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merged 2 commits into from
Mar 15, 2022
Merged

fix #3158 #3190

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b2a65be
fix #3158
antgonza Mar 15, 2022
d269b44
fix test_retrive_workflows
antgonza Mar 15, 2022
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21 changes: 15 additions & 6 deletions qiita_db/metadata_template/prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -858,12 +858,20 @@ def _get_predecessors(workflow, node):
pdp = pnode.default_parameter
pdp_cmd = pdp.command
params = pdp.values.copy()
reqp = {x: y[1][0]
for x, y in pdp_cmd.required_parameters.items()}
# verifying that the workflow.artifact_type is included
# in the command input types or raise an error
wkartifact_type = wk.artifact_type
reqp = dict()
for x, y in pdp_cmd.required_parameters.items():
if wkartifact_type not in y[1]:
raise ValueError(f'{wkartifact_type} is not part '
'of this preparation and cannot '
'be applied')
reqp[x] = wkartifact_type

cmds_to_create.append([pdp_cmd, params, reqp])

init_artifacts = {
self.artifact.artifact_type: self.artifact.id}
init_artifacts = {wkartifact_type: self.artifact.id}

cmds_to_create.reverse()
current_job = None
Expand All @@ -874,8 +882,9 @@ def _get_predecessors(workflow, node):
for iname, dname in rp.items():
if dname not in init_artifacts:
msg = (f'Missing Artifact type: "{dname}" in '
'this preparation; are you missing a '
'step to start?')
'this preparation; this might be due '
'to missing steps or not having the '
'correct raw data.')
# raises option c.
raise ValueError(msg)
req_params[iname] = init_artifacts[dname]
Expand Down
12 changes: 6 additions & 6 deletions qiita_db/metadata_template/test/test_prep_template.py
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Expand Up @@ -1412,13 +1412,13 @@ def test_artifact_setter(self):
pt.add_default_workflow(qdb.user.User('test@foo.bar'))

# now let's test that an error is raised when there is no valid initial
# input data; this moves the data type from FASTQ to taxa_summary
# input data; this moves the data type from FASTQ to taxa_summary for
# the default_workflow_id = 1
qdb.sql_connection.perform_as_transaction(
'UPDATE qiita.artifact SET artifact_type_id = 10 WHERE '
f'artifact_id = {pt.artifact.id}')
with self.assertRaisesRegex(ValueError, 'Missing Artifact type: '
'"FASTQ" in this preparation; are you '
'missing a step to start?'):
'UPDATE qiita.default_workflow SET artifact_type_id = 10 WHERE '
'default_workflow_id = 1')
with self.assertRaisesRegex(ValueError, 'taxa_summary is not part of '
'this preparation and cannot be applied'):
pt.add_default_workflow(qdb.user.User('test@foo.bar'))

# cleaning
Expand Down
17 changes: 17 additions & 0 deletions qiita_db/software.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1946,6 +1946,23 @@ def data_type(self):
qdb.sql_connection.TRN.add(sql, [self.id])
return qdb.sql_connection.TRN.execute_fetchflatten()

@property
def artifact_type(self):
"""Retrieves artifact_type that the workflow can be applied to

Returns
----------
str
The name of the artifact type this workflow can be applied to
"""
with qdb.sql_connection.TRN:
sql = """SELECT artifact_type
FROM qiita.artifact_type
LEFT JOIN qiita.default_workflow USING (artifact_type_id)
WHERE default_workflow_id = %s"""
qdb.sql_connection.TRN.add(sql, [self.id])
return qdb.sql_connection.TRN.execute_fetchflatten()[0]

@property
def graph(self):
"""Returns the graph that represents the workflow
Expand Down
11 changes: 11 additions & 0 deletions qiita_db/support_files/patches/85.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,14 @@ BEGIN
INSERT INTO qiita.command_parameter (command_id, parameter_name, parameter_type, required, default_value)
VALUES (cmd_id, 'categories', 'mchoice', True, NULL);
END $do$;

-- Feb 28, 2022
-- adding a new column to the default_workflow table to keep track of the
-- artifact type that is expecting vs. "guessing"

ALTER TABLE qiita.default_workflow ADD artifact_type_id BIGINT NOT NULL DEFAULT 3;
ALTER TABLE qiita.default_workflow
ADD CONSTRAINT fk_artifact_type_id
FOREIGN KEY (artifact_type_id)
REFERENCES qiita.artifact_type(artifact_type_id)
ON UPDATE CASCADE;
3 changes: 3 additions & 0 deletions qiita_db/test/test_software.py
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Expand Up @@ -632,6 +632,9 @@ def test_default_workflows(self):
obs = list(qdb.software.DefaultWorkflow.iter(False))
self.assertEqual(obs, exp)

self.assertEqual(
qdb.software.DefaultWorkflow(1).artifact_type, 'FASTQ')

qdb.software.DefaultWorkflow(1).active = False
obs = list(qdb.software.DefaultWorkflow.iter(False))
self.assertEqual(obs, exp)
Expand Down
12 changes: 11 additions & 1 deletion qiita_pet/handlers/software.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,13 +72,23 @@ def _default_parameters_parsing(node):
# output_type: output_node_name}, ...}
# for easy look up and merge of output_names
main_nodes = dict()
for x, y in graph.edges:
for i, (x, y) in enumerate(graph.edges):
connections = []
for a, _, c in graph[x][y]['connections'].connections:
connections.append("%s | %s" % (a, c))

vals_x, input_x, output_x = _default_parameters_parsing(x)
vals_y, input_y, output_y = _default_parameters_parsing(y)

