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Merged
merged 7 commits into from
Sep 12, 2018
Merged

Plugin outdate version #2664

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3d803d1
adding GUI changes for deprecated artifacts
antgonza Sep 10, 2018
500e340
fixing some tests
antgonza Sep 10, 2018
099e3f4
Merge branch 'dev' of https://github.com/biocore/qiita into plugin-ou…
antgonza Sep 11, 2018
3cb72ef
pull upstream dev
antgonza Sep 11, 2018
0d67fb2
addressing @ElDeveloper comments
antgonza Sep 12, 2018
bcd930e
fixing errors
antgonza Sep 12, 2018
61cc59d
fixing more errors
antgonza Sep 12, 2018
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2 changes: 2 additions & 0 deletions qiita_db/support_files/patches/python_patches/66.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@ def create_command(software, name, description, parameters, outputs=None,
sql_param_values = []
sql_artifact_params = []
for pname, vals in parameters.items():
# vals should always have 2 elements as it should be:
# param_name: [parameter_type, default]
if len(vals) != 2:
raise QiitaDBError(
"Malformed parameters dictionary, the format should be "
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17 changes: 9 additions & 8 deletions qiita_db/test/test_util.py
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Expand Up @@ -1062,23 +1062,24 @@ def test_get_artifacts_information(self):

exp = [
{'files': ['1_study_1001_closed_reference_otu_table.biom'],
'artifact_id': 4, 'data_type': '18S', 'target_gene': '16S rRNA',
'name': 'BIOM', 'target_subfragment': ['V4'],
'parameters': {
'artifact_id': 4, 'data_type': '18S', 'active': False,
'target_gene': '16S rRNA', 'name': 'BIOM',
'target_subfragment': ['V4'], 'parameters': {
'reference': '1', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'},
'algorithm': 'Pick closed-reference OTUs | Split libraries FASTQ',
'platform': 'Illumina',
'algorithm_az': 'd480799a0a7a2fbe0e9022bc9c602018',
'platform': 'Illumina', 'prep_samples': 27},
{'files': [], 'artifact_id': 7, 'data_type': '16S',
'prep_samples': 27},
{'files': [], 'artifact_id': 7, 'data_type': '16S', 'active': True,
'target_gene': '16S rRNA', 'name': 'BIOM',
'target_subfragment': ['V4'], 'parameters': {}, 'algorithm': '',
'algorithm_az': '', 'platform': 'Illumina', 'prep_samples': 27},
'platform': 'Illumina', 'algorithm_az': '', 'prep_samples': 27},
{'files': ['biom_table.biom'], 'artifact_id': 8,
'data_type': '18S', 'target_gene': 'not provided',
'data_type': '18S', 'active': True, 'target_gene': 'not provided',
'name': 'noname', 'target_subfragment': [], 'parameters': {},
'algorithm': '', 'algorithm_az': '', 'platform': 'not provided',
'algorithm': '', 'platform': 'not provided', 'algorithm_az': '',
'prep_samples': 0}]
self.assertItemsEqual(obs, exp)

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7 changes: 6 additions & 1 deletion qiita_db/util.py
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Expand Up @@ -1628,9 +1628,11 @@ def get_artifacts_information(artifact_ids, only_biom=True):
commands = {}
qdb.sql_connection.TRN.add(sql_params)
for cid, params in qdb.sql_connection.TRN.execute_fetchindex():
cmd = qdb.software.Command(cid)
commands[cid] = {
'params': params,
'merging_scheme': qdb.software.Command(cid).merging_scheme}
'merging_scheme': cmd.merging_scheme,
'active': cmd.software.active}

# now let's get the actual artifacts
ts = {}
Expand Down Expand Up @@ -1664,8 +1666,10 @@ def get_artifacts_information(artifact_ids, only_biom=True):

