def test_download(self):
# check success
response = self.get('/download/1')
self.assertEqual(response.code, 200)
self.assertEqual(response.body.decode('ascii'), (
"This installation of Qiita was not equipped with nginx, so it "
"is incapable of serving files. The file you attempted to "
"download is located at raw_data/1_s_G1_L001_sequences.fastq.gz"))
self.assertEqual(
response.headers['Content-Disposition'],
"attachment; filename=1_1_s_G1_L001_sequences.fastq.gz")
# other tests to validate the filename
response = self.get('/download/2')
self.assertEqual(
response.headers['Content-Disposition'],
"attachment; filename=1_1_s_G1_L001_sequences_barcodes.fastq.gz")
response = self.get('/download/3')
self.assertEqual(
response.headers['Content-Disposition'],
"attachment; filename=2_1_seqs.fna")
response = self.get('/download/18')
self.assertEqual(
response.headers['Content-Disposition'],
"attachment; filename=1_prep_1_19700101-000000.txt")
response = self.get('/download/22')
self.assertEqual(
response.headers['Content-Disposition'],
"attachment; filename=7_biom_table.biom")
# failure
response = self.get('/download/1000')
self.assertEqual(response.code, 403)
# directory
a = Artifact(1)
fd, fp = mkstemp(suffix='.html')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
dirpath = mkdtemp()
fd, fp2 = mkstemp(suffix='.txt', dir=dirpath)
close(fd)
with open(fp2, 'w') as f:
f.write('\n')
self._clean_up_files.append(dirpath)
a.set_html_summary(fp, support_dir=dirpath)
for x in a.filepaths:
if x['fp_type'] == 'html_summary_dir':
break
response = self.get('/download/%d' % x['fp_id'])
self.assertEqual(response.code, 200)
fp_name = basename(fp2)
dirname = basename(dirpath)
self.assertEqual(response.body.decode('ascii'),
"- 1 /protected/FASTQ/1/%s/%s FASTQ/1/%s/%s\n" % (
dirname, fp_name, dirname, fp_name))
def test_get_artifact_summary_handler(self):
a = Artifact(1)
# Add a summary to the artifact
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
summary = relpath(a.html_summary_fp[1], qiita_config.base_data_dir)
response = self.get('/artifact/html_summary/%s' % summary)
self.assertEqual(response.code, 200)
self.assertEqual(response.body, '<b>HTML TEST - not important</b>\n')
def test_download(self):
# check success
response = self.get('/download/1')
self.assertEqual(response.code, 200)
self.assertEqual(response.body, (
"This installation of Qiita was not equipped with nginx, so it "
"is incapable of serving files. The file you attempted to "
"download is located at raw_data/1_s_G1_L001_sequences.fastq.gz"))
# failure
response = self.get('/download/1000')
self.assertEqual(response.code, 403)
# directory
a = Artifact(1)
fd, fp = mkstemp(suffix='.html')
close(fd)
with open(fp, 'w') as f:
f.write('\n')
self._clean_up_files.append(fp)
dirpath = mkdtemp()
fd, fp2 = mkstemp(suffix='.txt', dir=dirpath)
close(fd)
with open(fp2, 'w') as f:
f.write('\n')
self._clean_up_files.append(dirpath)
a.set_html_summary(fp, support_dir=dirpath)
for fp_id, _, fp_type in a.filepaths:
if fp_type == 'html_summary_dir':
break
response = self.get('/download/%d' % fp_id)
self.assertEqual(response.code, 200)
fp_name = basename(fp2)
dirname = basename(dirpath)
self.assertEqual(
response.body, "- 1 /protected/FASTQ/1/%s/%s FASTQ/1/%s/%s\n"
% (dirname, fp_name, dirname, fp_name))
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
main_buttons = (
'<button onclick="if (confirm('
"\'Are you sure you want to make "
"public artifact id: 1?')) { set_artifact_visibility('public', 1) "
'}" class="btn btn-primary btn-sm">Make public</button> <button '
'onclick="if (confirm('
"'Are you sure you want to revert to "
"sandbox artifact id: 1?')) { set_artifact_visibility('sandbox', 1"
') }" class="btn btn-primary btn-sm">Revert to sandbox</button> ')
private_download_button = (
'<button class="btn btn-primary btn-sm" type="button" '
'aria-expanded="false" aria-controls="privateDownloadLink" '
'onclick="generate_private_download_link(%s)">Generate Download '
'Link</button><div class="collapse" id="privateDownloadLink"><div '
'class="card card-body" id="privateDownloadText">Generating '
'Download Link...</div></div>')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_files = [
(1, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)',
'2125826711', '58B'),
(2, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)',
'2125826711', '58B')
]
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'being_deleted': False,
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'being_deleted': False,
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': [job.id, 'queued', None],
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append((a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1]),
'1642196267', '33B'))
exp_summary_path = relpath(a.html_summary_fp[1],
qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'being_deleted': False,
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'being_deleted': False,
