Implement update mode for integration tests (#3536)

Author: MaksimDaniliuk

README.md

@@ -175,6 +175,22 @@ Befor running any test you have to build and install indigo-python
     python api/tests/integration/test.py -t 1 -p test_name
     ```
 
+    >to update all tests "ref/" using -u flag
+    ```
+    python api/tests/integration/test.py -u
+    ```
+
+    >to update all tests "ref/" without -u flag
+    ```
+    export INDIGO_UPDATE_TESTS="True"
+    python api/tests/integration/test.py
+    ```
+
+    >to update a single test's "ref/" by mask use `test_name` and -u flag
+    ```
+    python api/tests/integration/test.py -t 1 -p test_name -u
+    ```
+
 ### To run backend API test:
 1) Build and install indigo-python
 2) Set environment variable by running this command:

api/tests/integration/common/env_indigo.py

@@ -209,7 +209,7 @@ def moleculeLayoutDiff(
     ref,
     delta=0.01,
     ref_is_file=True,
-    update=False,
+    update=os.getenv("INDIGO_UPDATE_TESTS", "False") == "True",
     update_format="mol",
 ):
     if ref_is_file:
@@ -268,7 +268,7 @@ def reactionLayoutDiff(
     ref,
     delta=0.001,
     ref_is_file=True,
-    update=False,
+    update=os.getenv("INDIGO_UPDATE_TESTS", "False") == "True",
     update_format="mol",
 ):
     if ref_is_file:
@@ -297,6 +297,7 @@ def reactionLayoutDiff(
             r2.getMolecule(m.index()).molfile(),
             delta,
             ref_is_file=False,
+            update=False,
         )
         error_buf.append("Molecule #{}: {}".format(m.index(), res))
     return "\n   ".join(error_buf)

api/tests/integration/common/util.py

@@ -1,3 +1,4 @@
+import difflib
 import os
 import platform
 import re
@@ -207,3 +208,30 @@ def check_jna_sha1():
     except Exception as e:
         os.remove(output_path)
         raise e
+
+
+def find_diff(a, b):
+    return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))
+
+
+def compare_diff(ref_path, filename, data, stdout=True, diff_fn=find_diff):
+    path_to_file = os.path.join(ref_path, filename)
+
+    is_update_required = os.getenv("INDIGO_UPDATE_TESTS", "False") == "True"
+    if is_update_required:
+        with open(path_to_file, "w") as file:
+            file.write(data)
+
+    with open(path_to_file, "r") as file:
+        data_ref = file.read()
+
+    diff = diff_fn(data_ref, data)
+
+    if not stdout:
+        return diff
+
+    if not diff:
+        print(filename + ":SUCCEED")
+    else:
+        print(filename + ":FAILED")
+        print(diff)

api/tests/integration/ref/formats/2713-star-atom.py.out

@@ -1,3 +1,3 @@
 *** 2713 star atom support ***
-star_atom ket : SUCCEED
-star_atom scxmiles : SUCCEED
+star_atom.ket:SUCCEED
+*C.*N.*O |$star_e;;AH_p;;star_e;$|

