1+ /*
2+ * Copyright 2013-2024, Seqera Labs
3+ *
4+ * Licensed under the Apache License, Version 2.0 (the "License");
5+ * you may not use this file except in compliance with the License.
6+ * You may obtain a copy of the License at
7+ *
8+ * http://www.apache.org/licenses/LICENSE-2.0
9+ *
10+ * Unless required by applicable law or agreed to in writing, software
11+ * distributed under the License is distributed on an "AS IS" BASIS,
12+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13+ * See the License for the specific language governing permissions and
14+ * limitations under the License.
15+ */
16+
17+ package nextflow.script
18+
19+ import nextflow.Session
20+ import spock.lang.Specification
21+
22+ /**
23+ * Tests for ProcessEntryHandler parameter mapping functionality
24+ *
25+ * @author Paolo Di Tommaso <[email protected] > 26+ */
27+ class ProcessEntryHandlerTest extends Specification {
28+
29+ def ' should parse complex parameters with dot notation'
30+ given :
31+ def session = Mock (Session )
32+ def script = Mock (BaseScript )
33+ def meta = Mock (ScriptMeta )
34+ def handler = new ProcessEntryHandler (script, session, meta)
35+
36+ when :
37+ def result = handler. parseComplexParameters([
38+ ' meta.id' ' SAMPLE_001'
39+ ' meta.name' ' TestSample'
40+ ' meta.other' ' some-value'
41+ ' fasta' ' /path/to/file.fa'
42+ ])
43+
44+ then :
45+ result. meta instanceof Map
46+ result. meta. id == ' SAMPLE_001'
47+ result. meta. name == ' TestSample'
48+ result. meta. other == ' some-value'
49+ result. fasta == ' /path/to/file.fa'
50+ }
51+
52+ def ' should parse nested dot notation parameters'
53+ given :
54+ def session = Mock (Session )
55+ def script = Mock (BaseScript )
56+ def meta = Mock (ScriptMeta )
57+ def handler = new ProcessEntryHandler (script, session, meta)
58+
59+ when :
60+ def result = handler. parseComplexParameters([
61+ ' meta.sample.id' ' 123'
62+ ' meta.sample.name' ' test'
63+ ' meta.config.quality' ' high'
64+ ' output.dir' ' /results'
65+ ])
66+
67+ then :
68+ result. meta instanceof Map
69+ result. meta. sample instanceof Map
70+ result. meta. sample. id == ' 123'
71+ result. meta. sample. name == ' test'
72+ result. meta. config instanceof Map
73+ result. meta. config. quality == ' high'
74+ result. output instanceof Map
75+ result. output. dir == ' /results'
76+ }
77+
78+ def ' should handle simple parameters without dots'
79+ given :
80+ def session = Mock (Session )
81+ def script = Mock (BaseScript )
82+ def meta = Mock (ScriptMeta )
83+ def handler = new ProcessEntryHandler (script, session, meta)
84+
85+ when :
86+ def result = handler. parseComplexParameters([
87+ ' sampleId' ' SAMPLE_001'
88+ ' threads' ' 4'
89+ ' dataFile' ' /path/to/data.txt'
90+ ])
91+
92+ then :
93+ result. sampleId == ' SAMPLE_001'
94+ result. threads == ' 4'
95+ result. dataFile == ' /path/to/data.txt'
96+ }
97+
98+ def ' should get value for val input type'
99+ given :
100+ def session = Mock (Session )
101+ def script = Mock (BaseScript )
102+ def meta = Mock (ScriptMeta )
103+ def handler = new ProcessEntryHandler (script, session, meta)
104+
105+ when :
106+ def complexParams = [
107+ ' meta' id : ' SAMPLE_001' name : ' TestSample'
108+ ' sampleId' ' SIMPLE_001'
109+ ]
110+ def valInput = [type : ' val' name : ' meta'
111+ def simpleInput = [type : ' val' name : ' sampleId'
112+
113+ then :
114+ handler. getValueForInput(valInput, complexParams) == [id : ' SAMPLE_001' name : ' TestSample'
115+ handler. getValueForInput(simpleInput, complexParams) == ' SIMPLE_001'
116+ }
117+
118+ def ' should get value for path input type'
119+ given :
120+ def session = Mock (Session )
121+ def script = Mock (BaseScript )
122+ def meta = Mock (ScriptMeta )
123+ def handler = new ProcessEntryHandler (script, session, meta)
124+
125+ when :
126+ def complexParams = [
127+ ' fasta' ' /path/to/file.fa'
128+ ' dataFile' ' data.txt'
129+ ]
130+ def pathInput = [type : ' path' name : ' fasta'
131+ def fileInput = [type : ' file' name : ' dataFile'
132+
133+ then :
134+ def fastaResult = handler. getValueForInput(pathInput, complexParams)
135+ def fileResult = handler. getValueForInput(fileInput, complexParams)
136+
137+ // Should convert string paths to Path objects (mocked here)
138+ fastaResult. toString(). contains(' file.fa'
139+ fileResult. toString(). contains(' data.txt'
140+ }
141+
142+ def ' should throw exception for missing required parameter'
143+ given :
144+ def session = Mock (Session )
145+ def script = Mock (BaseScript )
146+ def meta = Mock (ScriptMeta )
147+ def handler = new ProcessEntryHandler (script, session, meta)
148+
149+ when :
150+ def complexParams = [
151+ ' meta' id : ' SAMPLE_001'
152+ ]
153+ def missingInput = [type : ' val' name : ' missing'
154+ handler. getValueForInput(missingInput, complexParams)
155+
156+ then :
157+ thrown(IllegalArgumentException )
158+ }
159+
160+ def ' should map tuple input structure correctly'
161+ given :
162+ def session = Mock (Session ) {
163+ getParams() >> [
164+ ' meta.id' ' SAMPLE_001'
165+ ' meta.name' ' TestSample'
166+ ' meta.other' ' some-value'
167+ ' fasta' ' /path/to/file.fa'
168+ ]
169+ }
170+ def script = Mock (BaseScript )
171+ def meta = Mock (ScriptMeta )
172+ def processDef = Mock (ProcessDef )
173+ def handler = new ProcessEntryHandler (script, session, meta)
174+
175+ when :
176+ // Mock input structures for tuple val(meta), path(fasta)
177+ def inputStructures = [
178+ [
179+ type : ' tuple'
180+ elements : [
181+ [type : ' val' name : ' meta'
182+ [type : ' path' name : ' fasta'
183+ ]
184+ ]
185+ ]
186+
187+ // Test the parameter mapping logic manually
188+ def complexParams = handler. parseComplexParameters(session. getParams())
189+ def tupleInput = inputStructures[0 ]
190+ def tupleElements = []
191+
192+ for ( def element : tupleInput. elements ) {
193+ def value = handler. getValueForInput(element, complexParams)
194+ tupleElements. add(value)
195+ }
196+
197+ then :
198+ complexParams. meta instanceof Map
199+ complexParams. meta. id == ' SAMPLE_001'
200+ complexParams. meta. name == ' TestSample'
201+ complexParams. meta. other == ' some-value'
202+ complexParams. fasta == ' /path/to/file.fa'
203+
204+ tupleElements. size() == 2
205+ tupleElements[0 ] instanceof Map // meta as map
206+ tupleElements[0 ]. id == ' SAMPLE_001'
207+ tupleElements[0 ]. name == ' TestSample'
208+ tupleElements[0 ]. other == ' some-value'
209+ // tupleElements[1] should be a Path object (mocked)
210+ tupleElements[1 ]. toString(). contains(' file.fa'
211+ }
212+ }
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