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feat: import samples additional attributes #2214

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feat: import samples additional attributes #2214

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@adambasha0 adambasha0 commented Oct 15, 2024 •
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  • rather 1-story 1-commit than sub-atomic commits

  • commit title is meaningful => git history search

  • commit description is helpful => helps the reviewer to understand the changes

  • code is up-to-date with the latest developments of the target branch (rebased to it or whatever) => ⏩-merge for linear history is favoured

  • added code is linted

  • tests are passing (at least locally): we still have some random test failure on CI. thinking of asking spec/examples.txt to be commited

  • in case the changes are visible to the end-user,  video or screenshots should be added to the PR => helps with user testing

  • testing coverage improvement is improved.

  • CHANGELOG :  add a bullet point on top (optional: reference to github issue/PR )

  • parallele PR for documentation  on docusaurus  if the feature/fix is tagged for a release

@adambasha0 adambasha0 self-assigned this Oct 15, 2024
github-actions[bot]
github-actions bot reviewed Oct 15, 2024
View reviewed changes
app/api/helpers/report_helpers.rb
@@ -556,7 +556,10 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false)
# deleted_at: ['wp.deleted_at', nil, 10],
molecule_name: ['mn."name"', '"molecule name"', 1],
molarity_value: ['s."molarity_value"', '"molarity_value"', 0],
molarity_unit: ['s."molarity_unit"', '"molarity_unit"', 0],
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Metrics/ModuleLength: Module has too many lines. [615/100]

lib/export/export_excel.rb
@@ -127,6 +127,12 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/AbcSize: Assignment Branch Condition size for filter_with_permission_and_detail_level is too high. [<13, 34, 28> 45.92/25]

lib/export/export_excel.rb
@@ -127,6 +127,12 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/CyclomaticComplexity: Cyclomatic complexity for filter_with_permission_and_detail_level is too high. [20/7]

lib/export/export_excel.rb
@@ -127,6 +127,12 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/MethodLength: Method has too many lines. [32/30]

lib/export/export_excel.rb
@@ -127,6 +127,12 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/PerceivedComplexity: Perceived complexity for filter_with_permission_and_detail_level is too high. [22/8]

lib/import/import_sdf.rb
sample['dry_solvent'] = row['dry_solvent'] if row['dry_solvent'].present?
sample['purity'] = row['purity'] if row['purity'].present?
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Metrics/BlockLength: Block has too many lines. [89/25]

spec/lib/export/export_excel_spec.rb Outdated
sample_json['refractive_index'] = refractive_index
sample_json['molarity_value'] = '2.45'
sample_json['molarity_unit'] = 'M'
exporter.instance_eval('@headers =["melting pt", "flash point", "refractive index", "molarity"]', __FILE__, __LINE__)
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Layout/LineLength: Line is too long. [123/120]

spec/lib/import/import_sdf_spec.rb Outdated
rows: [{
'inchikey' => 'DTHMTBUWTGVEFG-DDWIOCJRSA-N',
'molfile' => Rails.root.join('spec/fixtures/mf_with_data_01.sdf').read,
'description' => "MOLECULE_NAME\n(R)-Methyl-2-amino-2-phenylacetate hydrochloride ?96%; (R)-(?)-2-Phenylglycine methyl ester hydrochloride\n\nSAFETY_R_S\nH: 319; P: 305+351+338\n\nSMILES_STEREO\n[Cl-].COC(=O)[C@H](N)c1ccccc1.[H+]\n",
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Layout/LineLength: Line is too long. [241/120]

spec/lib/import/import_sdf_spec.rb Outdated
{ inchikey: 'DTHMTBUWTGVEFG-DDWIOCJRSA-N',
is_partial: false,
molfile_version: 'V2000',
}
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Layout/MultilineHashBraceLayout: Closing hash brace must be on the same line as the last hash element when opening brace is on the same line as the first hash element.

spec/lib/import/import_sdf_spec.rb Outdated
{ inchikey: 'DTHMTBUWTGVEFG-DDWIOCJRSA-N',
is_partial: false,
molfile_version: 'V2000',
}
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Style/TrailingCommaInArguments: Put a comma after the last parameter of a multiline method call.