api/tests/integration/ref/formats/cdx_export.py.out

@@ -1,41 +1,41 @@
 *** Mol to CDX ***
-enhanced_stereo1:success
-enhanced_stereo2:success
-enhanced_stereo3:success
-macro/sa-mono:success
-rgroup:success
-stereo_either-0020:success
-two_bn:success
+enhanced_stereo1.b64cdx:SUCCEED
+enhanced_stereo2.b64cdx:SUCCEED
+enhanced_stereo3.b64cdx:SUCCEED
+macro/sa-mono.b64cdx:SUCCEED
+rgroup.b64cdx:SUCCEED
+stereo_either-0020.b64cdx:SUCCEED
+two_bn.b64cdx:SUCCEED
 *** KET to CDX ***
-issue_1774:success
-issue_1775:success
+issue_1774.b64cdx:SUCCEED
+issue_1775.b64cdx:SUCCEED
 molecule json loader: 'any' bonds are allowed only for queries
 *** Try as Query ***
 CDXML loader: Queries not supported
-issue_1777:success
-agents:success
+issue_1777.b64cdx:SUCCEED
+agents.b64cdx:SUCCEED
 *** CDXML to CDX ***
-AlcoholOxidation_Rxn1:success
-AlcoholOxidation_Rxn2:success
-Amidation_Rxn1:success
-Amidation_Rxn2:success
-BuchwaldHartwig_Rxn1:success
-BuchwaldHartwig_Rxn2:success
-CarbonylReduction_Rxn1:success
-CarbonylReduction_Rxn2:success
-Esterification_Rxn1:success
-Esterification_Rxn2:success
-Grignard_Rxn1:success
-Grignard_Rxn2:success
-N-Alkylation_Rxn1:success
-N-Alkylation_Rxn2:success
-N-Sulfonylation_Rxn1:success
-N-Sulfonylation_Rxn2:success
-O-Alkylation_Rxn1:success
-O-Alkylation_Rxn2:success
-Reductive Amination_Rxn1:success
-Reductive Amination_Rxn2:success
-SnAr_Rxn1:success
-SnAr_Rxn2:success
-Suzuki_Rxn1:success
-Suzuki_Rxn2:success
+AlcoholOxidation_Rxn1.b64cdx:SUCCEED
+AlcoholOxidation_Rxn2.b64cdx:SUCCEED
+Amidation_Rxn1.b64cdx:SUCCEED
+Amidation_Rxn2.b64cdx:SUCCEED
+BuchwaldHartwig_Rxn1.b64cdx:SUCCEED
+BuchwaldHartwig_Rxn2.b64cdx:SUCCEED
+CarbonylReduction_Rxn1.b64cdx:SUCCEED
+CarbonylReduction_Rxn2.b64cdx:SUCCEED
+Esterification_Rxn1.b64cdx:SUCCEED
+Esterification_Rxn2.b64cdx:SUCCEED
+Grignard_Rxn1.b64cdx:SUCCEED
+Grignard_Rxn2.b64cdx:SUCCEED
+N-Alkylation_Rxn1.b64cdx:SUCCEED
+N-Alkylation_Rxn2.b64cdx:SUCCEED
+N-Sulfonylation_Rxn1.b64cdx:SUCCEED
+N-Sulfonylation_Rxn2.b64cdx:SUCCEED
+O-Alkylation_Rxn1.b64cdx:SUCCEED
+O-Alkylation_Rxn2.b64cdx:SUCCEED
+Reductive Amination_Rxn1.b64cdx:SUCCEED
+Reductive Amination_Rxn2.b64cdx:SUCCEED
+SnAr_Rxn1.b64cdx:SUCCEED
+SnAr_Rxn2.b64cdx:SUCCEED
+Suzuki_Rxn1.b64cdx:SUCCEED
+Suzuki_Rxn2.b64cdx:SUCCEED

api/tests/integration/ref/formats/genbank_to_seq.py.out

@@ -1,4 +1,4 @@
 *** GenBank/GenPept to Seq***
-1844-gen_bank.seq.seq:SUCCEED
-1844-gen_pept.seq.seq:SUCCEED
-2763-gen_spaces.seq.seq:SUCCEED
+1844-gen_bank.seq:SUCCEED
+1844-gen_pept.seq:SUCCEED
+2763-gen_spaces.seq:SUCCEED

