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Merged
merged 3 commits into from
Apr 4, 2017
Merged

Changing how artifact visibility works #2098

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3ff8a15
changing how artifact visibility works
antgonza Apr 3, 2017
88c1358
fixing code
antgonza Apr 3, 2017
17e8db1
fix errors
antgonza Apr 3, 2017
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30 changes: 17 additions & 13 deletions qiita_db/artifact.py
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Expand Up @@ -260,9 +260,11 @@ def create(cls, filepaths, artifact_type, name=None, prep_template=None,

Notes
-----
The visibility of the artifact is set by default to `sandbox`
The timestamp of the artifact is set by default to `datetime.now()`
The value of `submitted_to_vamps` is set by default to `False`
The visibility of the artifact is set by default to `sandbox` if
prep_template is passed but if parents is passed we will inherit the
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is passed but -> is passed and if?

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I think I also understand this as well.

most closed visibility.
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most closed -> closest?

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I understand now, what you mean here.

The timestamp of the artifact is set by default to `datetime.now()`.
The value of `submitted_to_vamps` is set by default to `False`.
"""
# We need at least one file
if not filepaths:
Expand Down Expand Up @@ -617,19 +619,21 @@ def visibility(self, value):
only applies when the new visibility is more open than before.
"""
with qdb.sql_connection.TRN:
# In order to correctly propagate the visibility we need to find
# the root of this artifact and then propagate to all the artifacts
sql = "SELECT * FROM qiita.find_artifact_roots(%s)"
qdb.sql_connection.TRN.add(sql, [self.id])
root_id = qdb.sql_connection.TRN.execute_fetchlast()
root = qdb.artifact.Artifact(root_id)
# these are the ids of all the children from the root
ids = [a.id for a in root.descendants.nodes()]

sql = """UPDATE qiita.artifact
SET visibility_id = %s
WHERE artifact_id = %s"""
qdb.sql_connection.TRN.add(
sql, [qdb.util.convert_to_id(value, "visibility"), self.id])
WHERE artifact_id IN %s"""
vis_id = qdb.util.convert_to_id(value, "visibility")
qdb.sql_connection.TRN.add(sql, [vis_id, tuple(ids)])
qdb.sql_connection.TRN.execute()
# In order to correctly propagate the visibility upstream, we need
# to go one step at a time. By setting up the visibility of our
# parents first, we accomplish that, since they will propagate
# the changes to its parents
for p in self.parents:
visibilites = [[d.visibility] for d in p.descendants.nodes()]
p.visibility = qdb.util.infer_status(visibilites)

@property
def artifact_type(self):
Expand Down
5 changes: 5 additions & 0 deletions qiita_db/support_files/patches/53.sql
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@@ -0,0 +1,5 @@
-- Apr 1, 2017
-- setting visibility of all artifacts to be the most open of the full
-- processing tree

SELECT 42;
19 changes: 19 additions & 0 deletions qiita_db/support_files/patches/python_patches/53.py
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@@ -0,0 +1,19 @@
from qiita_db.study import Study

studies = Study.get_by_status('private').union(
Study.get_by_status('public')).union(Study.get_by_status('sandbox'))
raw_data = [pt.artifact for s in studies for pt in s.prep_templates()]

for rd in raw_data:
# getting the most open visibility of all the children in the pipeline
children = rd.descendants.nodes()
vis = [a.visibility for a in children]
vis.append(rd.visibility)

new_vis = 'sandbox'
if 'public' in vis:
new_vis = 'public'
elif 'private' in vis:
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are there situations where an artifact was bumped to private but where the user expects all other artifacts to remain sandboxed?

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in praxis no ... at least based on what we have seen so far ...

new_vis = 'private'

rd.visibility = new_vis
17 changes: 8 additions & 9 deletions qiita_db/test/test_artifact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -966,8 +966,8 @@ def test_visibility_setter(self):
# /- 2 (private) -|- 5 (private)
# 1 (private) -| \- 6 (private)
# \- 3 (private)
# By changing the visibility of 4 to public, the visibility of 1 and
# 2 also changes to public
# By changing the visibility of 4 to public, the visibility of all
# should change
a1 = qdb.artifact.Artifact(1)
a2 = qdb.artifact.Artifact(2)
a3 = qdb.artifact.Artifact(3)
Expand All @@ -979,17 +979,16 @@ def test_visibility_setter(self):

self.assertEqual(a1.visibility, "public")
self.assertEqual(a2.visibility, "public")
self.assertEqual(a3.visibility, "private")
self.assertEqual(a3.visibility, "public")
self.assertEqual(a4.visibility, "public")
self.assertEqual(a5.visibility, "private")
self.assertEqual(a6.visibility, "private")
self.assertEqual(a5.visibility, "public")
self.assertEqual(a6.visibility, "public")

