feat: Rdkit cart substructure search #2055

headri · 2024-08-05T08:43:38Z

Upgraded the Postgres 14 database to Postgres 16 with the RDKit cartridge. This includes:

The Dockerfile for the new database image
A seed file to call the migrations on demand
migrations to create the necessary tables

Added a new structured search option with the new RDKit.

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

@@ -110,45 +112,61 @@ class Sample < ApplicationRecord
  pg_search_scope :search_by_cas, against: { xref: 'cas' }

  # scopes for suggestions
-  scope :by_residues_custom_info, ->(info, val) { joins(:residues).where("residues.custom_info -> '#{info}' ILIKE ?", "%#{sanitize_sql_like(val)}%")}
+  scope :by_residues_custom_info, lambda { |info, val|
+                                    joins(:residues).where("residues.custom_info -> '#{info}' ILIKE ?", "%#{sanitize_sql_like(val)}%")


Layout/LineLength: Line is too long. [134/120]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

+                                     joins(:reactions_product_samples).where(reactions_samples: { reaction_id: ids })
+                                   }
+  scope :by_reaction_material_ids, lambda { |ids|
+                                     joins(:reactions_starting_material_samples).where(reactions_samples: { reaction_id: ids })


Layout/LineLength: Line is too long. [127/120]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

-  scope :sample_or_startmat_or_products, -> {
-    joins("left join reactions_samples rs on rs.sample_id = samples.id").where("rs.id isnull or rs.\"type\" in ('ReactionsProductSample', 'ReactionsStartingMaterialSample')")
+  scope :sample_or_startmat_or_products, lambda {
+    joins('left join reactions_samples rs on rs.sample_id = samples.id').where("rs.id isnull or rs.\"type\" in ('ReactionsProductSample', 'ReactionsStartingMaterialSample')")


Layout/LineLength: Line is too long. [174/120]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

-      nil
+    if sample_svg_file.present?
+      "/images/samples/#{sample_svg_file}"
+    elsif molecule&.molecule_svg_file&.present?


Lint/RedundantSafeNavigation: Redundant safe navigation detected, use . instead.

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

  end

  def init_elemental_compositions
-    residue = self.residues[0]
-    return unless molecule_sum_formular.present?
+    residue = residues[0]


Metrics/AbcSize: Assignment Branch Condition size for init_elemental_compositions is too high. [<10, 34, 17> 39.31/25]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

  end

  def init_elemental_compositions
-    residue = self.residues[0]
-    return unless molecule_sum_formular.present?
+    residue = residues[0]


Metrics/PerceivedComplexity: Perceived complexity for init_elemental_compositions is too high. [15/8]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

    end
  end

  def check_molfile_polymer_section
    return if decoupled
-    return unless self.molfile.include? 'R#'
+    return unless molfile.include? 'R#'


Metrics/AbcSize: Assignment Branch Condition size for check_molfile_polymer_section is too high. [<9, 37, 10> 39.37/25]

github-actions · 2024-08-06T09:07:14Z

app/models/sample.rb

    end
  end

  def check_molfile_polymer_section
    return if decoupled
-    return unless self.molfile.include? 'R#'
+    return unless molfile.include? 'R#'


Metrics/CyclomaticComplexity: Cyclomatic complexity for check_molfile_polymer_section is too high. [10/7]

github-actions · 2024-08-06T09:07:15Z

app/models/sample.rb

    end
  end

  def check_molfile_polymer_section
    return if decoupled
-    return unless self.molfile.include? 'R#'
+    return unless molfile.include? 'R#'


Metrics/PerceivedComplexity: Perceived complexity for check_molfile_polymer_section is too high. [11/8]

github-actions · 2024-08-06T09:07:15Z

app/models/sample.rb

-    self.creator.increment_counter 'samples'
+    return unless /^#{creator.name_abbreviation}-\d+$/.match?(short_label)
+
+    creator.increment_counter 'samples'


Rails/SkipsModelValidations: Avoid using increment_counter because it skips validations.

JanCBrammer

The substructure search does not seem to be tested on the current main. This PR would be a good opportunity to add these tests (for the existing substructure search methods as well as the new one that's being added here).

CHANGELOG.md

app/packs/src/components/navigation/search/Search.js

config/application.rb

JanCBrammer · 2024-08-06T12:09:20Z

app/api/chemotion/search_api.rb

@@ -97,10 +97,13 @@ def sample_structure_search(c_id = @c_id, not_permitted = @dl_s && @dl_s < 1)

        # TODO: implement this: http://pubs.acs.org/doi/abs/10.1021/ci600358f
        scope =
-          if params[:selection][:search_type] == 'similar'
+          case params[:selection][:search_type]


This switch case seems to be replicating the switch case under usecases/search/structure_search.rb. Why?

usecases/search/structure_search.rb removed

github-actions · 2024-08-08T08:34:18Z

spec/api/chemotion/search_api_spec.rb

  let(:screen) { create(:screen, name: 'Screen') }
  let(:other_screen) { create(:screen, name: 'Other Screen') }
  let!(:cell_line) { create(:cellline_sample, name: 'another-cellline-search-example', collections: [collection]) }
+  let!(:mof3000_1) { Rails.root.join('spec/fixtures/mof_v3000_1.mol').read }


RSpec/IndexedLet: This let statement uses index in its name. Please give it a meaningful name.

github-actions · 2024-08-08T08:34:18Z

spec/api/chemotion/search_api_spec.rb

  let(:screen) { create(:screen, name: 'Screen') }
  let(:other_screen) { create(:screen, name: 'Other Screen') }
  let!(:cell_line) { create(:cellline_sample, name: 'another-cellline-search-example', collections: [collection]) }
+  let!(:mof3000_1) { Rails.root.join('spec/fixtures/mof_v3000_1.mol').read }


