fix: creating molecules with invalid molfile using faulty smiles #2255

adambasha0 · 2024-12-06T16:15:58Z

ensure the status of request to pubchem for getting mol from smiles is OK.
Otherwise return nil

github-actions · 2024-12-06T16:17:23Z

app/api/chemotion/molecule_api.rb

@@ -42,15 +42,16 @@ class MoleculeAPI < Grape::API
            molfile = babel_info[:molfile] if babel_info
            begin
              rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
-              rd_mol = rw_mol.mol_to_mol_block  unless rw_mol.nil?
+              rd_mol = rw_mol.mol_to_mol_block unless rw_mol.nil?


Metrics/ClassLength: Class has too many lines. [291/200]

github-actions · 2024-12-06T16:36:48Z

LCOV of commit `c5bf635` during Continuous Integration #4208

Summary coverage rate:
  lines......: 65.5% (14059 of 21452 lines)
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github-actions · 2024-12-09T11:13:08Z

spec/lib/chemotion/molfile_validation_spec.rb

+      let(:faulty_smiles) { Chemotion::OpenBabelService.get_smiles_from_molfile(invalid_molfile) }
+
+      before do
+        allow(Chemotion::PubchemService).to receive(:molfile_from_smiles).with(faulty_smiles).and_return(corrupt_molfile)


Layout/LineLength: Line is too long. [121/120]

github-actions · 2024-12-09T12:17:55Z

LCOV of commit `648c42c` during Continuous Integration #4221

Summary coverage rate:
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github-actions · 2024-12-10T08:38:00Z

LCOV of commit `d2fb6be` during Continuous Integration #4226

Summary coverage rate:
  lines......: 66.4% (14232 of 21426 lines)
  functions..: no data found
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Files changed coverage rate: n/a

github-actions · 2024-12-12T09:16:58Z

app/api/chemotion/molecule_api.rb

@@ -42,15 +42,15 @@ class MoleculeAPI < Grape::API
            molfile = babel_info[:molfile] if babel_info
            begin
              rw_mol = RDKitChem::RWMol.mol_from_smiles(smiles)
-              rd_mol = rw_mol.mol_to_mol_block  unless rw_mol.nil?
+              rd_mol = rw_mol.mol_to_mol_block unless rw_mol.nil?


Metrics/ClassLength: Class has too many lines. [290/200]

github-actions · 2024-12-12T09:36:33Z

LCOV of commit `b17441a` during Continuous Integration #4237

Summary coverage rate:
  lines......: 66.5% (14249 of 21424 lines)
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github-actions · 2024-12-12T09:49:17Z

LCOV of commit `16992a1` during Continuous Integration #4238

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adambasha0 · 2024-12-12T12:21:35Z

This bug fix introduces a routine to do the following:

prevent the creation of faulty molecule (meaning invalid/corrupt molfile) using molecule :smiles API endpoint.

fix: return nil when response status is 400 for get_molfile_by_smiles

github-actions · 2025-01-09T20:45:34Z

lib/pub_chem.rb

@@ -80,7 +80,10 @@ def self.get_molfile_by_smiles(smiles)
    @auth = { username: '', password: '' }
    options = { timeout: 10, headers: { 'Content-Type' => 'text/json' } }
    encoded_smiles = URI.encode(smiles, '[]/()+-.@#=\\')
-    HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options).body
+    response = HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options)


Metrics/ModuleLength: Module has too many lines. [192/100]

github-actions · 2025-01-09T20:45:34Z

lib/pub_chem.rb

@@ -80,7 +80,10 @@ def self.get_molfile_by_smiles(smiles)
    @auth = { username: '', password: '' }
    options = { timeout: 10, headers: { 'Content-Type' => 'text/json' } }
    encoded_smiles = URI.encode(smiles, '[]/()+-.@#=\\')
-    HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options).body
+    response = HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options)


Style/StringConcatenation: Prefer string interpolation to string concatenation.

github-actions · 2025-01-09T20:45:35Z

lib/pub_chem.rb

@@ -80,7 +80,10 @@ def self.get_molfile_by_smiles(smiles)
    @auth = { username: '', password: '' }
    options = { timeout: 10, headers: { 'Content-Type' => 'text/json' } }
    encoded_smiles = URI.encode(smiles, '[]/()+-.@#=\\')
-    HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options).body
+    response = HTTParty.get(http_s + PUBCHEM_HOST + '/rest/pug/compound/smiles/' + encoded_smiles + '/record/SDF', options)


