pharmaobservatory 0.1.3 → 0.1.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (175) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +101 -4
  3. data/docs/BiomarkerBqpAssertionsRow.md +1 -1
  4. data/docs/BiomarkerEvidenceRow.md +1 -1
  5. data/docs/BiomarkerLiteratureRow.md +1 -1
  6. data/docs/BiomarkerRelationsResponse.md +58 -0
  7. data/docs/BiomarkerRelationsRow.md +54 -0
  8. data/docs/BiomarkerSampleCoverageResponse.md +58 -0
  9. data/docs/BiomarkerSampleCoverageRow.md +36 -0
  10. data/docs/BiomarkerSamplePrevalenceResponse.md +58 -0
  11. data/docs/BiomarkerSamplePrevalenceRow.md +56 -0
  12. data/docs/BiomarkerValidationResponse.md +58 -0
  13. data/docs/BiomarkerValidationRow.md +70 -0
  14. data/docs/BiomarkersApi.md +320 -0
  15. data/docs/BiomarkersRow.md +2 -2
  16. data/docs/CellLinesRow.md +1 -1
  17. data/docs/CompaniesApi.md +410 -0
  18. data/docs/CompaniesRecord.md +1 -1
  19. data/docs/CompaniesRecordAttributes.md +18 -0
  20. data/docs/CompaniesRow.md +7 -3
  21. data/docs/CompanyAssetsResponse.md +58 -0
  22. data/docs/CompanyAssetsRow.md +42 -0
  23. data/docs/CompanyFundingEventsResponse.md +58 -0
  24. data/docs/CompanyFundingEventsRow.md +62 -0
  25. data/docs/CompanyFundingSummaryResponse.md +58 -0
  26. data/docs/CompanyFundingSummaryRow.md +46 -0
  27. data/docs/CompanyProgramsRow.md +2 -2
  28. data/docs/ConditionAdverseEventsResponse.md +58 -0
  29. data/docs/ConditionAdverseEventsRow.md +24 -0
  30. data/docs/ConditionBurdenResponse.md +58 -0
  31. data/docs/ConditionBurdenRow.md +32 -0
  32. data/docs/ConditionDeliveryResponse.md +58 -0
  33. data/docs/ConditionDeliveryRow.md +44 -0
  34. data/docs/ConditionDrugsResponse.md +58 -0
  35. data/docs/ConditionDrugsRow.md +26 -0
  36. data/docs/ConditionPrevalenceResponse.md +58 -0
  37. data/docs/ConditionPrevalenceRow.md +62 -0
  38. data/docs/ConditionPublicationsResponse.md +58 -0
  39. data/docs/ConditionPublicationsRow.md +32 -0
  40. data/docs/ConditionSitesResponse.md +58 -0
  41. data/docs/ConditionSitesRow.md +28 -0
  42. data/docs/ConditionTrialsResponse.md +58 -0
  43. data/docs/ConditionTrialsRow.md +58 -0
  44. data/docs/ConditionsApi.md +953 -0
  45. data/docs/ConditionsRecord.md +38 -0
  46. data/docs/ConditionsRecordAttributes.md +20 -0
  47. data/docs/ConditionsResponse.md +58 -0
  48. data/docs/ConditionsRow.md +32 -0
  49. data/docs/DrugPatentCliffRow.md +1 -1
  50. data/docs/InstitutionalHoldingsRow.md +3 -1
  51. data/docs/LegalEntitiesApi.md +160 -0
  52. data/docs/LegalEntitiesRow.md +1 -1
  53. data/docs/OwnershipPositionsResponse.md +58 -0
  54. data/docs/OwnershipPositionsRow.md +100 -0
  55. data/docs/PdufaDatesRow.md +2 -2
  56. data/docs/SiteCroTrialsRow.md +1 -1
  57. data/docs/SiteTrialConditionsRow.md +1 -1
  58. data/docs/SiteTrialDrugsRow.md +1 -1
  59. data/docs/SiteTrialsRow.md +1 -1
  60. data/docs/SponsorRecruitmentByPhaseRow.md +2 -2
  61. data/docs/SponsorRecruitmentDurationRow.md +1 -1
  62. data/docs/SponsorTrialsRow.md +2 -2
  63. data/docs/TrialAdverseEventsResponse.md +58 -0
  64. data/docs/TrialAdverseEventsRow.md +28 -0
  65. data/docs/TrialChangesResponse.md +58 -0
  66. data/docs/TrialChangesRow.md +36 -0
  67. data/docs/TrialDeliveryResponse.md +58 -0
  68. data/docs/TrialDeliveryRow.md +64 -0
  69. data/docs/TrialDemographicsResponse.md +58 -0
  70. data/docs/TrialDemographicsRow.md +32 -0
  71. data/docs/TrialDrugsResponse.md +58 -0
  72. data/docs/TrialDrugsRow.md +30 -0
  73. data/docs/TrialEnrollmentHistoryResponse.md +58 -0
  74. data/docs/TrialEnrollmentHistoryRow.md +36 -0
  75. data/docs/TrialEnrollmentRateResponse.md +58 -0
  76. data/docs/TrialEnrollmentRateRow.md +58 -0
  77. data/docs/TrialExtractedEndpointsResponse.md +58 -0
  78. data/docs/TrialExtractedEndpointsRow.md +40 -0
  79. data/docs/TrialOutcomeMeasuresResponse.md +58 -0
  80. data/docs/TrialOutcomeMeasuresRow.md +28 -0
  81. data/docs/TrialSitesResponse.md +58 -0
  82. data/docs/TrialSitesRow.md +46 -0
  83. data/docs/TrialsApi.md +1033 -0
  84. data/docs/TrialsRecord.md +38 -0
