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Allow multiple artifact commands #69

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merged 3 commits into from
Jun 8, 2022
Merged

Allow multiple artifact commands #69

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de018a9
allow multiple artifact commands
antgonza Jun 7, 2022
8b9c38b
Merge branch 'master' of github.com:qiita-spots/qp-qiime2 into allow-…
antgonza Jun 7, 2022
a0e10b5
fix tests
antgonza Jun 8, 2022
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10 changes: 3 additions & 7 deletions qp_qiime2/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,8 @@
req_params[ename] = ('choice:[%s]' % qp_qiime2_dbs, default)
req_params['qp-hide-param' + ename] = ('string', pname)
else:
ename = element.description
ename = f'{element.description} [{pname}]'

# this is an odd one, first encountered:
# feature-classifier fit-classifier-naive-bayes
if ename == element.NOVALUE:
Expand Down Expand Up @@ -232,12 +233,6 @@
# As of qiime2-2022.2 this filters out:
# filtered_sequences filter_seqs
continue
elif total_inputs > 1:
# As of qiime2-2022.2 this filters out:
# 2
# biplot pcoa_biplot
# visualization mantel
continue

for pname, element in parameters.items():
tqt, predicate = get_qiime2_type_name_and_predicate(element)
Expand Down Expand Up @@ -307,6 +302,7 @@
opt_params[name] = ('string', 'qp-hide-metadata-field')
else:
ename = '%s (%s)' % (element.description, pname)

if element.has_default():
opt_params[ename] = (data_type, default)
# we need to add the actual name of the parameter so we
Expand Down
13 changes: 9 additions & 4 deletions qp_qiime2/qp_qiime2.py
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Expand Up @@ -48,13 +48,14 @@
'expression': []},
'alpha_vector': {
'name': 'SampleData',
'expression': ['AlphaDiversity']},
'expression': ['AlphaDiversity', 'ClassifierPredictions',
'Probabilities']},
'phylogeny': {
'name': 'Phylogeny',
'expression': ['Rooted']},
'FeatureData': {
'name': 'FeatureData',
'expression': ['Taxonomy', 'Sequence']},
'expression': ['Taxonomy', 'Sequence', 'Importance']},
'TaxonomicClassifier': {
'name': 'TaxonomicClassifier',
'expression': []},
Expand Down Expand Up @@ -310,8 +311,12 @@ def call_qiime2(qclient, job_id, parameters, out_dir):
if mkey.view_type is set:
val = {val}
else:
val = qiime2.sdk.util.parse_primitive(
mkey.qiime_type.to_ast(), val)
# if ast['name'] == 'List', we need to make sure to take
# the user give val and make it a list
ast = mkey.qiime_type.to_ast()
if 'name' in ast and ast['name'] == 'List':
val = [val]
val = qiime2.sdk.util.parse_primitive(ast, val)

q2params[key] = val
elif k in ('qp-hide-metadata', 'qp-hide-FeatureData[Taxonomy]'):
Expand Down
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