def fixture_balsamic_context(
cg_context: CGConfig,
helpers: StoreHelpers,
balsamic_lims: MockLimsAPI,
balsamic_housekeeper: HousekeeperAPI,
trailblazer_api: MockTB,
hermes_api: HermesApi,
cg_dir,
) -> CGConfig:
"""context to use in cli"""
cg_context.housekeeper_api_ = balsamic_housekeeper
cg_context.lims_api_ = balsamic_lims
cg_context.trailblazer_api_ = trailblazer_api
cg_context.meta_apis["analysis_api"] = BalsamicAnalysisAPI(
config=cg_context)
status_db: Store = cg_context.status_db
# Create tgs application version
helpers.ensure_application_version(store=status_db,
application_tag="TGSA",
application_type="tgs")
# Create wes application version
helpers.ensure_application_version(store=status_db,
application_tag="WESA",
application_type="wes")
# Create textbook case for WGS PAIRED with enough reads
case_wgs_paired_enough_reads = helpers.add_case(
store=status_db,
internal_id="balsamic_case_wgs_paired_enough_reads",
name="balsamic_case_wgs_paired_enough_reads",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wgs_paired_tumor_enough_reads = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_tumor_enough_reads",
is_tumour=True,
application_type="wgs",
reads=10,
sequenced_at=dt.datetime.now(),
)
sample_case_wgs_paired_normal_enough_reads = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_normal_enough_reads",
is_tumour=False,
application_type="wgs",
reads=10,
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_wgs_paired_enough_reads,
sample=sample_case_wgs_paired_tumor_enough_reads,
)
helpers.add_relationship(
status_db,
case=case_wgs_paired_enough_reads,
sample=sample_case_wgs_paired_normal_enough_reads,
)
# Create textbook case for WGS PAIRED
case_wgs_paired = helpers.add_case(
store=status_db,
internal_id="balsamic_case_wgs_paired",
name="balsamic_case_wgs_paired",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wgs_paired_tumor = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_tumor",
is_tumour=True,
application_type="wgs",
reads=10,
sequenced_at=dt.datetime.now(),
)
sample_case_wgs_paired_normal = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_normal",
is_tumour=False,
application_type="wgs",
reads=10,
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_wgs_paired,
sample=sample_case_wgs_paired_tumor)
helpers.add_relationship(status_db,
case=case_wgs_paired,
sample=sample_case_wgs_paired_normal)
# Create textbook case for TGS PAIRED without enough reads
case_tgs_paired = helpers.add_case(
status_db,
internal_id="balsamic_case_tgs_paired",
name="balsamic_case_tgs_paired",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_tgs_paired_tumor = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_paired_tumor",
is_tumour=True,
application_tag="TGSA",
application_type="tgs",
reads=10,
sequenced_at=dt.datetime.now(),
)
sample_case_tgs_paired_normal = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_paired_normal",
is_tumour=False,
application_tag="TGSA",
application_type="tgs",
reads=0,
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_tgs_paired,
sample=sample_case_tgs_paired_tumor)
helpers.add_relationship(status_db,
case=case_tgs_paired,
sample=sample_case_tgs_paired_normal)
# Create textbook case for WGS TUMOR ONLY
case_wgs_single = helpers.add_case(
status_db,
internal_id="balsamic_case_wgs_single",
name="balsamic_case_wgs_single",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wgs_single_tumor = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_single_tumor",
is_tumour=True,
application_type="wgs",
reads=100,
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_wgs_single,
sample=sample_case_wgs_single_tumor)
# Create textbook case for TGS TUMOR ONLY
case_tgs_single = helpers.add_case(
status_db,
internal_id="balsamic_case_tgs_single",
name="balsamic_case_tgs_single",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_tgs_single_tumor = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_single_tumor",
is_tumour=True,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_tgs_single,
sample=sample_case_tgs_single_tumor)
# Create ERROR case for TGS NORMAL ONLY
case_tgs_single_error = helpers.add_case(