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_info': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# testing sandbox
a.visibility = 'sandbox'
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'being_deleted': False,
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'sandbox',
'editable': True,
'buttons': private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_files = [(3, '1_seqs.fna (preprocessed fasta)', '', '0B'),
(4, '1_seqs.qual (preprocessed fastq)', '', '0B'),
(5, '1_seqs.demux (preprocessed demux)', '', '0B')]
exp = {
'name':
'Demultiplexed 1',
'artifact_id':
2,
'artifact_type':
'Demultiplexed',
'being_deleted':
False,
'artifact_timestamp':
'2012-10-01 10:10',
'visibility':
'private',
'editable':
True,
'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="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a> ' +
private_download_button % 2),
'processing_info': {
'command_active': True,
'software_deprecated': False,
'command': 'Split libraries FASTQ',
'processing_parameters': {
'max_barcode_errors': '1.5',
'sequence_max_n': '0',
'max_bad_run_length': '3',
'phred_offset': 'auto',
'rev_comp': 'False',
'phred_quality_threshold': '3',
'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12'
},
'software_version': '1.9.1',
'software': 'QIIME'
},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# the buttons shouldn't be present when the study is autoloaded
study = a.study
study.autoloaded = True
exp['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> ' + private_download_button % 2)
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
self.assertEqual(obs, exp)
study.autoloaded = False
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {
'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
'being_deleted': False,
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': private_download_button % 8,
'processing_info': {},
'files': [(22, 'biom_table.biom (biom)', '1756512010', '1.0M')],
'is_from_analysis': True,
'summary': None,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1})
)
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': [job.id, 'queued', None],
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
exp_summary_path = relpath(
a.html_summary_fp[1], qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_info': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_files = [
(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {'name': 'Demultiplexed 1',
'artifact_id': 2,
'artifact_type': 'Demultiplexed',
'artifact_timestamp': '2012-10-01 10:10',
'visibility': 'private',
'editable': True,
'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="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_info': {
'command': 'Split libraries FASTQ',
'software': 'QIIME',
'software_version': '1.9.1',
'processing_parameters': {
'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'phred_offset': u'auto',
'rev_comp': 'False', 'phred_quality_threshold': '3',
'input_data': '1', 'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': u'golay_12'}},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': '',
'processing_info': {},
'files': [(27, 'biom_table.biom (biom)')],
'is_from_analysis': True,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_p_jobs = [[
'063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None
],
[
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'Split libraries', 'running', 'demultiplexing', None
]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')
]
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job': [job.id, 'queued', None],
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
exp_summary_path = relpath(a.html_summary_fp[1],
qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'artifact_type':
'FASTQ',
'artifact_timestamp':
'2012-10-01 09:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
exp_summary_path,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_parameters': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_p_jobs = [[
'd19f76ee-274e-4c1b-b3a2-a12d73507c55',
'Pick closed-reference OTUs', 'error', 'generating demux file',
'Error message'
]]
exp_files = [(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {
'name':
'Demultiplexed 1',
'artifact_id':
2,
'artifact_type':
'Demultiplexed',
'artifact_timestamp':
'2012-10-01 10:10',
'visibility':
'private',
'editable':
True,
'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="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_parameters': {
'max_barcode_errors': 1.5,
'sequence_max_n': 0,
'max_bad_run_length': 3,
'phred_offset': u'auto',
'rev_comp': False,
'phred_quality_threshold': 3,
'input_data': 1,
'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
'barcode_type': u'golay_12'
},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {
'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': '',
'processing_parameters': {},
'files': [(27, 'biom_table.biom (biom)')],
'is_from_analysis': True,
'summary': None,
'job': None,
'processing_jobs': [],
'errored_jobs': []
}
self.assertEqual(obs, exp)