Naming/VariableNumber: Use normalcase for symbol numbers.

github-actions · 2024-08-08T08:34:18Z

spec/api/chemotion/search_api_spec.rb

  let(:screen) { create(:screen, name: 'Screen') }
  let(:other_screen) { create(:screen, name: 'Other Screen') }
  let!(:cell_line) { create(:cellline_sample, name: 'another-cellline-search-example', collections: [collection]) }
+  let!(:mof3000_1) { Rails.root.join('spec/fixtures/mof_v3000_1.mol').read }
+  let!(:mof3000_2) { Rails.root.join('spec/fixtures/mof_v3000_2.mol').read }


RSpec/IndexedLet: This let statement uses index in its name. Please give it a meaningful name.

github-actions · 2024-08-08T08:34:18Z

spec/api/chemotion/search_api_spec.rb

  let(:screen) { create(:screen, name: 'Screen') }
  let(:other_screen) { create(:screen, name: 'Other Screen') }
  let!(:cell_line) { create(:cellline_sample, name: 'another-cellline-search-example', collections: [collection]) }
+  let!(:mof3000_1) { Rails.root.join('spec/fixtures/mof_v3000_1.mol').read }
+  let!(:mof3000_2) { Rails.root.join('spec/fixtures/mof_v3000_2.mol').read }


Naming/VariableNumber: Use normalcase for symbol numbers.

Required: RDKit library installed. The system variable: One system environment variable PG_CART_INSTALLED is added with the default value as false. If RDKit is installed and you want to turn on this feature for user, remember to set RDKIT_INSTALLED as true. The migration files: 1. They are executed only if RDKit is installed in Postgresql. 2. A new column is added to the table: samples. The script for generating the data into the new column is included.

JanCBrammer · 2024-08-13T10:46:30Z

app/api/chemotion/search_api.rb

            Sample.by_collection_id(c_id).search_by_fingerprint_sub(molfile)
+          when 'subRDKit'
+            Sample.by_collection_id(c_id).search_by_rdkit_sub(molfile)
          end


We discussed adding a fallback / default case for invalid search_type.

The search type has a whitelist: "optional :search_type, type: String, values: %w[similar sub subRDKit]"
Do we still need a fallback / default case?

JanCBrammer · 2024-08-13T10:55:45Z

db/seeds/development.rb

@@ -1,4 +1,5 @@
 require_relative "shared/admin.seed.rb"
 require_relative "shared/molecules.seed.rb"
-require_relative "shared/text_templates.seed.rb"
+# require_relative "shared/text_templates.seed.rb"


Add "TODO" comment with a reminder to comment this back in or remove it.
Maybe also add context on why this is commented out.

JanCBrammer

How will the RDKit cartridge be introduced in test (CI) and production environments?
This PR sets it up for the development environment. Question also for @PiTrem.
Is there going to be documentation over at https://github.com/ComPlat/chemotion_saurus?

app/api/chemotion/search_api.rb

app/usecases/search/structure_search.rb

docker-compose.dev.yml

JanCBrammer

I've clicked through the feature in the UI. It seems to be working fine.

db/seeds/development.rb

headri requested review from PiTrem and JanCBrammer August 5, 2024 08:44

PiTrem changed the title ~~Rdkit cart substructure search~~ feat: Rdkit cart substructure search Aug 5, 2024

PiTrem changed the base branch from main to v1.9 August 5, 2024 11:20

PiTrem changed the base branch from v1.9 to main August 6, 2024 07:29

headri force-pushed the rdkit_cart_substructure_search branch from f0e03e4 to e461766 Compare August 6, 2024 09:05

github-actions bot reviewed Aug 6, 2024

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JanCBrammer reviewed Aug 6, 2024

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cllde8 and others added 12 commits August 8, 2024 10:47

feat: added postgres 16 with rdkit

341419b

feat: rdkit frontend switchable by env var

33011db

feat: sql statement for rdkit search

e52370a

added postgres dockerfile

2643193

reafctor: remove unneeded packages

a957ac6

feat: added seed and updated trigger

eee482a

feat: added trigger generation to seed

4cb0a54

corrected search clause & rubocop changes

c27daa0

fix: corrected bug in update trigger

3b069bb

refactor: changed env var to PG_CARTRIDGE=RDKit

a54abd1

Added tests for structured search

027895b

headri force-pushed the rdkit_cart_substructure_search branch from 5e3c6ec to 027895b Compare August 8, 2024 08:49

refactor: added rdkit seed to migration

15c1f3f

JanCBrammer reviewed Aug 13, 2024

View reviewed changes

JanCBrammer requested changes Aug 13, 2024

View reviewed changes

refactor: removed usecase structure search

2b23d03

JanCBrammer reviewed Aug 13, 2024

View reviewed changes

app/api/chemotion/search_api.rb Show resolved Hide resolved

JanCBrammer reviewed Aug 13, 2024

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app/usecases/search/structure_search.rb Show resolved Hide resolved

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docker-compose.dev.yml Outdated Show resolved Hide resolved

fix: corrected fallback for env fetch

2921577

JanCBrammer reviewed Aug 22, 2024

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headri and others added 2 commits August 27, 2024 09:40

Merge branch 'main' into rdkit_cart_substructure_search

df9b4fc

added seed to test and prod

38a719d

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feat: Rdkit cart substructure search #2055

feat: Rdkit cart substructure search #2055

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feat: Rdkit cart substructure search #2055

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