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LCOV of commit f97123b during Continuous Integration #4003

Summary coverage rate:
  lines......: 65.6% (14117 of 21517 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@adambasha0 adambasha0 linked an issue Oct 15, 2024 that may be closed by this pull request
Add purity and additional fields to chemical import feature and XLSX template #1644
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LCOV of commit b1fe655 during Continuous Integration #4019

Summary coverage rate:
  lines......: 65.7% (14133 of 21517 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

github-actions[bot]
github-actions bot reviewed Oct 16, 2024
View reviewed changes
lib/import/import_chemicals.rb Outdated
key = to_snake_case(column_header)
format_value = value.strip
def self.build_chemical_data(map_column, chemical, key, formated_value)

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Layout/EmptyLinesAroundMethodBody: Extra empty line detected at method body beginning.

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LCOV of commit 7734b77 during Continuous Integration #4028

Summary coverage rate:
  lines......: 65.6% (14128 of 21530 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@PiTrem PiTrem marked this pull request as draft October 29, 2024 08:27
@adambasha0 adambasha0 force-pushed the enhance-import-samples-feature branch from 7734b77 to f0f7636 Compare November 5, 2024 15:55
github-actions[bot]
github-actions bot reviewed Nov 5, 2024
View reviewed changes
lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/AbcSize: Assignment Branch Condition size for filter_with_permission_and_detail_level is too high. [<13, 35, 30> 47.9/25]

lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/CyclomaticComplexity: Cyclomatic complexity for filter_with_permission_and_detail_level is too high. [21/7]

lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/MethodLength: Method has too many lines. [34/30]

lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/PerceivedComplexity: Perceived complexity for filter_with_permission_and_detail_level is too high. [23/8]

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github-actions bot commented Nov 5, 2024

LCOV of commit f0f7636 during Continuous Integration #4108

Summary coverage rate:
  lines......: 65.6% (14120 of 21515 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@adambasha0 adambasha0 force-pushed the enhance-import-samples-feature branch from f0f7636 to 0c7a6b7 Compare November 5, 2024 16:46
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github-actions bot commented Nov 5, 2024

LCOV of commit 0c7a6b7 during Continuous Integration #4109

Summary coverage rate:
  lines......: 65.6% (14117 of 21511 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@adambasha0
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adambasha0 commented Nov 6, 2024 •
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enhancement to import fields like Location, Melting Point, Boiling Point, flash point, refractive index, density, and molarity and chemical volume with units, and fix existing bugs.

@adambasha0
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Chemotion.dev.12.webm

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github-actions bot commented Nov 6, 2024

LCOV of commit 485f974 during Continuous Integration #4115

Summary coverage rate:
  lines......: 65.6% (14117 of 21511 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@PiTrem PiTrem changed the title enhance import samples feature and spec tests and additional samples attributes (flash point and refractive index) feat: import samples additional attributes - flash point and refractive index Nov 7, 2024
@adambasha0 adambasha0 force-pushed the enhance-import-samples-feature branch from 485f974 to 17dda99 Compare November 7, 2024 14:57
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github-actions bot commented Nov 7, 2024

LCOV of commit 17dda99 during Continuous Integration #4124

Summary coverage rate:
  lines......: 65.6% (14118 of 21510 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@PiTrem PiTrem marked this pull request as ready for review January 8, 2025 08:32
@adambasha0 adambasha0 changed the title feat: import samples additional attributes - flash point and refractive index feat: import samples additional attributes Jan 16, 2025
@PiTrem PiTrem self-assigned this Jan 16, 2025
@PiTrem PiTrem added this to the v2.0.0 milestone Jan 21, 2025
@adambasha0 adambasha0 force-pushed the enhance-import-samples-feature branch from 17dda99 to adc1c66 Compare January 23, 2025 19:00
github-actions[bot]
github-actions bot reviewed Jan 23, 2025
View reviewed changes
app/api/helpers/report_helpers.rb
@@ -556,7 +556,10 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false)
# deleted_at: ['wp.deleted_at', nil, 10],
molecule_name: ['mn."name"', '"molecule name"', 1],
molarity_value: ['s."molarity_value"', '"molarity_value"', 0],
molarity_unit: ['s."molarity_unit"', '"molarity_unit"', 0],
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Metrics/ModuleLength: Module has too many lines. [617/100]