  85. data/docs/TrialsRecordAttributes.md +24 -0
  86. data/docs/TrialsResponse.md +58 -0
  87. data/docs/TrialsRow.md +116 -0
  88. data/lib/pharmaobservatory/api/biomarkers_api.rb +336 -0
  89. data/lib/pharmaobservatory/api/companies_api.rb +455 -0
  90. data/lib/pharmaobservatory/api/conditions_api.rb +1001 -0
  91. data/lib/pharmaobservatory/api/legal_entities_api.rb +168 -0
  92. data/lib/pharmaobservatory/api/trials_api.rb +1085 -0
  93. data/lib/pharmaobservatory/models/biomarker_bqp_assertions_row.rb +1 -1
  94. data/lib/pharmaobservatory/models/biomarker_evidence_row.rb +1 -1
  95. data/lib/pharmaobservatory/models/biomarker_literature_row.rb +1 -1
  96. data/lib/pharmaobservatory/models/biomarker_relations_response.rb +478 -0
  97. data/lib/pharmaobservatory/models/biomarker_relations_row.rb +421 -0
  98. data/lib/pharmaobservatory/models/biomarker_sample_coverage_response.rb +478 -0
  99. data/lib/pharmaobservatory/models/biomarker_sample_coverage_row.rb +322 -0
  100. data/lib/pharmaobservatory/models/biomarker_sample_prevalence_response.rb +478 -0
  101. data/lib/pharmaobservatory/models/biomarker_sample_prevalence_row.rb +436 -0
  102. data/lib/pharmaobservatory/models/biomarker_validation_response.rb +478 -0
  103. data/lib/pharmaobservatory/models/biomarker_validation_row.rb +509 -0
  104. data/lib/pharmaobservatory/models/biomarkers_row.rb +2 -2
  105. data/lib/pharmaobservatory/models/cell_lines_row.rb +1 -1
  106. data/lib/pharmaobservatory/models/companies_record.rb +1 -1
  107. data/lib/pharmaobservatory/models/companies_record_attributes.rb +220 -0
  108. data/lib/pharmaobservatory/models/companies_row.rb +29 -7
  109. data/lib/pharmaobservatory/models/company_assets_response.rb +478 -0
  110. data/lib/pharmaobservatory/models/company_assets_row.rb +355 -0
  111. data/lib/pharmaobservatory/models/company_funding_events_response.rb +478 -0
  112. data/lib/pharmaobservatory/models/company_funding_events_row.rb +465 -0
  113. data/lib/pharmaobservatory/models/company_funding_summary_response.rb +478 -0
  114. data/lib/pharmaobservatory/models/company_funding_summary_row.rb +377 -0
  115. data/lib/pharmaobservatory/models/company_programs_row.rb +2 -2
  116. data/lib/pharmaobservatory/models/condition_adverse_events_response.rb +478 -0
  117. data/lib/pharmaobservatory/models/condition_adverse_events_row.rb +256 -0
  118. data/lib/pharmaobservatory/models/condition_burden_response.rb +478 -0
  119. data/lib/pharmaobservatory/models/condition_burden_row.rb +300 -0
  120. data/lib/pharmaobservatory/models/condition_delivery_response.rb +478 -0
  121. data/lib/pharmaobservatory/models/condition_delivery_row.rb +366 -0
  122. data/lib/pharmaobservatory/models/condition_drugs_response.rb +478 -0
  123. data/lib/pharmaobservatory/models/condition_drugs_row.rb +267 -0
  124. data/lib/pharmaobservatory/models/condition_prevalence_response.rb +478 -0
  125. data/lib/pharmaobservatory/models/condition_prevalence_row.rb +465 -0
  126. data/lib/pharmaobservatory/models/condition_publications_response.rb +478 -0
  127. data/lib/pharmaobservatory/models/condition_publications_row.rb +300 -0
  128. data/lib/pharmaobservatory/models/condition_sites_response.rb +478 -0
  129. data/lib/pharmaobservatory/models/condition_sites_row.rb +278 -0
  130. data/lib/pharmaobservatory/models/condition_trials_response.rb +478 -0
  131. data/lib/pharmaobservatory/models/condition_trials_row.rb +443 -0
  132. data/lib/pharmaobservatory/models/conditions_record.rb +385 -0
  133. data/lib/pharmaobservatory/models/conditions_record_attributes.rb +229 -0
  134. data/lib/pharmaobservatory/models/conditions_response.rb +478 -0
  135. data/lib/pharmaobservatory/models/conditions_row.rb +304 -0
  136. data/lib/pharmaobservatory/models/drug_patent_cliff_row.rb +1 -1
  137. data/lib/pharmaobservatory/models/institutional_holdings_row.rb +13 -2
  138. data/lib/pharmaobservatory/models/legal_entities_row.rb +1 -1
  139. data/lib/pharmaobservatory/models/ownership_positions_response.rb +478 -0