# generating algorithm, by default is ''
algorithm = ''
active = True
if cid is not None:
ms = commands[cid]['merging_scheme']
active = commands[cid]['active']
eparams = []
if ms['parameters']:
eparams.append(','.join(['%s: %s' % (k, aparams[k])
Expand Down Expand Up @@ -1733,6 +1737,7 @@ def get_artifacts_information(artifact_ids, only_biom=True):
'parameters': aparams,
'algorithm': algorithm,
'algorithm_az': algorithm_az[algorithm],
'active': active,
'files': filepaths})

return results
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4 changes: 2 additions & 2 deletions qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py
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Expand Up @@ -76,7 +76,7 @@ def test_analyisis_graph_handler_get_request(self):
exp = {'edges': [(8, job_id), (job_id, 9)],
'nodes': [
('job', 'job', job_id, 'Single Rarefaction', 'success'),
('artifact', 'BIOM', 9, 'noname\n(BIOM)', 'artifact'),
('artifact', 'BIOM', 9, 'noname\n(BIOM)', 'deprecated'),
('artifact', 'BIOM', 8, 'noname\n(BIOM)', 'artifact')],
'workflow': None}
self.assertItemsEqual(obs, exp)
Expand Down Expand Up @@ -160,7 +160,7 @@ def test_get_analysis_graph_handler(self):
exp = {'edges': [[8, job_id], [job_id, 9]],
'nodes': [
['job', 'job', job_id, 'Single Rarefaction', 'success'],
['artifact', 'BIOM', 9, 'noname\n(BIOM)', 'artifact'],
['artifact', 'BIOM', 9, 'noname\n(BIOM)', 'deprecated'],
['artifact', 'BIOM', 8, 'noname\n(BIOM)', 'artifact']],
'workflow': None}
self.assertItemsEqual(obs, exp)
Expand Down
32 changes: 16 additions & 16 deletions qiita_pet/handlers/api_proxy/tests/test_artifact.py
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Expand Up @@ -228,33 +228,33 @@ def test_artifact_get_info(self):
data = [
{'files': ['1_study_1001_closed_reference_otu_table_Silva.biom'],
'artifact_id': 6, 'data_type': '16S',
'timestamp': '2012-10-02 17:30:00', 'target_gene': '16S rRNA',
'name': 'BIOM', 'target_subfragment': ['V4'],
'parameters': {
'reference': '2', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'},
'timestamp': '2012-10-02 17:30:00', 'active': False,
'target_gene': '16S rRNA', 'name': 'BIOM',
'target_subfragment': ['V4'], 'parameters': {
'reference': '2', 'similarity': '0.97', 'sortmerna_e_value': '1',
'sortmerna_max_pos': '10000', 'threads': '1',
'sortmerna_coverage': '0.97'},
'algorithm': 'Pick closed-reference OTUs | Split libraries FASTQ',
'platform': 'Illumina',
'algorithm_az': 'd480799a0a7a2fbe0e9022bc9c602018',
'prep_samples': 27},
{'files': ['1_study_1001_closed_reference_otu_table.biom'],
'artifact_id': 5, 'data_type': '18S',
'timestamp': '2012-10-02 17:30:00', 'target_gene': '16S rRNA',
'name': 'BIOM', 'target_subfragment': ['V4'],
'parameters': {
'reference': '1', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'},
'timestamp': '2012-10-02 17:30:00', 'active': False,
'target_gene': '16S rRNA', 'name': 'BIOM',
'target_subfragment': ['V4'], 'parameters': {
'reference': '1', 'similarity': '0.97', 'sortmerna_e_value': '1',
'sortmerna_max_pos': '10000', 'threads': '1',
'sortmerna_coverage': '0.97'},
'algorithm': 'Pick closed-reference OTUs | Split libraries FASTQ',
'platform': 'not provided',
'algorithm_az': 'd480799a0a7a2fbe0e9022bc9c602018',
'prep_samples': 27},
{'files': [], 'artifact_id': 7, 'data_type': '16S',
'timestamp': '2012-10-02 17:30:00', 'target_gene': '16S rRNA',
'name': 'BIOM', 'target_subfragment': ['V4'], 'parameters': {},
'algorithm': '', 'platform': 'Illumina', 'algorithm_az': '',
