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Merge pull request #7 from nilchia/flexy0.2.16
fix strict test
2 parents 5ac2026 + d914b89 commit 8ee186c

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‎tools/flexynesis/.lint_skip‎

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TestsCaseValidation

‎tools/flexynesis/flexynesis.xml‎

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Original file line numberDiff line numberDiff line change
@@ -193,24 +193,24 @@
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<tests>
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<test>
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<param name="non_commercial_use" value="True"/>
196-
<param name="train_clin" value="train/clin" ftype="csv"/>
197-
<param name="test_clin" value="test/clin" ftype="csv"/>
198-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
199-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
202-
<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="training_type">
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<param name="model" value="s_train"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
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<param name="train_omics_main" value="train/gex" ftype="csv"/>
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<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="model_class">
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<param name="model_class" value="DirectPred"/>
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</conditional>
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<param name="target_variables" value="Erlotinib"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -263,19 +263,19 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
268-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
269-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<conditional name="training_type">
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<param name="model" value="s_train"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
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<param name="train_omics_main" value="train/gex" ftype="csv"/>
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<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<conditional name="model_class">
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<param name="model_class" value="DirectPred"/>
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</conditional>
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<param name="target_variables" value="Erlotinib"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -323,24 +323,24 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
327-
<param name="test_clin" value="test/clin" ftype="csv"/>
328-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
329-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="training_type">
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<param name="model" value="s_train"/>
328+
<param name="train_clin" value="train/clin" ftype="csv"/>
329+
<param name="test_clin" value="test/clin" ftype="csv"/>
330+
<param name="train_omics_main" value="train/gex" ftype="csv"/>
331+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
332+
<param name="assay_main" value="bar"/>
333+
<repeat name="omics">
334+
<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
336+
<param name="assay" value="foo"/>
337+
</repeat>
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<conditional name="model_class">
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<param name="model_class" value="DirectPred"/>
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</conditional>
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<param name="target_variables" value="Irinotecan"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -393,21 +393,21 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
396-
<param name="train_clin" value="train/clin" ftype="csv"/>
397-
<param name="test_clin" value="test/clin" ftype="csv"/>
398-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
399-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
401-
<repeat name="omics">
402-
<param name="train_omics" value="train/cnv" ftype="csv"/>
403-
<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
405-
</repeat>
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<conditional name="training_type">
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<param name="model" value="us_train"/>
398+
<param name="train_clin" value="train/clin" ftype="csv"/>
399+
<param name="test_clin" value="test/clin" ftype="csv"/>
400+
<param name="train_omics_main" value="train/gex" ftype="csv"/>
401+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
402+
<param name="assay_main" value="bar"/>
403+
<repeat name="omics">
404+
<param name="train_omics" value="train/cnv" ftype="csv"/>
405+
<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<param name="model_class" value="supervised_vae"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -433,23 +433,23 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
436-
<param name="train_clin" value="train/clin" ftype="csv"/>
437-
<param name="test_clin" value="test/clin" ftype="csv"/>
438-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
439-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
440-
<param name="assay_main" value="bar"/>
441-
<param name="layer_main" value="input"/>
442-
<repeat name="omics">
443-
<param name="train_omics" value="train/cnv" ftype="csv"/>
444-
<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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<param name="layer" value="output"/>
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</repeat>
448436
<conditional name="training_type">
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<param name="model" value="cm_train"/>
438+
<param name="train_clin" value="train/clin" ftype="csv"/>
439+
<param name="test_clin" value="test/clin" ftype="csv"/>
440+
<param name="train_omics_main" value="train/gex" ftype="csv"/>
441+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
442+
<param name="assay_main" value="bar"/>
443+
<param name="layer_main" value="input"/>
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<repeat name="omics">
445+
<param name="train_omics" value="train/cnv" ftype="csv"/>
446+
<param name="test_omics" value="test/cnv" ftype="csv"/>
447+
<param name="assay" value="foo"/>
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<param name="layer" value="output"/>
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</repeat>
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<param name="model_class" value="CrossModalPred"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
452-
<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -485,27 +485,27 @@
485485
</test>
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<test>
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<param name="non_commercial_use" value="True"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