  140. data/lib/pharmaobservatory/models/ownership_positions_row.rb +674 -0
  141. data/lib/pharmaobservatory/models/pdufa_dates_row.rb +2 -2
  142. data/lib/pharmaobservatory/models/site_cro_trials_row.rb +1 -1
  143. data/lib/pharmaobservatory/models/site_trial_conditions_row.rb +1 -1
  144. data/lib/pharmaobservatory/models/site_trial_drugs_row.rb +1 -1
  145. data/lib/pharmaobservatory/models/site_trials_row.rb +1 -1
  146. data/lib/pharmaobservatory/models/sponsor_recruitment_by_phase_row.rb +2 -2
  147. data/lib/pharmaobservatory/models/sponsor_recruitment_duration_row.rb +1 -1
  148. data/lib/pharmaobservatory/models/sponsor_trials_row.rb +2 -2
  149. data/lib/pharmaobservatory/models/trial_adverse_events_response.rb +478 -0
  150. data/lib/pharmaobservatory/models/trial_adverse_events_row.rb +278 -0
  151. data/lib/pharmaobservatory/models/trial_changes_response.rb +478 -0
  152. data/lib/pharmaobservatory/models/trial_changes_row.rb +328 -0
  153. data/lib/pharmaobservatory/models/trial_delivery_response.rb +478 -0
  154. data/lib/pharmaobservatory/models/trial_delivery_row.rb +476 -0
  155. data/lib/pharmaobservatory/models/trial_demographics_response.rb +478 -0
  156. data/lib/pharmaobservatory/models/trial_demographics_row.rb +300 -0
  157. data/lib/pharmaobservatory/models/trial_drugs_response.rb +478 -0
  158. data/lib/pharmaobservatory/models/trial_drugs_row.rb +291 -0
  159. data/lib/pharmaobservatory/models/trial_enrollment_history_response.rb +478 -0
  160. data/lib/pharmaobservatory/models/trial_enrollment_history_row.rb +322 -0
  161. data/lib/pharmaobservatory/models/trial_enrollment_rate_response.rb +478 -0
  162. data/lib/pharmaobservatory/models/trial_enrollment_rate_row.rb +443 -0
  163. data/lib/pharmaobservatory/models/trial_extracted_endpoints_response.rb +478 -0
  164. data/lib/pharmaobservatory/models/trial_extracted_endpoints_row.rb +346 -0
  165. data/lib/pharmaobservatory/models/trial_outcome_measures_response.rb +478 -0
  166. data/lib/pharmaobservatory/models/trial_outcome_measures_row.rb +278 -0
  167. data/lib/pharmaobservatory/models/trial_sites_response.rb +478 -0
  168. data/lib/pharmaobservatory/models/trial_sites_row.rb +377 -0
  169. data/lib/pharmaobservatory/models/trials_record.rb +385 -0
  170. data/lib/pharmaobservatory/models/trials_record_attributes.rb +247 -0
  171. data/lib/pharmaobservatory/models/trials_response.rb +478 -0
  172. data/lib/pharmaobservatory/models/trials_row.rb +784 -0
  173. data/lib/pharmaobservatory/version.rb +1 -1
  174. data/lib/pharmaobservatory.rb +63 -0
  175. metadata +127 -1
@@ -0,0 +1,267 @@
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+ =begin
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+ #Pharma Observatory Public REST API
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+
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+ #Read-only REST API over the Pharma Observatory biomedical data platform. Reference: https://pharmaobservatory.com/api-reference
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+
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+ The version of the OpenAPI document: 1.0.0
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+
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+ Generated by: https://openapi-generator.tech
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+ Generator version: 7.13.0
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+
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+ =end
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+
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+ require 'date'
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+ require 'time'
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+
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+ module PharmaObservatory
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+ # One row of the condition_drugs dataset: one row per condition and resolved molecule. A grouped request returns the group columns and the measures instead, as additional properties.