if i == 0:
# we are in the first element so we can specifically select
# the type we are looking for
at = w.artifact_type
if at in input_x[0][1]:
input_x[0][1] = at
else:
input_x[0][1] = '** WARNING, NOT DEFINED **'

name_x = vals_x[0]
name_y = vals_y[0]
if vals_x not in (nodes):
Expand Down
22 changes: 12 additions & 10 deletions qiita_pet/test/test_software.py
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Expand Up @@ -144,6 +144,8 @@ def test_retrive_workflows(self):
'rev_comp_mapping_barcodes': 'True', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'barcode_type': 'golay_12',
'max_barcode_errors': '1.5', 'phred_offset': 'auto'}],
['input_params_7_FASTQ | per_sample_FASTQ', 1,
'FASTQ | per_sample_FASTQ'],
['output_params_7_demultiplexed | Demultiplexed', 1,
'demultiplexed | Demultiplexed'],
['params_8', 3, 'Pick closed-reference OTUs', 'Defaults', {
Expand All @@ -152,7 +154,7 @@ def test_retrive_workflows(self):
'sortmerna_coverage': '0.97', 'threads': '1'}],
['output_params_8_OTU table | BIOM', 3, 'OTU table | BIOM']])
exp[0]['edges'].extend([
['input_params_1_FASTQ | per_sample_FASTQ', 'params_7'],
['input_params_7_FASTQ | per_sample_FASTQ', 'params_7'],
['params_7', 'output_params_7_demultiplexed | Demultiplexed'],
['output_params_7_demultiplexed | Demultiplexed', 'params_8'],
['params_8', 'output_params_8_OTU table | BIOM']])
Expand Down Expand Up @@ -180,8 +182,8 @@ def test_retrive_workflows(self):
'rev_comp_mapping_barcodes': 'False', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'barcode_type': 'golay_12',
'max_barcode_errors': '1.5', 'phred_offset': 'auto'}],
['input_params_1_FASTQ | per_sample_FASTQ', 1,
'FASTQ | per_sample_FASTQ'],
['input_params_1_FASTQ', 1,
'FASTQ'],
['output_params_1_demultiplexed | Demultiplexed', 1,
'demultiplexed | Demultiplexed'],
['params_2', 3, 'Pick closed-reference OTUs', 'Defaults', {
Expand All @@ -190,7 +192,7 @@ def test_retrive_workflows(self):
'sortmerna_coverage': '0.97', 'threads': '1'}],
['output_params_2_OTU table | BIOM', 3, 'OTU table | BIOM']],
'edges': [
['input_params_1_FASTQ | per_sample_FASTQ', 'params_1'],
['input_params_1_FASTQ', 'params_1'],
['params_1', 'output_params_1_demultiplexed | Demultiplexed'],
['output_params_1_demultiplexed | Demultiplexed', 'params_2'],
['params_2', 'output_params_2_OTU table | BIOM']]},
Expand All @@ -206,8 +208,8 @@ def test_retrive_workflows(self):
'qual_score_window': '0', 'disable_primers': 'False',
'reverse_primers': 'disable', 'reverse_primer_mismatches': '0',
'truncate_ambi_bases': 'False'}],
['input_params_3_FASTA | FASTA_Sanger | SFF', 2,
'FASTA | FASTA_Sanger | SFF'],
['input_params_3_** WARNING, NOT DEFINED **', 2,
'** WARNING, NOT DEFINED **'],
['output_params_3_demultiplexed | Demultiplexed', 2,
'demultiplexed | Demultiplexed'],
['params_4', 3, 'Pick closed-reference OTUs', 'Defaults', {
Expand All @@ -216,7 +218,7 @@ def test_retrive_workflows(self):
'sortmerna_coverage': '0.97', 'threads': '1'}],
['output_params_4_OTU table | BIOM', 3, 'OTU table | BIOM']],
'edges': [
['input_params_3_FASTA | FASTA_Sanger | SFF', 'params_3'],
['input_params_3_** WARNING, NOT DEFINED **', 'params_3'],
['params_3', 'output_params_3_demultiplexed | Demultiplexed'],
['output_params_3_demultiplexed | Demultiplexed', 'params_4'],
['params_4', 'output_params_4_OTU table | BIOM']]},
Expand All @@ -229,8 +231,8 @@ def test_retrive_workflows(self):
'rev_comp_mapping_barcodes': 'False', 'rev_comp': 'False',
'phred_quality_threshold': '3', 'barcode_type': 'not-barcoded',
'max_barcode_errors': '1.5', 'phred_offset': 'auto'}],
['input_params_5_FASTQ | per_sample_FASTQ', 1,
'FASTQ | per_sample_FASTQ'],
['input_params_5_FASTQ', 1,
'FASTQ'],
['output_params_5_demultiplexed | Demultiplexed', 1,
'demultiplexed | Demultiplexed'],
['params_6', 3, 'Pick closed-reference OTUs', 'Defaults', {
Expand All @@ -239,7 +241,7 @@ def test_retrive_workflows(self):
'sortmerna_coverage': '0.97', 'threads': '1'}],
['output_params_6_OTU table | BIOM', 3, 'OTU table | BIOM']],
'edges': [
['input_params_5_FASTQ | per_sample_FASTQ', 'params_5'],
['input_params_5_FASTQ', 'params_5'],
['params_5', 'output_params_5_demultiplexed | Demultiplexed'],
['output_params_5_demultiplexed | Demultiplexed', 'params_6'],
['params_6', 'output_params_6_OTU table | BIOM']]}]
Expand Down