status_db,
internal_id="balsamic_case_tgs_single_error",
name="balsamic_case_tgs_single_error",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_tgs_single_normal_error = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_single_normal_error",
is_tumour=False,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_tgs_single_error,
sample=sample_case_tgs_single_normal_error,
)
# Create ERROR case for TGS TWO TUMOR ONE NORMAL
case_tgs_paired_error = helpers.add_case(
status_db,
internal_id="balsamic_case_tgs_paired_error",
name="balsamic_case_tgs_paired_error",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_tgs_paired_tumor_error = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_paired_tumor_error",
is_tumour=True,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
sample_case_tgs_paired_tumor2_error = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_paired_tumor2_error",
is_tumour=True,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
sample_case_tgs_paired_normal_error = helpers.add_sample(
status_db,
internal_id="sample_case_tgs_paired_normal_error",
is_tumour=False,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_tgs_paired_error,
sample=sample_case_tgs_paired_tumor_error,
)
helpers.add_relationship(
status_db,
case=case_tgs_paired_error,
sample=sample_case_tgs_paired_tumor2_error,
)
helpers.add_relationship(
status_db,
case=case_tgs_paired_error,
sample=sample_case_tgs_paired_normal_error,
)
# Create ERROR case for MIXED application type
case_mixed_paired_error = helpers.add_case(
status_db,
internal_id="balsamic_case_mixed_paired_error",
name="balsamic_case_mixed_paired_error",
data_analysis=Pipeline.BALSAMIC,
)
mixed_sample_case_wgs_paired_tumor_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_wgs_paired_tumor_error",
is_tumour=True,
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
mixed_sample_case_tgs_paired_normal_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_tgs_paired_normal_error",
is_tumour=False,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_mixed_paired_error,
sample=mixed_sample_case_wgs_paired_tumor_error,
)
helpers.add_relationship(
status_db,
case=case_mixed_paired_error,
sample=mixed_sample_case_tgs_paired_normal_error,
)
# Create ERROR case for MIXED application type NOT BALSAMIC APPLICATION
case_mixed_wgs_mic_paired_error = helpers.add_case(
status_db,
internal_id="balsamic_case_mixed_wgs_mic_paired_error",
name="balsamic_case_mixed_wgs_mic_paired_error",
data_analysis=Pipeline.BALSAMIC,
)
mixed_sample_case_wgs_mic_paired_tumor_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_wgs_mic_paired_tumor_error",
is_tumour=True,
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
mixed_sample_case_wgs_mic_paired_normal_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_wgs_mic_paired_normal_error",
is_tumour=False,
application_tag="MICA",
application_type="mic",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_mixed_wgs_mic_paired_error,
sample=mixed_sample_case_wgs_mic_paired_tumor_error,
)
helpers.add_relationship(
status_db,
case=case_mixed_wgs_mic_paired_error,
sample=mixed_sample_case_wgs_mic_paired_normal_error,
)
# Create ERROR case for MIXED TARGET BED
case_mixed_bed_paired_error = helpers.add_case(
status_db,
internal_id="balsamic_case_mixed_bed_paired_error",
name="balsamic_case_mixed_bed_paired_error",
data_analysis=Pipeline.BALSAMIC,
)
mixed_sample_case_mixed_bed_paired_tumor_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_mixed_bed_paired_tumor_error",
is_tumour=True,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
mixed_sample_case_mixed_bed_paired_normal_error = helpers.add_sample(
status_db,
internal_id="mixed_sample_case_mixed_bed_paired_normal_error",
is_tumour=False,
application_tag="TGSA",
application_type="tgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_mixed_bed_paired_error,
sample=mixed_sample_case_mixed_bed_paired_tumor_error,
)
helpers.add_relationship(
status_db,
case=case_mixed_bed_paired_error,
sample=mixed_sample_case_mixed_bed_paired_normal_error,
)