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+ class ConditionDrugsRow
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+ # The condition key, a MeSH (Medical Subject Headings) descriptor id (D followed by six to nine digits).
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+ attr_accessor :condition_id
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+
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+ # The drug key (a canonical drug id; the same value as molecule_id on this dataset).
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+ attr_accessor :drug_id
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+
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+ # The molecule key the drug resolves to.
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+ attr_accessor :molecule_id
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+
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+ # The molecule's display name.
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+ attr_accessor :drug_name
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+
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+ # Trials for this condition that test the molecule.
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+ attr_accessor :n_trials
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+
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+ # Attribute mapping from ruby-style variable name to JSON key.
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+ def self.attribute_map
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+ {
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+ :'condition_id' => :'condition_id',
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+ :'drug_id' => :'drug_id',
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+ :'molecule_id' => :'molecule_id',
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+ :'drug_name' => :'drug_name',
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+ :'n_trials' => :'n_trials'
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+ }
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+ end
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+
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+ # Returns attribute mapping this model knows about
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+ def self.acceptable_attribute_map
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+ attribute_map
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+ end
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+
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+ # Returns all the JSON keys this model knows about
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+ def self.acceptable_attributes
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+ acceptable_attribute_map.values
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+ end
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+
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+ # Attribute type mapping.
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+ def self.openapi_types
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+ {
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+ :'condition_id' => :'String',
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+ :'drug_id' => :'String',
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+ :'molecule_id' => :'String',
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+ :'drug_name' => :'String',
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+ :'n_trials' => :'Integer'
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+ }
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+ end
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+
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+ # List of attributes with nullable: true
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+ def self.openapi_nullable
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+ Set.new([
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+ :'condition_id',
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+ :'drug_id',
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+ :'molecule_id',
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+ :'drug_name',
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+ :'n_trials'
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+ ])
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+ end
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+
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+ # Initializes the object
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+ # @param [Hash] attributes Model attributes in the form of hash
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+ def initialize(attributes = {})
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+ if (!attributes.is_a?(Hash))
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+ fail ArgumentError, "The input argument (attributes) must be a hash in `PharmaObservatory::ConditionDrugsRow` initialize method"
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+ end
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+
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+ # check to see if the attribute exists and convert string to symbol for hash key
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+ acceptable_attribute_map = self.class.acceptable_attribute_map
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+ attributes = attributes.each_with_object({}) { |(k, v), h|
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+ if (!acceptable_attribute_map.key?(k.to_sym))
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+ fail ArgumentError, "`#{k}` is not a valid attribute in `PharmaObservatory::ConditionDrugsRow`. Please check the name to make sure it's valid. List of attributes: " + acceptable_attribute_map.keys.inspect
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+ end
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+ h[k.to_sym] = v
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+ }
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+
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+ if attributes.key?(:'condition_id')
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+ self.condition_id = attributes[:'condition_id']
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+ end
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+
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+ if attributes.key?(:'drug_id')
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+ self.drug_id = attributes[:'drug_id']
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+ end
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+
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+ if attributes.key?(:'molecule_id')
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+ self.molecule_id = attributes[:'molecule_id']
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+ end
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+
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+ if attributes.key?(:'drug_name')
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+ self.drug_name = attributes[:'drug_name']
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+ end
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+
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+ if attributes.key?(:'n_trials')
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+ self.n_trials = attributes[:'n_trials']
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+ end
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+ end
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+
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+ # Show invalid properties with the reasons. Usually used together with valid?
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+ # @return Array for valid properties with the reasons
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+ def list_invalid_properties
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+ warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
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+ invalid_properties = Array.new
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+ invalid_properties
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+ end
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+
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+ # Check to see if the all the properties in the model are valid
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+ # @return true if the model is valid
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+ def valid?