# However, if we change it back to private,
# it should remain public
# Same if we go back
a4.visibility = 'private'

self.assertEqual(a1.visibility, "public")
self.assertEqual(a2.visibility, "public")
self.assertEqual(a1.visibility, "private")
self.assertEqual(a2.visibility, "private")
self.assertEqual(a3.visibility, "private")
self.assertEqual(a4.visibility, "private")
self.assertEqual(a5.visibility, "private")
Expand Down
188 changes: 109 additions & 79 deletions qiita_db/test/test_util.py
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Expand Up @@ -968,89 +968,119 @@ def test_generate_study_list(self):

qdb.artifact.Artifact(4).visibility = 'public'
exp_info[0]['status'] = 'public'
exp_info[0]['proc_data_info'] = [{
'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)',
'pid': 4,
'processed_date': '2012-10-02 17:30:00',
'params': {
'similarity': 0.97,
'reference_name': 'Greengenes',
'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000,
'threads': 1,
'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}]
exp_info[0]['proc_data_info'] = [
{'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 4,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, u'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
{'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 5,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, 'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
{'data_type': '16S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 6,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Silva',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, 'sortmerna_coverage': 0.97,
'reference_version': 'test'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}]
obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True,
public_only=True)
self.assertEqual(obs_info, exp_info)

exp_info[0]['proc_data_info'].extend(
[{
'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)',
'pid': 5,
'processed_date': '2012-10-02 17:30:00',
'params': {
'similarity': 0.97,
'reference_name': 'Greengenes',
'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000,
'threads': 1,
'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}, {
'data_type': '16S',
'algorithm': 'QIIME (Pick closed-reference OTUs)',
'pid': 6,
'processed_date': '2012-10-02 17:30:00',
'params': {
'similarity': 0.97,
'reference_name': 'Silva',
'sortmerna_e_value': 1,
'sortmerna_max_pos': 10000,
'threads': 1,
'sortmerna_coverage': 0.97,
'reference_version': 'test'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']}, {
'processed_date': '2012-10-02 17:30:00',
'pid': 7,
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'],
'data_type': '16S'}])

exp_info[0]['proc_data_info'] = [
{'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 4,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, 'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
{'data_type': '18S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 5,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Greengenes',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, 'sortmerna_coverage': 0.97,
'reference_version': '13_8'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
{'data_type': '16S',
'algorithm': 'QIIME (Pick closed-reference OTUs)', 'pid': 6,
'processed_date': '2012-10-02 17:30:00',
'params': {'similarity': 0.97, 'reference_name': 'Silva',
'sortmerna_e_value': 1, u'sortmerna_max_pos': 10000,
'threads': 1, 'sortmerna_coverage': 0.97,
'reference_version': 'test'},
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']},
{'processed_date': '2012-10-02 17:30:00', 'pid': 7,
'samples': ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195',
'1.SKB4.640189', '1.SKB5.640181', '1.SKB6.640176',
'1.SKB7.640196', '1.SKB8.640193', '1.SKB9.640200',
'1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190',
'1.SKD7.640191', '1.SKD8.640184', '1.SKD9.640182',
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197',
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'],
'data_type': '16S'}]
obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True)
self.assertEqual(obs_info, exp_info)

Expand Down
21 changes: 9 additions & 12 deletions qiita_pet/handlers/api_proxy/tests/test_artifact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@ def test_artifact_summary_get_request(self):
'files': exp_files,
'errored_jobs': [],
'editable': True,
'visibility': 'private',
'visibility': 'sandbox',
'job': None,
'message': '',
'name': 'Demultiplexed 1',
Expand All @@ -316,17 +316,14 @@ def test_artifact_summary_get_request(self):
'min_per_read_length_fraction': 0.75,
'barcode_type': u'golay_12'},
'summary': None,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'buttons': (
'<button onclick="if (confirm(\'Are you sure you want to '
'request approval for artifact id: 2?\')) { '
'set_artifact_visibility(\'awaiting_approval\', 2) }" '
'class="btn btn-primary btn-sm">Request approval</button> '
'<a class="btn btn-primary btn-sm" href="/vamps/2"><span '
'class="glyphicon glyphicon-export"></span> Submit to '
'VAMPS</a>'),
'study_id': 1,
'prep_id': 1}
self.assertEqual(obs, exp)
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/handlers/api_proxy/tests/test_prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -332,7 +332,7 @@ def test_prep_template_graph_get_req(self):
obs = prep_template_graph_get_req(1, 'demo@microbio.me')
self.assertEqual(obs['message'], '')
self.assertEqual(obs['status'], 'success')
self.assertEqual(8, len(obs['node_labels']))
self.assertEqual(11, len(obs['node_labels']))
self.assertIn(('artifact', 1, 'Raw data 1 - FASTQ'),
obs['node_labels'])
self.assertIn(('artifact', 2, 'Demultiplexed 1 - Demultiplexed'),
Expand Down