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Merged
merged 20 commits into from
Apr 14, 2015
Merged

List proc data in search #1039

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28e6f57
return proc data info as part of json and start rendering it
squirrelo Apr 2, 2015
59286a7
Merge branch 'cart-analysis-changes', remote-tracking branch 'origin'…
squirrelo Apr 4, 2015
9227ee3
show proc data for each study properly
squirrelo Apr 6, 2015
6f08836
update tests with proc_data_info
squirrelo Apr 6, 2015
7b386c3
Merge branch 'cart-branch' of https://github.com/biocore/qiita into l…
squirrelo Apr 7, 2015
545a213
refactor building datatable
squirrelo Apr 9, 2015
07c9da2
Merge branch 'master' of https://github.com/biocore/qiita into list-p…
squirrelo Apr 9, 2015
350b864
more client-side rendering
squirrelo Apr 9, 2015
7e8c447
update tests
squirrelo Apr 9, 2015
7eedf17
flake8
squirrelo Apr 9, 2015
48c6760
Merge branch 'cart-branch' of https://github.com/biocore/qiita into l…
squirrelo Apr 9, 2015
dba9942
fix data retrieval for rendering
squirrelo Apr 9, 2015
917c003
break up functions and add tests
squirrelo Apr 9, 2015
10b0c5c
rename and add docstrings
squirrelo Apr 12, 2015
3fe2af9
clean up tests
squirrelo Apr 13, 2015
c16b429
implement suggestions
squirrelo Apr 13, 2015
ccd7d4a
flake8
squirrelo Apr 13, 2015
179b582
more changes for suggestions
squirrelo Apr 13, 2015
b6c0f44
fix building study info to match search results
squirrelo Apr 14, 2015
fbcd86c
update tests
squirrelo Apr 14, 2015
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implement suggestions
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@squirrelo
squirrelo committed Apr 13, 2015
commit c16b4294ad7f1bcf09c11dc337304d990d6ce927
12 changes: 6 additions & 6 deletions qiita_pet/handlers/study_handlers/listing_handlers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def _get_shared_links_for_study(study):
return ", ".join(shared)


def _build_single_study_info(study, info):
def _build_single_study_info(study, info, study_proc, proc_samples):
"""Clean up and add to the study info for HTML purposes

Parameters
Expand Down Expand Up @@ -75,6 +75,9 @@ def _build_single_study_info(study, info):
info["pi"] = study_person_linkifier((PI.email, PI.name))
del info["principal_investigator_id"]
del info["email"]
# Build the proc data info list for the child row in datatable
info["proc_data_info"] = _build_single_proc_data_info(
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Thanks for moving this here!

study, study_proc, proc_samples)
return info


Expand Down Expand Up @@ -174,11 +177,8 @@ def _build_study_info(user, study_proc=None, proc_samples=None):
for pid in proc_data:
proc_samples[pid] = ProcessedData(pid).samples

study_info = _build_single_study_info(study, info)
# Build the proc data info list for the child row in datatable
study_info["proc_data_info"] = _build_single_proc_data_info(
study, study_proc, proc_samples)

study_info = _build_single_study_info(study, info, study_proc,
proc_samples)
infolist.append(study_info)
return infolist

Expand Down
66 changes: 9 additions & 57 deletions qiita_pet/test/test_study_handlers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,34 +15,6 @@ class TestHelpers(TestHandlerBase):
database = True

def setUp(self):
self.single_exp = {
'study_id': 1,
'status': 'private',
'study_abstract':
'This is a preliminary study to examine the microbiota '
'associated with the Cannabis plant. Soils samples '
'from the bulk soil, soil associated with the roots, '
'and the rhizosphere were extracted and the DNA '
'sequenced. Roots from three independent plants of '
'different strains were examined. These roots were '
'obtained November 11, 2011 from plants that had been '
'harvested in the summer. Future studies will attempt '
'to analyze the soils and rhizospheres from the same '
'location at different time points in the plant '
'lifecycle.',
'metadata_complete': True,
'study_title':
'Identification of the Microbiomes for Cannabis Soils',
'num_raw_data': 4,
'number_samples_collected': 27,
'shared':
'<a target="_blank" href="mailto:shared@foo.bar">Shared</a>',
'pmid': '<a target="_blank" href="http://www.ncbi.nlm.nih.gov/'
'pubmed/123456">123456</a>, <a target="_blank" href="http:'
'//www.ncbi.nlm.nih.gov/pubmed/7891011">7891011</a>',
'pi': '<a target="_blank" href="mailto:PI_dude@foo.bar">'
'PIDude</a>'
}
self.proc_data_exp = [{
'pid': 1,
'processed_date': '2012-10-01 09:30:27',
Expand All @@ -66,9 +38,9 @@ def setUp(self):
'1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192']
}]
self.exp = [{
self.single_exp = {
'study_id': 1,
'status': 'public',
'status': 'private',
'study_abstract':
'This is a preliminary study to examine the microbiota '
'associated with the Cannabis plant. Soils samples '
Expand All @@ -93,30 +65,9 @@ def setUp(self):
'//www.ncbi.nlm.nih.gov/pubmed/7891011">7891011</a>',
'pi': '<a target="_blank" href="mailto:PI_dude@foo.bar">'
'PIDude</a>',
'proc_data_info': [{
'pid': 1,
'processed_date': '2012-10-01 09:30:27',
'data_type': '18S',
'algorithm': 'uclust',
'reference_name': 'Greengenes',
'reference_version': '13_8',
'taxonomy_filepath': 'GreenGenes_13_8_97_otu_taxonomy.txt',
'sequence_filepath': 'GreenGenes_13_8_97_otus.fasta',
'tree_filepath': 'GreenGenes_13_8_97_otus.tree',
'similarity': 0.97,
'enable_rev_strand_match': True,
'suppress_new_clusters': True,
'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']
}]
}]
'proc_data_info': self.proc_data_exp
}
self.exp = [self.single_exp]
super(TestHelpers, self).setUp()

def test_get_shared_links_for_study(self):
Expand All @@ -125,6 +76,8 @@ def test_get_shared_links_for_study(self):
self.assertEqual(obs, exp)

def test_build_single_study_info(self):
study_proc = {1: [1]}
proc_samples = {1: self.proc_data_exp[0]['samples']}
study_info = {
'study_id': 1,
'email': 'test@foo.bar',
Expand All @@ -147,7 +100,8 @@ def test_build_single_study_info(self):
'location at different time points in the plant '
'lifecycle.'
}
obs = _build_single_study_info(Study(1), study_info)
obs = _build_single_study_info(Study(1), study_info, study_proc,
proc_samples)
self.assertEqual(obs, self.single_exp)

def test_build_single_proc_data_info(self):
Expand All @@ -157,12 +111,10 @@ def test_build_single_proc_data_info(self):
self.assertEqual(obs, self.proc_data_exp)

def test_build_study_info(self):
ProcessedData(1).status = 'public'
obs = _build_study_info(User('test@foo.bar'))
self.assertEqual(obs, self.exp)

def test_build_study_info_new_study(self):
ProcessedData(1).status = 'public'
info = {
'timeseries_type_id': 1,
'portal_type_id': 1,
Expand Down