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+ warn '[DEPRECATED] the `valid?` method is obsolete'
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+ true
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+ end
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+
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+ # Checks equality by comparing each attribute.
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+ # @param [Object] Object to be compared
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+ def ==(o)
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+ return true if self.equal?(o)
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+ self.class == o.class &&
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+ condition_id == o.condition_id &&
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+ drug_id == o.drug_id &&
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+ molecule_id == o.molecule_id &&
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+ drug_name == o.drug_name &&
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+ n_trials == o.n_trials
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+ end
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+
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+ # @see the `==` method
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+ # @param [Object] Object to be compared
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+ def eql?(o)
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+ self == o
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+ end
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+
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+ # Calculates hash code according to all attributes.
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+ # @return [Integer] Hash code
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+ def hash
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+ [condition_id, drug_id, molecule_id, drug_name, n_trials].hash
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+ end
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+
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+ # Builds the object from hash
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+ # @param [Hash] attributes Model attributes in the form of hash
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+ # @return [Object] Returns the model itself
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+ def self.build_from_hash(attributes)
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+ return nil unless attributes.is_a?(Hash)
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+ attributes = attributes.transform_keys(&:to_sym)
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+ transformed_hash = {}
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+ openapi_types.each_pair do |key, type|
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+ if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
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+ transformed_hash["#{key}"] = nil
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+ elsif type =~ /\AArray<(.*)>/i
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+ # check to ensure the input is an array given that the attribute
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+ # is documented as an array but the input is not
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+ if attributes[attribute_map[key]].is_a?(Array)
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+ transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
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+ end
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+ elsif !attributes[attribute_map[key]].nil?
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+ transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
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+ end
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+ end
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+ new(transformed_hash)
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+ end
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+
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+ # Deserializes the data based on type
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+ # @param string type Data type
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+ # @param string value Value to be deserialized
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+ # @return [Object] Deserialized data
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+ def self._deserialize(type, value)
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+ case type.to_sym
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+ when :Time
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+ Time.parse(value)
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+ when :Date
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+ Date.parse(value)
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+ when :String
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+ value.to_s
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+ when :Integer
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+ value.to_i
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+ when :Float
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+ value.to_f
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+ when :Boolean
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+ if value.to_s =~ /\A(true|t|yes|y|1)\z/i
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+ true
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+ else
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+ false
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+ end
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+ when :Object
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+ # generic object (usually a Hash), return directly
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+ value
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+ when /\AArray<(?<inner_type>.+)>\z/
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+ inner_type = Regexp.last_match[:inner_type]
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+ value.map { |v| _deserialize(inner_type, v) }
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+ when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
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+ k_type = Regexp.last_match[:k_type]
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+ v_type = Regexp.last_match[:v_type]
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+ {}.tap do |hash|
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+ value.each do |k, v|
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+ hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
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+ end
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+ end
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+ else # model
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+ # models (e.g. Pet) or oneOf
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+ klass = PharmaObservatory.const_get(type)
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+ klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
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+ end
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+ end
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+
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+ # Returns the string representation of the object
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+ # @return [String] String presentation of the object
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+ def to_s
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+ to_hash.to_s
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+ end
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+
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+ # to_body is an alias to to_hash (backward compatibility)
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+ # @return [Hash] Returns the object in the form of hash
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+ def to_body
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+ to_hash
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+ end
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+
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+ # Returns the object in the form of hash
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+ # @return [Hash] Returns the object in the form of hash
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+ def to_hash
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+ hash = {}
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+ self.class.attribute_map.each_pair do |attr, param|
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+ value = self.send(attr)
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+ if value.nil?
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+ is_nullable = self.class.openapi_nullable.include?(attr)
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+ next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
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+ end
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+
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+ hash[param] = _to_hash(value)
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+ end
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+ hash
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+ end
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+
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+ # Outputs non-array value in the form of hash
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+ # For object, use to_hash. Otherwise, just return the value
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+ # @param [Object] value Any valid value
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+ # @return [Hash] Returns the value in the form of hash
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+ def _to_hash(value)
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+ if value.is_a?(Array)
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+ value.compact.map { |v| _to_hash(v) }
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+ elsif value.is_a?(Hash)
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+ {}.tap do |hash|
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+ value.each { |k, v| hash[k] = _to_hash(v) }
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+ end
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+ elsif value.respond_to? :to_hash
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+ value.to_hash
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+ else
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+ value
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+ end
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+ end
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+
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+ end
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+
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+ end