lib/export/export_chemicals.rb Outdated
product_link_thermofischer host_building host_room host_cabinet host_group important_notes
borrowed_by current_building current_room current_cabinet current_group disposal_info
chemical_sample_id cas status vendor order_number amount volume price person required_date
ordered_date storage_temperature expiration_date required_by pictograms h_statements p_statements safety_sheet_link_merck
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Layout/LineLength: Line is too long. [127/120]

lib/export/export_chemicals.rb Outdated
format_chemical_column = ['p statements', 'h statements', 'amount', 'storage temperature',
'safety sheet link thermofischer', 'safety sheet link merck',
'product link thermofischer', 'product link merck'].freeze
format_chemical_column = ['p statements', 'h statements', 'amount', 'volume', 'storage temperature', 'safety sheet link thermofischer',
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Layout/LineLength: Line is too long. [141/120]

lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/CyclomaticComplexity: Cyclomatic complexity for filter_with_permission_and_detail_level is too high. [21/7]

lib/export/export_excel.rb
@@ -127,6 +127,14 @@ def filter_with_permission_and_detail_level(sample)
string.split(',').join(' - ')
elsif column == 'solvent'
extract_label_from_solvent_column(sample[column]) || ''
elsif column == 'refractive index'
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Metrics/PerceivedComplexity: Perceived complexity for filter_with_permission_and_detail_level is too high. [23/8]

lib/export/export_sdf.rb
column_data = format_field(column, sample[column])
data.concat(column_data)
end
data = concatenate_data(sample, data)
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Metrics/CyclomaticComplexity: Cyclomatic complexity for filter_with_permission_and_detail_level is too high. [10/7]

lib/export/export_sdf.rb
column_data = format_field(column, sample[column])
data.concat(column_data)
end
data = concatenate_data(sample, data)
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Metrics/PerceivedComplexity: Perceived complexity for filter_with_permission_and_detail_level is too high. [11/8]

lib/import/import_sdf.rb
sample['dry_solvent'] = row['dry_solvent'] if row['dry_solvent'].present?
sample['purity'] = row['purity'] if row['purity'].present?
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Metrics/CyclomaticComplexity: Cyclomatic complexity for create_samples is too high. [66/7]

lib/import/import_sdf.rb
sample['dry_solvent'] = row['dry_solvent'] if row['dry_solvent'].present?
sample['purity'] = row['purity'] if row['purity'].present?
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Metrics/PerceivedComplexity: Perceived complexity for create_samples is too high. [71/8]

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LCOV of commit 33c374f during Continuous Integration #4354

Summary coverage rate:
  lines......: 67.0% (14517 of 21673 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@adambasha0 adambasha0 force-pushed the enhance-import-samples-feature branch from 33c374f to 9daaccb Compare January 24, 2025 09:21
github-actions[bot]
github-actions bot reviewed Jan 24, 2025
View reviewed changes
lib/export/export_chemicals.rb
'safety sheet link thermofischer', 'safety sheet link merck',
'product link thermofischer', 'product link merck'].freeze
format_chemical_column = ['p statements', 'h statements', 'amount', 'volume', 'storage temperature',
'safety sheet link thermofischer', 'safety sheet link merck', 'product link thermofischer',
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Layout/LineLength: Line is too long. [123/120]

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LCOV of commit 9daaccb during Continuous Integration #4355

Summary coverage rate:
  lines......: 67.0% (14517 of 21673 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

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@TasnimMehzabin TasnimMehzabin TasnimMehzabin approved these changes

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Add purity and additional fields to chemical import feature and XLSX template
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@adambasha0 @TasnimMehzabin @PiTrem