api/tests/integration/ref/formats/ket_to_ket.py.out

@@ -1,29 +1,29 @@
 *** KET to KET ***
 3087-star-process.ket:SUCCEED
 images.ket:SUCCEED
-ambiguous_monomer.ket doc loadKetDocument: SUCCEED
-ambiguous_monomer.ket mol loadMolecule: SUCCEED
-ambiguous_monomer.ket mol loadQueryMolecule: SUCCEED
-expanded_monomer.ket doc loadKetDocument: SUCCEED
-expanded_monomer.ket mol loadMolecule: SUCCEED
-expanded_monomer.ket mol loadQueryMolecule: SUCCEED
-helm_alias.ket doc loadKetDocument: SUCCEED
-helm_alias.ket mol loadMolecule: SUCCEED
-helm_alias.ket mol loadQueryMolecule: SUCCEED
-helm_annotation.ket doc loadKetDocument: SUCCEED
-helm_annotation.ket mol loadMolecule: SUCCEED
-helm_annotation.ket mol loadQueryMolecule: SUCCEED
-modification_types.ket doc loadKetDocument: SUCCEED
-modification_types.ket mol loadMolecule: SUCCEED
-modification_types.ket mol loadQueryMolecule: SUCCEED
-monomer_shape.ket doc loadKetDocument: SUCCEED
-monomer_shape.ket mol loadMolecule: SUCCEED
-monomer_shape.ket mol loadQueryMolecule: SUCCEED
-monomer_transform.ket doc loadKetDocument: SUCCEED
-monomer_transform.ket mol loadMolecule: SUCCEED
-monomer_transform.ket mol loadQueryMolecule: SUCCEED
-2707_subst_count.ket ket: SUCCEED
-2707_subst_count.ket mol: SUCCEED
+ambiguous_monomer_doc.ket loadKetDocument:SUCCEED
+ambiguous_monomer_mol.ket loadMolecule:SUCCEED
+ambiguous_monomer_mol.ket loadQueryMolecule:SUCCEED
+expanded_monomer_doc.ket loadKetDocument:SUCCEED
+expanded_monomer_mol.ket loadMolecule:SUCCEED
+expanded_monomer_mol.ket loadQueryMolecule:SUCCEED
+helm_alias_doc.ket loadKetDocument:SUCCEED
+helm_alias_mol.ket loadMolecule:SUCCEED
+helm_alias_mol.ket loadQueryMolecule:SUCCEED
+helm_annotation_doc.ket loadKetDocument:SUCCEED
+helm_annotation_mol.ket loadMolecule:SUCCEED
+helm_annotation_mol.ket loadQueryMolecule:SUCCEED
+modification_types_doc.ket loadKetDocument:SUCCEED
+modification_types_mol.ket loadMolecule:SUCCEED
+modification_types_mol.ket loadQueryMolecule:SUCCEED
+monomer_shape_doc.ket loadKetDocument:SUCCEED
+monomer_shape_mol.ket loadMolecule:SUCCEED
+monomer_shape_mol.ket loadQueryMolecule:SUCCEED
+monomer_transform_doc.ket loadKetDocument:SUCCEED
+monomer_transform_mol.ket loadMolecule:SUCCEED
+monomer_transform_mol.ket loadQueryMolecule:SUCCEED
+2707_subst_count.ket:SUCCEED
+2707_subst_count.mol:SUCCEED
 3069-reaction.ket:SUCCEED
 multi_merge4.ket:SUCCEED
 mixed_reaction.ket:SUCCEED