# Create ERROR case for WGS TUMOR ONLY MIP CLI_OPTION_ANALYSIS ONLY
mip_case_wgs_single = helpers.add_case(
status_db,
internal_id="mip_case_wgs_single",
name="mip_case_wgs_single",
data_analysis=Pipeline.MIP_DNA,
)
mip_sample_case_wgs_single_tumor = helpers.add_sample(
status_db,
internal_id="mip_sample_case_wgs_single_tumor",
is_tumour=True,
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=mip_case_wgs_single,
sample=mip_sample_case_wgs_single_tumor,
)
# Create ERROR case for WGS ONE TUMOR TWO NORMAL
case_wgs_paired_two_normal_error = helpers.add_case(
status_db,
internal_id="balsamic_case_wgs_paired_two_normal_error",
name="balsamic_case_wgs_paired_two_normal_error",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wgs_paired_two_normal_tumor_error = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_two_normal_tumor_error",
is_tumour=True,
application_tag="WGSA",
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
sample_case_wgs_paired_two_normal_normal1_error = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_two_normal_normal1_error",
is_tumour=False,
application_tag="WGSA",
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
sample_case_wgs_paired_two_normal_normal2_error = helpers.add_sample(
status_db,
internal_id="sample_case_wgs_paired_two_normal_normal2_error",
is_tumour=False,
application_tag="WGSA",
application_type="wgs",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(
status_db,
case=case_wgs_paired_two_normal_error,
sample=sample_case_wgs_paired_two_normal_tumor_error,
)
helpers.add_relationship(
status_db,
case=case_wgs_paired_two_normal_error,
sample=sample_case_wgs_paired_two_normal_normal1_error,
)
helpers.add_relationship(
status_db,
case=case_wgs_paired_two_normal_error,
sample=sample_case_wgs_paired_two_normal_normal2_error,
)
# Create WES case with 1 tumor sample
case_wes_tumor = helpers.add_case(
status_db,
internal_id="balsamic_case_wes_tumor",
name="balsamic_case_wes_tumor",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wes_tumor = helpers.add_sample(
status_db,
internal_id="sample_case_wes_tumor",
is_tumour=True,
application_tag="WESA",
application_type="wes",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_wes_tumor,
sample=sample_case_wes_tumor)
# Create ERROR case for WES when no panel is found
case_wes_panel_error = helpers.add_case(
status_db,
internal_id="balsamic_case_wes_panel_error",
name="balsamic_case_wes_panel_error",
data_analysis=Pipeline.BALSAMIC,
)
sample_case_wes_panel_error = helpers.add_sample(
status_db,
internal_id="sample_case_wes_panel_error",
is_tumour=True,
application_tag="WESA",
application_type="wes",
sequenced_at=dt.datetime.now(),
)
helpers.add_relationship(status_db,
case=case_wes_panel_error,
sample=sample_case_wes_panel_error)
# Create ERROR case with NO SAMPLES
helpers.add_case(status_db,
internal_id="no_sample_case",
name="no_sample_case")
# Create BED1 version 1
bed1_name = "BalsamicBed1"
bed1_filename = "balsamic_bed_1.bed"
Path(cg_dir, bed1_filename).touch(exist_ok=True)
bed1 = status_db.add_bed(name=bed1_name)
status_db.add_commit(bed1)
version1 = status_db.add_bed_version(bed=bed1,
version=1,
filename=bed1_filename,
shortname=bed1_name)
status_db.add_commit(version1)
# Create BED2 version 1
bed2_name = "BalsamicBed2"
bed2_filename = "balsamic_bed_2.bed"
Path(cg_dir, bed2_filename).touch(exist_ok=True)
bed2 = status_db.add_bed(name=bed2_name)
status_db.add_commit(bed2)
version2 = status_db.add_bed_version(bed=bed2,
version=1,
filename=bed2_filename,
shortname=bed2_name)
status_db.add_commit(version2)
return cg_context
def base_context(cg_context: CGConfig) -> CGConfig:
"""context to use in cli"""
cg_context.lims_api_ = MockLims()
return cg_context
def base_context(cg_context: CGConfig, helpers: StoreHelpers, lims_api):
"""The click context for the microsalt cli"""
helpers.add_microbial_sample(cg_context.status_db)
cg_context.lims_api_ = lims_api
cg_context.meta_apis["analysis_api"] = MicrosaltAnalysisAPI(cg_context)
return cg_context
def fixture_sample_sheet_context(cg_context: CGConfig,
lims_api: LimsAPI) -> CGConfig:
cg_context.lims_api_ = lims_api
return cg_context