489-
<param name="test_clin" value="test/clin" ftype="csv"/>
490-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
491-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
492-
<param name="assay_main" value="bar"/>
493-
<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="training_type">
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<param name="model" value="s_train"/>
490+
<param name="train_clin" value="train/clin" ftype="csv"/>
491+
<param name="test_clin" value="test/clin" ftype="csv"/>
492+
<param name="train_omics_main" value="train/gex" ftype="csv"/>
493+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
495+
<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="model_class">
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<param name="model_class" value="GNN"/>
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</conditional>
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<param name="gnn_conv_type" value="GC"/>
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<param name="string_organism" value="9606"/>
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<param name="string_node_name" value="gene_name"/>
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<param name="target_variables" value="Erlotinib"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -558,21 +558,21 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
561-
<param name="train_clin" value="train/clin" ftype="csv"/>
562-
<param name="test_clin" value="test/clin" ftype="csv"/>
563-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
564-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="b ar"/>
566-
<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="f oo"/>
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</repeat>
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<conditional name="training_type">
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<param name="model" value="us_train"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
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<param name="train_omics_main" value="train/gex" ftype="csv"/>
566+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="b ar"/>
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<repeat name="omics">
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<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="f oo"/>
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</repeat>
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<param name="model_class" value="supervised_vae"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.embeddings_test">
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<assert_contents>
@@ -598,24 +598,24 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
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<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
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<param name="train_omics_main" value="train/gex" ftype="csv"/>
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<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
607-
<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="training_type">
612602
<param name="model" value="s_train"/>
603+
<param name="train_clin" value="train/clin" ftype="csv"/>
604+
<param name="test_clin" value="test/clin" ftype="csv"/>
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<param name="train_omics_main" value="train/gex" ftype="csv"/>
606+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
609+
<param name="train_omics" value="train/cnv" ftype="csv"/>
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<param name="test_omics" value="test/cnv" ftype="csv"/>
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<param name="assay" value="foo"/>
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</repeat>
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<conditional name="model_class">
614614
<param name="model_class" value="XGBoost"/>
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</conditional>
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<param name="target_variables" value="Erlotinib"/>
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<param name="hpo_iter" value="1"/>
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</conditional>
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<param name="hpo_iter" value="1"/>
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<output_collection name="results" type="list">
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<element name="job.stats">
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<assert_contents>
@@ -628,26 +628,26 @@
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</test>
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<test>
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<param name="non_commercial_use" value="True"/>
631-
<param name="train_clin" value="train/clin" ftype="csv"/>
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<param name="test_clin" value="test/clin" ftype="csv"/>
633-
<param name="train_omics_main" value="train/gex" ftype="csv"/>
634-
<param name="test_omics_main" value="test/gex" ftype="csv"/>
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<param name="assay_main" value="bar"/>
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<repeat name="omics">
637-
<param name="train_omics" value="train/cnv" ftype="csv"/>
638-
<param name="test_omics" value="test/cnv" ftype="csv"/>
639-
<param name="assay" value="foo"/>
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</repeat>
641631
<conditional name="training_type">
642632
<param name="model" value="s_train"/>
633+
<param name="train_clin" value="train/clin" ftype="csv"/>
634+
<param name="test_clin" value="test/clin" ftype="csv"/>
635+
<param name="train_omics_main" value="train/gex" ftype="csv"/>
636+
<param name="test_omics_main" value="test/gex" ftype="csv"/>
637+
<param name="assay_main" value="bar"/>
638+
<repeat name="omics">
639+
<param name="train_omics" value="train/cnv" ftype="csv"/>
640+
<param name="test_omics" value="test/cnv" ftype="csv"/>
641+
<param name="assay" value="foo"/>
642+
</repeat>
643643
<conditional name="model_class">
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<param name="model_class" value="DirectPred"/>
645645
</conditional>
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<param name="target_variables" value="Erlotinib"/>
647+
<param name="hpo_iter" value="1"/>
648+
<param name="feature_importance_method" value="IntegratedGradients"/>
649+
<param name="val_size" value="0.2"/>
647650
</conditional>
648-
<param name="hpo_iter" value="1"/>
649-
<param name="feature_importance_method" value="IntegratedGradients"/>
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<param name="val_size" value="0.2"/>
651651
<output_collection name="results" type="list">
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<element name="job.embeddings_test">
653653
<assert_contents>

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