf_sv_path=sv_vcf_path,
-        nr_sv_variants=nr_sv_variants,
-        vcf_individuals=vcf_inds,
-        vcf_path=vcf_path,
-        nr_variants=nr_variants,
-    )
-
-    ## THEN assert that the case has the correct id
-    assert case_obj["case_id"] == family_obj.family_id
-
-    for ind_obj in case_obj["individuals"]:
-        assert ind_obj["ind_id"] in vcf_inds
-
-    for ind_obj in case_obj["sv_individuals"]:
-        assert ind_obj["ind_id"] in sv_vcf_inds
-
-    ## THEN assert that the vcf_path was added
-    assert case_obj["vcf_path"] == vcf_path
-    assert case_obj["vcf_sv_path"] == sv_vcf_path
-
-    ## THEN assert that the nr variants is correct
-    assert case_obj["nr_variants"] == nr_variants
-    assert case_obj["nr_sv_variants"] == nr_sv_variants

tests/build_models/test_build_variant.py

@@ -1,15 +0,0 @@
-from loqusdb.build_models.variant import get_coords, build_variant
-
-
-def test_build_het_variant(het_variant, case_obj):
-    variant_obj = build_variant(variant=het_variant, case_obj=case_obj)
-    assert variant_obj["chrom"] == het_variant.CHROM
-    assert variant_obj["homozygote"] == 0
-    assert variant_obj["hemizygote"] == 0
-
-
-def test_get_coords_for_BND(bnd_variant):
-    coords = get_coords(bnd_variant)
-    assert coords["pos"] == coords["end"]
-    assert coords["sv_length"] == float("inf")
-    assert coords["sv_type"] == "BND"

tests/build_models/test_is_greater.py

@@ -1,49 +0,0 @@
-from loqusdb.build_models.variant import Position, is_greater
-
-
-def test_is_greater_different_chrom():
-    ## GIVEN two positions where a is smaller than b. Different chroms
-    a = Position("1", 100)
-    b = Position("3", 100)
-
-    ## WHEN testing if a is greater than b
-    res = is_greater(a, b)
-    ## THEN assert a was not greater than b
-    assert res is False
-
-    ## WHEN testing if b is greater than a
-    res = is_greater(b, a)
-    ## THEN assert b was greater than a
-    assert res is True
-
-
-def test_is_greater_same_chrom():
-    ## GIVEN two positions where a is smaller than b. Same chroms
-    a = Position("1", 100)
-    b = Position("1", 300)
-
-    ## WHEN testing if a is greater than b
-    res = is_greater(a, b)
-    ## THEN assert a was not greater than b
-    assert res is False
-
-    ## WHEN testing if b is greater than a
-    res = is_greater(b, a)
-    ## THEN assert b was greater than a
-    assert res is True
-
-
-def test_is_greater_wierd_chrom():
-    ## GIVEN two positions where one chrom is unknown b
-    a = Position("1", 100)
-    b = Position("GRLrs2", 300)
-
-    ## WHEN testing if a is greater than b
-    res = is_greater(a, b)
-    ## THEN assert a was not greater than b
-    assert res is False
-
-    ## WHEN testing if b is greater than a
-    res = is_greater(b, a)
-    ## THEN assert a was not greater than b
-    assert res is False

tests/commands/test_export.py

@@ -1,16 +0,0 @@
-from click.testing import CliRunner
-
-from loqusdb.commands.cli import cli as base_command
-
-
-def test_export_base(real_db_name: str):
-    """Test the base command that exports variants."""
-
-    runner = CliRunner()
-
-    # WHEN the base command to export cases is run
-    command = ["--database", real_db_name, "export"]
-
-    ## THEN it should return success
-    result = runner.invoke(base_command, command)
-    assert result.exit_code == 0

tests/commands/test_identity.py

@@ -1,19 +0,0 @@
-from click.testing import CliRunner
-
-from loqusdb.commands.cli import cli as base_command
-
-
-def test_identity(real_db_name: str):
-    """Test the SV identity base command."""
-
-    runner = CliRunner()
-
-    # WHEN the base identity command is run on an empty database
-    command = ["--database", real_db_name, "identity", "-v", "1_7890024_TGA_GGG"]
-
-    # THEN the command should return success
-    result = runner.invoke(base_command, command)
-    assert result.exit_code == 0
-
-    # AND no variant found message
-    assert "No hits for variant" in result.output

tests/commands/test_view.py

@@ -1,19 +0,0 @@
-from click.testing import CliRunner
-
-from loqusdb.commands.cli import cli as base_command
-from loqusdb.plugins.mongo.adapter import MongoAdapter
-
-
-def test_view_cases_base(real_mongo_adapter: MongoAdapter, real_db_name: str):
-    """Test the base command that returns database cases."""
-
-    ## GIVEN an empty database
-    assert sum([1 for _ in real_mongo_adapter.cases()]) == 0
-
-    runner = CliRunner()
-
-    # THEN the case command should return No cases found error
-    command = ["--database", real_db_name, "cases"]
-    result = runner.invoke(base_command, command)
-    assert result.exit_code == 1
-    assert "No cases found in database" in result.output