Layout/LineLength: Line is too long. [123/120]

github-actions · 2025-01-09T20:45:35Z

spec/api/molecule_api_spec.rb

+      before do
+        allow(Chemotion::OpenBabelService).to receive(:molfile_clear_hydrogens)
+          .with(any_args)
+          .and_return("Status: 400\n OpenBabel01092512342D\nMessage: Unable to standardize the given structure - perhaps some special charac\n  0  0  0  0  0  0  0  0  0  0999 V2000\nM  END\n")


Layout/LineLength: Line is too long. [193/120]

github-actions · 2025-01-09T20:45:35Z

spec/api/molecule_api_spec.rb

+      end
+
+      JSON.parse(File.read('spec/fixtures/structures/bad_smiles.json')).each_value do |data|
+        context 'when testing SMILES entry' do


RSpec/NestedGroups: Maximum example group nesting exceeded [4/3].

github-actions · 2025-01-09T20:45:35Z

spec/spec_helper.rb

+    error_body = "<<~BODY
+      Status: 400
+      Code: PUGREST.BadRequest
+      Message: Unable to standardize the given structure - perhaps some special characters need to be escaped or data packed in a MIME form?


Layout/LineLength: Line is too long. [140/120]

github-actions · 2025-01-09T21:05:59Z

LCOV of commit `4cd48c2` during Continuous Integration #4294

Summary coverage rate:
  lines......: 67.1% (14469 of 21571 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

github-actions · 2025-01-10T09:04:52Z

LCOV of commit `bbaa130` during Continuous Integration #4296

Summary coverage rate:
  lines......: 67.1% (14471 of 21571 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

github-actions · 2025-01-10T09:21:55Z

LCOV of commit `5930336` during Continuous Integration #4295

Summary coverage rate:
  lines......: 67.1% (14470 of 21570 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

adambasha0 self-assigned this Dec 6, 2024

adambasha0 added the bug label Dec 6, 2024

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adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch 2 times, most recently from d057483 to d2fb6be Compare December 10, 2024 08:16

adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch from d2fb6be to b17441a Compare December 12, 2024 09:15

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adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch from b17441a to 16992a1 Compare December 12, 2024 09:27

adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch from 16992a1 to 4cd48c2 Compare January 9, 2025 20:43

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adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch from 4cd48c2 to 5930336 Compare January 10, 2025 08:22

fix: prevent create molecules with invalid molfile using faulty smiles

bbaa130

adambasha0 force-pushed the prevent-creation-of-faulty-molecules-with-incorrect-smiles branch from 5930336 to bbaa130 Compare January 10, 2025 08:43

PiTrem changed the title ~~fix: prevent create molecules with invalid molfile using faulty smiles~~ fix: creating molecules with invalid molfile using faulty smiles Jan 16, 2025

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fix: creating molecules with invalid molfile using faulty smiles #2255

fix: creating molecules with invalid molfile using faulty smiles #2255

adambasha0 commented Dec 6, 2024 •

edited by PiTrem

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fix: creating molecules with invalid molfile using faulty smiles #2255

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fix: creating molecules with invalid molfile using faulty smiles #2255

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adambasha0 commented Dec 6, 2024 • edited by PiTrem Loading

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LCOV of commit c5bf635 during Continuous Integration #4208

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github-actions bot commented Dec 9, 2024

LCOV of commit 648c42c during Continuous Integration #4221

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LCOV of commit d2fb6be during Continuous Integration #4226

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LCOV of commit b17441a during Continuous Integration #4237

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LCOV of commit 16992a1 during Continuous Integration #4238

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LCOV of commit 4cd48c2 during Continuous Integration #4294

github-actions bot commented Jan 10, 2025

LCOV of commit bbaa130 during Continuous Integration #4296

github-actions bot commented Jan 10, 2025

LCOV of commit 5930336 during Continuous Integration #4295

adambasha0 commented Dec 6, 2024 •

edited by PiTrem

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LCOV of commit `c5bf635` during Continuous Integration #4208

LCOV of commit `648c42c` during Continuous Integration #4221

LCOV of commit `d2fb6be` during Continuous Integration #4226

LCOV of commit `b17441a` during Continuous Integration #4237

LCOV of commit `16992a1` during Continuous Integration #4238

adambasha0 commented Dec 12, 2024 •

edited

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LCOV of commit `4cd48c2` during Continuous Integration #4294

LCOV of commit `bbaa130` during Continuous Integration #4296

LCOV of commit `5930336` during Continuous Integration #4295