api/tests/integration/ref/formats/ket_to_mol.py.out

@@ -1,59 +1,59 @@
 *** KET to MOL ***
-3068-star-issue.ket:SUCCEED
-3178-any-bond.ket:SUCCEED
-3227-copolymer.ket:SUCCEED
-3343-dir-expanded.ket:SUCCEED
-5amd.ket:SUCCEED
-accl_no_class.ket:SUCCEED
-acgt_1412.ket:SUCCEED
-anacyclamide.ket:SUCCEED
-chem.ket:SUCCEED
-chem_rna_hydro.ket:SUCCEED
-conj_no_class.ket:SUCCEED
-conjugate.ket:SUCCEED
-cysteine.ket:SUCCEED
-dala.ket:SUCCEED
-dcysteine.ket:SUCCEED
-dna_mod.ket:SUCCEED
-dthymine.ket:SUCCEED
-exp-valence-0.ket:SUCCEED
-flip_rotate.ket:SUCCEED
-flip_rotate_2000.ket:SUCCEED
-flip_rotate_rna.ket:SUCCEED
-fmoc.ket:SUCCEED
-hydro_atp_ch.ket:SUCCEED
-issue_1476.ket:SUCCEED
-issue_2699_rlogic.ket:SUCCEED
-issue_2702.ket:SUCCEED
-macro/R2R3R4.ket:SUCCEED
-macro/conjugates/pep-chem-rna.ket:SUCCEED
-macro/conjugates/peptide_rna.ket:SUCCEED
-macro/dendromers/dendro-peptide.ket:SUCCEED
-macro/disulfide/disulfide_peptide_cycle.ket:SUCCEED
-macro/hundred-monomers.ket:SUCCEED
-macro/left_phosphate/left_phosphate.ket:SUCCEED
-macro/linear/linear_dna.ket:SUCCEED
-macro/linear/linear_multi.ket:SUCCEED
-macro/linear/linear_peptide.ket:SUCCEED
-macro/linear/linear_rna.ket:SUCCEED
-macro/modified/mod_dna.ket:SUCCEED
-macro/modified/mod_peptide.ket:SUCCEED
-macro/modified/mod_rna.ket:SUCCEED
-macro/modified/mod_rna_peptide.ket:SUCCEED
-macro/peptide-rna/peptide-rna.ket:SUCCEED
-macro/peptide-rna/peptide-rna-ac.ket:SUCCEED
-macro/polyphosphate/polyphosphate_rna.ket:SUCCEED
-macro/sa-mono.ket:SUCCEED
-macro/terminators/terms_peptide.ket:SUCCEED
-mon_long_id.ket:SUCCEED
-pepchem.ket:SUCCEED
-peptides.ket:SUCCEED
-query_explicit_val.ket:SUCCEED
-rna_mod.ket:SUCCEED
-sgroup_class.ket:SUCCEED
-sgroups_mul.ket:SUCCEED
-suplabel.ket:SUCCEED
-taspoglutide.ket:SUCCEED
-thymine.ket:SUCCEED
-empty_apid.ket:SUCCEED
-ket-reaction-arrow.ket:SUCCEED
+3068-star-issue.mol:SUCCEED
+3178-any-bond.mol:SUCCEED
+3227-copolymer.mol:SUCCEED
+3343-dir-expanded.mol:SUCCEED
+5amd.mol:SUCCEED
+accl_no_class.mol:SUCCEED
+acgt_1412.mol:SUCCEED
+anacyclamide.mol:SUCCEED
+chem.mol:SUCCEED
+chem_rna_hydro.mol:SUCCEED
+conj_no_class.mol:SUCCEED
+conjugate.mol:SUCCEED
+cysteine.mol:SUCCEED
+dala.mol:SUCCEED
+dcysteine.mol:SUCCEED
+dna_mod.mol:SUCCEED
+dthymine.mol:SUCCEED
+exp-valence-0.mol:SUCCEED
+flip_rotate.mol:SUCCEED
+flip_rotate_2000.mol:SUCCEED
+flip_rotate_rna.mol:SUCCEED
+fmoc.mol:SUCCEED
+hydro_atp_ch.mol:SUCCEED
+issue_1476.mol:SUCCEED
+issue_2699_rlogic.mol:SUCCEED
+issue_2702.mol:SUCCEED
+macro/R2R3R4.mol:SUCCEED
+macro/conjugates/pep-chem-rna.mol:SUCCEED
+macro/conjugates/peptide_rna.mol:SUCCEED
+macro/dendromers/dendro-peptide.mol:SUCCEED
+macro/disulfide/disulfide_peptide_cycle.mol:SUCCEED
+macro/hundred-monomers.mol:SUCCEED
+macro/left_phosphate/left_phosphate.mol:SUCCEED
+macro/linear/linear_dna.mol:SUCCEED
+macro/linear/linear_multi.mol:SUCCEED
+macro/linear/linear_peptide.mol:SUCCEED
+macro/linear/linear_rna.mol:SUCCEED
+macro/modified/mod_dna.mol:SUCCEED
+macro/modified/mod_peptide.mol:SUCCEED
+macro/modified/mod_rna.mol:SUCCEED
+macro/modified/mod_rna_peptide.mol:SUCCEED
+macro/peptide-rna/peptide-rna.mol:SUCCEED
+macro/peptide-rna/peptide-rna-ac.mol:SUCCEED
+macro/polyphosphate/polyphosphate_rna.mol:SUCCEED
+macro/sa-mono.mol:SUCCEED
+macro/terminators/terms_peptide.mol:SUCCEED
+mon_long_id.mol:SUCCEED
+pepchem.mol:SUCCEED
+peptides.mol:SUCCEED
+query_explicit_val.mol:SUCCEED
+rna_mod.mol:SUCCEED
+sgroup_class.mol:SUCCEED
+sgroups_mul.mol:SUCCEED
+suplabel.mol:SUCCEED
+taspoglutide.mol:SUCCEED
+thymine.mol:SUCCEED
+empty_apid.mol:SUCCEED
+ket-reaction-arrow.mol:SUCCEED

api/tests/integration/ref/formats/ket_to_seq3letter.py.out

@@ -1,4 +1,4 @@
 *** KET to 3 LETTER SEQUENCE ***
-peptides_3letter : SUCCEED
+peptides_3letter.seq3:SUCCEED
 Test 'issue_3200': got expected error 'Only amino acids can be saved as three letter amino acid codes'
 Test 'peptides_molecule': got expected error 'Sequence saver: Can't save micro-molecules to sequence format'

api/tests/integration/ref/formats/ket_w_mult_group2mol.py.out

@@ -1,2 +1,2 @@
 *** KET to MOL ***
-ket_with_mult_group.ket:SUCCEED
+ket_with_mult_group.mol:SUCCEED