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Merge 78597c4 into 748287c
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@sbreiff
sbreiff committed May 8, 2019
2 parents 748287c + 78597c4 commit c3a1794
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Showing 2 changed files with 44 additions and 101 deletions.
18 changes: 17 additions & 1 deletion chalicelib/check_setup.json
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Original file line number Diff line number Diff line change
Expand Up @@ -181,6 +181,14 @@
"hotseat": {
"kwargs": {"primary": true},
"dependencies": []
},
"staging": {
"kwargs": {"primary": true},
"dependencies": []
},
"data": {
"kwargs": {"primary": true},
"dependencies": []
}
}
}
Expand All @@ -192,7 +200,15 @@
"morning_checks": {
"hotseat": {
"kwargs": {"primary": true},
"dependencies": []
"dependencies": ["yellow_flag_biosamples"]
},
"staging": {
"kwargs": {"primary": true},
"dependencies": ["yellow_flag_biosamples"]
},
"data": {
"kwargs": {"primary": true},
"dependencies": ["yellow_flag_biosamples"]
}
}
}
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127 changes: 27 additions & 100 deletions chalicelib/checks/badge_checks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,6 +155,16 @@ def patch_badges(full_output, badge_name, ffenv, single_message=''):

@check_function()
def yellow_flag_biosamples(connection, **kwargs):
'''
Checks biosamples for required metadata:
1. Culture harvest date, doubling number, passage number, culture duration
2. Morphology image
3. Karyotyping (authentication doc or string field) for any biosample derived
from pluripotent cell line that has been passaged more than 10 times beyond
the first thaw of the original vial.
4. Differentiation authentication for differentiated cells.
5. HAP-1 biosamples must have ploidy authentication.
'''
check = init_check_res(connection, 'yellow_flag_biosamples')

results = ff_utils.search_metadata('search/?type=Biosample', ff_env=connection.ff_env)
Expand Down Expand Up @@ -184,8 +194,12 @@ def yellow_flag_biosamples(connection, **kwargs):
diff_auth = True
elif auth_type == 'Ploidy Authentication':
ploidy = True
if 'tem cell' in ''.join(bs_types) and bcc.get('passage_number', 0) > 10 and not karyotype:
messages.append('Biosample is a stem cell line over 10 passages but missing karyotype')
passages = bcc.get('passage_number', 0)
if 'tem cell' in ''.join(bs_types) and not karyotype:
if passages > 10:
messages.append('Biosample is a stem cell line over 10 passages but missing karyotype')
elif not passages:
messages.append('Biosample is a stem cell line with unknown passage number missing karyotype')
if result.get('biosample_type') == 'In vitro differentiated cells' and not diff_auth:
messages.append('Differentiated biosample missing differentiation authentication')
if 'HAP-1' in result.get('biosource_summary') and not ploidy:
Expand Down Expand Up @@ -218,7 +232,6 @@ def yellow_flag_biosamples(connection, **kwargs):
'Keep badge and edit messages': to_edit,
'Keep badge (no change)': ok}
check.brief_output[RELEASED_KEY] = {
#'Add badge': list(to_add.keys()),
'Add badge': ['{} missing {}'.format(
k, ', '.join([item[item.index('missing') + 8:] for item in flagged[k]])
) for k in to_add.keys()],
Expand Down Expand Up @@ -252,22 +265,9 @@ def gold_biosamples(connection, **kwargs):
'''
Gold level commendation criteria:
1. Tier 1 or Tier 2 Cells obtained from the approved 4DN source and grown
precisely according to the approved SOP as specified including any additional
authentication eg. HAP-1 haploid line requires a FACs plot demonstrating less
than 5% diploid cells.
2. Culture start and harvest dates
3. Passage number
4. Total Days in Culture
5. Doubling number
6. Karyotyping is required for gold commendation for any biosample derived from
a 4DN pluripotent cell line that have been passaged more than 10 times beyond
the first thaw of the original vial. Karyotype reports obtained in house or
by a service should be submitted as authentication. However, for some genomics
experiments karyotype information can be derived from sequencing data and a
description of the derived karyotype can be submitted.
7. For differentiated cells that are derived from any tiered cell lines
1) the 4DN SOP must be precisely followed and
2) authentication as specified in the SOP must be submitted (links to SOPs).
precisely according to the approved SOP including any additional
authentication (eg. HAP-1 haploid line requires ploidy authentication).
2. All required metadata present (does not have a biosample warning badge).
'''
check = init_check_res(connection, 'gold_biosamples')