'prep_samples': 27}]
'timestamp': '2012-10-02 17:30:00', 'active': True,
'target_gene': '16S rRNA', 'name': 'BIOM',
'target_subfragment': ['V4'], 'parameters': {}, 'algorithm': '',
'platform': 'Illumina', 'algorithm_az': '', 'prep_samples': 27}]
exp = {'status': 'success', 'msg': '', 'data': data}
self.assertItemsEqual(obs.keys(), exp.keys())
self.assertEqual(obs['status'], exp['status'])
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14 changes: 7 additions & 7 deletions qiita_pet/handlers/api_proxy/tests/test_prep_template.py
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Expand Up @@ -306,17 +306,17 @@ def test_prep_template_graph_get_req(self):
obs['nodes'])
self.assertIn(
('artifact', 'Demultiplexed', 2,
'Demultiplexed 1\n(Demultiplexed)', 'artifact'),
'Demultiplexed 1\n(Demultiplexed)', 'deprecated'),
obs['nodes'])
self.assertIn(
('artifact', 'Demultiplexed', 3,
'Demultiplexed 2\n(Demultiplexed)', 'artifact'),
'Demultiplexed 2\n(Demultiplexed)', 'deprecated'),
obs['nodes'])
self.assertIn(('artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'artifact'),
self.assertIn(('artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'deprecated'),
obs['nodes'])
self.assertIn(('artifact', 'BIOM', 5, 'BIOM\n(BIOM)', 'artifact'),
self.assertIn(('artifact', 'BIOM', 5, 'BIOM\n(BIOM)', 'deprecated'),
obs['nodes'])
self.assertIn(('artifact', 'BIOM', 6, 'BIOM\n(BIOM)', 'artifact'),
self.assertIn(('artifact', 'BIOM', 6, 'BIOM\n(BIOM)', 'deprecated'),
obs['nodes'])
self.assertEqual(3, len([n for dt, _, _, n, _ in obs['nodes']
if n == 'Pick closed-reference OTUs' and
Expand Down Expand Up @@ -346,9 +346,9 @@ def test_prep_template_graph_get_req(self):
obs['nodes'])
self.assertIn(
('artifact', 'Demultiplexed', 2,
'Demultiplexed 1\n(Demultiplexed)', 'artifact'),
'Demultiplexed 1\n(Demultiplexed)', 'deprecated'),
obs['nodes'])
self.assertIn(('artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'artifact'),
self.assertIn(('artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'deprecated'),
obs['nodes'])
self.assertEqual(3, len([n for dt, _, _, n, _ in obs['nodes']
if n == 'Pick closed-reference OTUs' and
Expand Down
3 changes: 2 additions & 1 deletion qiita_pet/handlers/artifact_handlers/base_handlers.py
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Expand Up @@ -196,7 +196,8 @@ def artifact_summary_get_request(user, artifact_id):
'command': cmd.name,
'software': sw.name,
'software_version': sw.version,
'processing_parameters': proc_params.values
'processing_parameters': proc_params.values,
'software_active': sw.active
}
else:
processing_info = {}
Expand Down
21 changes: 10 additions & 11 deletions qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py
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Expand Up @@ -227,17 +227,16 @@ def test_artifact_summary_get_request(self):
'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'}},
'software_active': 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,
Expand Down
12 changes: 6 additions & 6 deletions qiita_pet/handlers/study_handlers/tests/test_artifact.py
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Expand Up @@ -168,18 +168,18 @@ def test_post(self):
'data_type': '16S', 'timestamp': u'2012-10-02 17:30:00',
'platform': 'Illumina',
'algorithm_az': 'd480799a0a7a2fbe0e9022bc9c602018',
'prep_samples': 27,
'prep_samples': 27, 'active': False,
'algorithm': 'Pick closed-reference OTUs | Split libraries FASTQ',
'parameters': {
'reference': u'2', 'similarity': '0.97',
'sortmerna_e_value': '1', 'sortmerna_max_pos': '10000',
'threads': '1', 'sortmerna_coverage': '0.97'},
'reference': '2', 'similarity': '0.97', 'sortmerna_e_value': '1',
'sortmerna_max_pos': '10000', 'threads': '1',
'sortmerna_coverage': '0.97'},
'target_gene': '16S rRNA', 'name': 'BIOM'},
{'files': [], 'target_subfragment': ['V4'], 'artifact_id': 7,
'data_type': '16S', 'timestamp': '2012-10-02 17:30:00',
'platform': 'Illumina', 'algorithm_az': '', 'prep_samples': 27,
'algorithm': '', 'parameters': {}, 'target_gene': '16S rRNA',
'name': 'BIOM'}]
'active': True, 'algorithm': '', 'parameters': {},
'target_gene': '16S rRNA', u'name': u'BIOM'}]
exp = {'status': 'success', 'msg': '', 'data': data}
obs = loads(response.body)
self.assertItemsEqual(obs.keys(), exp.keys())
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25 changes: 14 additions & 11 deletions qiita_pet/static/js/networkVue.js
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Expand Up @@ -1067,15 +1067,17 @@ Vue.component('processing-graph', {
vm.countdownPoll = 15;
$('#countdown-span').html(vm.countdownPoll);
vm.colorScheme = {
'success': {border: '#00cc00', background: '#7FE57F', highlight: {border: '#00cc00', background: '#a5eda5'}},
'running': {border: '#b28500', background: '#ffbf00', highlight: {border: '#b28500', background: '#ffdc73'}},
'error': {border: '#ff3333', background: '#ff5b5b', highlight: {border: '#ff3333', background: '#ff8484'}},
'in_construction': {border: '#634a00', background: '#e59400', highlight: {border: '#634a00', background: '#efbe66'}},
'queued': {border: '#4f5b66', background: '#a7adba', highlight: {border: '#4f5b66', background: '#c0c5ce'}},
'waiting': {border: '#4f5b66', background: '#a7adba', highlight: {border: '#4f5b66', background: '#c0c5ce'}},
'artifact': {border: '#BBBBBB', background: '#FFFFFF', highlight: {border: '#999999', background: '#FFFFFF'}},
'type': {border: '#BBBBBB', background: '#CCCCCC', highlight: {border: '#999999', background: '#DDDDDD'}},
'deleting': {border: '#ff3333', background: '#ff6347', highlight: {border: '#ff3333', background: '#ff6347'}}};
'success': {border: '#00cc00', background: '#7FE57F', highlight: {border: '#00cc00', background: '#a5eda5'}, 'color': '#333333'},
'running': {border: '#b28500', background: '#ffbf00', highlight: {border: '#b28500', background: '#ffdc73'}, 'color': '#333333'},
'error': {border: '#ff3333', background: '#ff5b5b', highlight: {border: '#ff3333', background: '#ff8484'}, 'color': '#333333'},
'in_construction': {border: '#634a00', background: '#e59400', highlight: {border: '#634a00', background: '#efbe66'}, 'color': '#333333'},
'queued': {border: '#4f5b66', background: '#a7adba', highlight: {border: '#4f5b66', background: '#c0c5ce'}, 'color': '#333333'},
'waiting': {border: '#4f5b66', background: '#a7adba', highlight: {border: '#4f5b66', background: '#c0c5ce'}, 'color': '#333333'},
'artifact': {border: '#BBBBBB', background: '#FFFFFF', highlight: {border: '#999999', background: '#FFFFFF'}, 'color': '#333333'},
'type': {border: '#BBBBBB', background: '#CCCCCC', highlight: {border: '#999999', background: '#DDDDDD'}, 'color': '#333333'},
'deleting': {border: '#ff3333', background: '#ff6347', highlight: {border: '#ff3333', background: '#ff6347'}, 'color': '#333333'},
'deprecated': {border: '#000000', background: '#000000', highlight: {border: '#000000', background: '#333333'}, 'color': '#ffffff'}
};