Expand All @@ -276,18 +276,21 @@ def gold_biosamples(connection, **kwargs):
results = ff_utils.search_metadata(search_url, ff_env=connection.ff_env)
gold = []
for result in results:
# follows SOP w/ no deviations
# follows SOP w/ no deviations
sop = True if all([bcc.get('follows_sop', '') == 'Yes' for bcc in result.get('cell_culture_details', [])]) else False
if sop and result.get('status') not in REV:
gold.append(result['@id'])
# correct source
to_add, to_remove, ok = compare_badges(gold, 'Biosample', 'gold-biosample', connection.ff_env)
check.action = 'patch_gold_biosample_badges'
if to_add or to_remove:
check.status = 'WARN'
check.allow_action = True
check.summary = 'Gold biosample badges need patching'
check.description = '{} biosamples need gold badges patched'.format(len(to_add) + len(to_remove.keys()))
check.description = '{} biosamples need gold badges patched. '.format(len(to_add) + len(to_remove.keys()))
check.description += 'Yellow_flag_biosamples check must pass before patching.'
yellow_check = init_check_res(connection, 'yellow_flag_biosamples')
latest_yellow = yellow_check.get_latest_result()
if latest_yellow['status'] == 'PASS':
check.allow_action = True
else:
check.status = 'PASS'
check.summary = 'Gold biosample badges up-to-date'
Expand Down Expand Up @@ -381,6 +384,7 @@ def repsets_have_bio_reps(connection, **kwargs):
check.description = '{} replicate experiment sets need replicate badges patched'.format(
len(to_add.values()) + len(to_remove.values()) + len(to_edit.values())
)
check.allow_action = True
else:
check.status = 'PASS'
check.summary = 'Replicate number badges up-to-date'
Expand All @@ -401,8 +405,6 @@ def repsets_have_bio_reps(connection, **kwargs):
check.brief_output[RELEASED_KEY][key][k].append(item)
if name in check.full_output['Keep badge (no change)']:
check.brief_output[RELEASED_KEY]['Keep badge (no change)'][k].append(item)
if to_add or to_remove or to_edit:
check.allow_action = True
return check


Expand All @@ -421,81 +423,6 @@ def patch_badges_for_replicate_numbers(connection, **kwargs):
return action


@check_function()
def tier1_metadata_present(connection, **kwargs):
'''
Check for Tier 1 Biosample badges that are missing one or more of the following
pieces of required metadata:
1) culture_start_date
2) culture_harvest_date
3) culture_duration
4) morphology_image
5) a linked cell_culture_details item
Action patches badges with a message detailing which of the above pieces of
metadata is missing.
'''
check = init_check_res(connection, 'tier1_metadata_present')

results = ff_utils.search_metadata('search/?biosource.cell_line_tier=Tier+1&type=Biosample',
ff_env=connection.ff_env)
missing = {REV_KEY: {}, RELEASED_KEY: {}}
msg_dict = {'culture_start_date': 'Tier 1 Biosample missing Culture Start Date',
# item will fail validation if missing a start date - remove this part of check?
'culture_duration': 'Tier 1 Biosample missing Culture Duration',
'morphology_image': 'Tier 1 Biosample missing Morphology Image'}
for result in results:
if len(result.get('biosource')) != 1:
continue
elif not result.get('cell_culture_details'):
missing[result['@id']] = 'Tier 1 Biosample missing Cell Culture Details'
else:
messages = [val for key, val in msg_dict.items() if not result['cell_culture_details'].get(key)]
if messages:
if result.get('status') in REV:
missing[REV_KEY][result['@id']] = '; '.join(messages)
else:
missing[RELEASED_KEY][result['@id']] = '; '.join(messages)

to_add, to_remove, to_edit, ok = compare_badges_and_messages(
missing[RELEASED_KEY], 'Biosample', 'tier1-metadata-missing', connection.ff_env
)
check.action = 'patch_badges_for_tier1_metadata'
if to_add or to_remove or to_edit:
check.status = 'WARN'
check.summary = 'Tier 1 metadata badges need patching'
check.description = '{} tier 1 biosamples need metadata_missing badges patched'.format(
len(to_add.values()) + len(to_remove.values()) + len(to_edit.values())
)
else:
check.status = 'PASS'
check.summary = 'Tier 1 metadata badges up-to-date'
check.description = 'No tier 1 biosamples need metadata_missing badges patched'
check.full_output = {'Add badge': to_add,
'Keep badge (no change)': ok,
'Remove badge': to_remove,
'Keep badge and edit messages': to_edit}
check.brief_output = missing
# if to_add or to_remove or to_edit:
# check.allow_action = True
return check


@action_function()
def patch_badges_for_tier1_metadata(connection, **kwargs):
action = init_action_res(connection, 'patch_badges_for_tier1_metadata')
tier1_check_result = action.get_associated_check_result(kwargs)

action.output = patch_badges(tier1_check_result['full_output'], 'tier1-metadata-missing', connection.ff_env)
if [action.output[key] for key in list(action.output.keys()) if 'failure' in key and action.output[key]]:
action.status = 'FAIL'
action.description = 'Some items failed to patch. See below for details.'
else:
action.status = 'DONE'
action.description = 'Patching badges successful for missing tier1 metadata.'
return action


@check_function()
def exp_has_raw_files(connection, **kwargs):
'''
Expand Down

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