show_loading('processing-network-div');
$("#processing-network-div").hide();
Expand All @@ -1091,9 +1093,10 @@ Vue.component('processing-graph', {
var circle_statuses = [];
var circle_types = [];
for (var circle_name in vm.colorScheme) {
var text = '<td style="padding: 5px; background-color:' + vm.colorScheme[circle_name]['background'] +
var text = '<td style="padding: 5px; color:' + vm.colorScheme[circle_name]['color'] +
'; background-color:' + vm.colorScheme[circle_name]['background'] +
';"><small>' + circle_name + '</small></td>';
if (circle_name === 'artifact' || circle_name === 'type'){
if (circle_name === 'artifact' || circle_name === 'type' || circle_name === 'deprecated'){
circle_types.push(text);
} else {
circle_statuses.push(text);
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21 changes: 12 additions & 9 deletions qiita_pet/static/js/qiita.js
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Expand Up @@ -314,17 +314,20 @@ function format_biom_rows(data, row, for_study_list = true, samples = null) {

// grouping by processing_method, data_type and parameters
$.each(data, function (idx, info) {
if (typeof info !== 'string' && !(info instanceof String)) {
var algorithm = info.algorithm;
if (!(algorithm in processing_method)) {
processing_method[algorithm] = {};
}
// ignore the artifacts that were generated with software that is not active
if (info['active']) {
if (typeof info !== 'string' && !(info instanceof String)) {
var algorithm = info.algorithm;
if (!(algorithm in processing_method)) {
processing_method[algorithm] = {};
}

var data_type = info.data_type + ' (' + info.target_subfragment.join(', ') + ')';
if (!(data_type in processing_method[algorithm])) {
processing_method[algorithm][data_type] = [];
var data_type = info.data_type + ' (' + info.target_subfragment.join(', ') + ')';
if (!(data_type in processing_method[algorithm])) {
processing_method[algorithm][data_type] = [];
}
processing_method[algorithm][data_type].push(info);
}
processing_method[algorithm][data_type].push(info);
}
});

Expand Down
5 changes: 5 additions & 0 deletions qiita_pet/templates/artifact_ajax/artifact_summary.html
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Expand Up @@ -111,6 +111,11 @@
<div class='row'>
<div class='col-md-12'>
<h4>
{% if processing_info and not processing_info['software_active'] %}
<div class="alert alert-warning" role="alert">
Warning, this artifact is deprecated!
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Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

It would be useful to state what this means exactly for the user, either to link to a help page or to spell things out in this message.

</div>
{% end %}
<i id='summary-title'>{{name}}</i><i> (ID: {{artifact_id}}) Visibility: {{visibility}}</i>
{% if editable %}
<a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit name</a>
Expand Down
10 changes: 5 additions & 5 deletions qiita_pet/test/test_prep_template.py
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Expand Up @@ -90,17 +90,17 @@ def test_get(self):
obs['nodes'])
self.assertIn(
['artifact', 'Demultiplexed', 2,
'Demultiplexed 1\n(Demultiplexed)', 'artifact'],
'Demultiplexed 1\n(Demultiplexed)', 'deprecated'],
obs['nodes'])
self.assertIn(
['artifact', 'Demultiplexed', 3,
'Demultiplexed 2\n(Demultiplexed)', 'artifact'],
'Demultiplexed 2\n(Demultiplexed)', 'deprecated'],
obs['nodes'])
self.assertIn(['artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'artifact'],
self.assertIn(['artifact', 'BIOM', 4, 'BIOM\n(BIOM)', 'deprecated'],
obs['nodes'])
self.assertIn(['artifact', 'BIOM', 5, 'BIOM\n(BIOM)', 'artifact'],
self.assertIn(['artifact', 'BIOM', 5, 'BIOM\n(BIOM)', 'deprecated'],
obs['nodes'])
self.assertIn(['artifact', 'BIOM', 6, 'BIOM\n(BIOM)', 'artifact'],
self.assertIn(['artifact', 'BIOM', 6, 'BIOM\n(BIOM)', 'deprecated'],
obs['nodes'])
self.assertEqual(3, len([n for dt, _, _, n, _ in obs['nodes']
if n == 'Pick closed-reference OTUs' and
Expand Down
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