pharmaobservatory 0.1.1 → 0.1.3

data/docs/BiomarkersResponse.md

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+# PharmaObservatory::BiomarkersResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<BiomarkersRow>**](BiomarkersRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkersResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/BiomarkersRow.md

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+# PharmaObservatory::BiomarkersRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **biomarker_id** | **String** | The biomarker key. | [optional] |
+| **route_key** | **String** | The biomarker's route key, the id the web page uses and the one entry key every biomarker dataset takes (the gene symbol for a gene biomarker). | [optional] |
+| **biomarker_kind** | **String** | gene, protein_variant or another feature kind. | [optional] |
+| **identity_status** | **String** | Whether the biomarker's identity is confirmed. | [optional] |
+| **display_name** | **String** | The biomarker's display name. | [optional] |
+| **parent_biomarker_id** | **String** | The parent biomarker (a variant's gene). | [optional] |
+| **gene_symbol** | **String** | The gene symbol. | [optional] |
+| **amino_acid_change** | **String** | The amino-acid change, for a variant. | [optional] |
+| **target_id** | **String** | The target's Ensembl gene id. | [optional] |
+| **hgnc_id** | **String** | The HGNC gene id. | [optional] |
+| **uniprot_accession** | **String** | The UniProt accession. | [optional] |
+| **feature_code** | **String** | Feature code for a non-gene feature. | [optional] |
+| **feature_type** | **String** | Feature type for a non-gene feature. | [optional] |
+| **evidence_tier** | **Integer** | Strongest evidence tier: 1 FDA companion diagnostic through 6 no evidence. | [optional] |
+| **evidence_tier_label** | **String** | The tier's name. | [optional] |
+| **n_fda_cdx_assertions** | **Integer** | FDA companion diagnostic assertions. | [optional] |
+| **n_fda_bqp_assertions** | **Integer** | FDA biomarker qualification project assertions. | [optional] |
+| **n_cancer_actionable_cgi** | **Integer** | Cancer Genome Interpreter actionable rows. | [optional] |
+| **n_ot_association** | **Integer** | Open Targets target-disease associations. | [optional] |
+| **n_trial_mention** | **Integer** | Trials that name the biomarker. | [optional] |
+| **n_publication_variant_mentions** | **Integer** | Publication variant mentions. | [optional] |
+| **has_clinical_validation_evidence** | **Boolean** | Whether clinical validation evidence exists. | [optional] |
+| **has_analytical_validation_evidence** | **Boolean** | Whether analytical validation evidence exists. | [optional] |
+| **n_assay_provider_papers** | **Integer** | Papers naming an assay provider for the biomarker. | [optional] |
+| **n_assay_provider_suppliers** | **Integer** | Assay-provider suppliers named. | [optional] |
+| **n_diagnostic_provider_suppliers** | **Integer** | Of those, diagnostic providers. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkersRow.new(
+  biomarker_id: null,
+  route_key: null,
+  biomarker_kind: null,
+  identity_status: null,
+  display_name: null,
+  parent_biomarker_id: null,
+  gene_symbol: null,
+  amino_acid_change: null,
+  target_id: null,
+  hgnc_id: null,
+  uniprot_accession: null,
+  feature_code: null,
+  feature_type: null,
+  evidence_tier: null,
+  evidence_tier_label: null,
+  n_fda_cdx_assertions: null,
+  n_fda_bqp_assertions: null,
+  n_cancer_actionable_cgi: null,
+  n_ot_association: null,
+  n_trial_mention: null,
+  n_publication_variant_mentions: null,
+  has_clinical_validation_evidence: null,
+  has_analytical_validation_evidence: null,
+  n_assay_provider_papers: null,
+  n_assay_provider_suppliers: null,
+  n_diagnostic_provider_suppliers: null
+)
+```
+

data/docs/CellLinesApi.md

@@ -0,0 +1,153 @@
+# PharmaObservatory::CellLinesApi
+
+All URIs are relative to *https://pharmaobservatory.com*
+
+| Method | HTTP request | Description |
+| ------ | ------------ | ----------- |
+| [**cell_lines_get**](CellLinesApi.md#cell_lines_get) | **GET** /api/v1/cell_lines/{id} | One cell line |
+| [**cell_lines_list**](CellLinesApi.md#cell_lines_list) | **GET** /api/v1/cell_lines | List cell lines |
+
+
+## cell_lines_get
+
+> <CellLinesRecord> cell_lines_get(id)
+
+One cell line
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::CellLinesApi.new
+id = 'SCI-CONF' # String | 
+
+begin
+  # One cell line
+  result = api_instance.cell_lines_get(id)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling CellLinesApi->cell_lines_get: #{e}"
+end
+```
+
+#### Using the cell_lines_get_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<CellLinesRecord>, Integer, Hash)> cell_lines_get_with_http_info(id)
+
+```ruby
+begin
+  # One cell line
+  data, status_code, headers = api_instance.cell_lines_get_with_http_info(id)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <CellLinesRecord>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling CellLinesApi->cell_lines_get_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **id** | **String** |  |  |
+
+### Return type
+
+[**CellLinesRecord**](CellLinesRecord.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+
+
+## cell_lines_list
+
+> <CellLinesResponse> cell_lines_list(opts)
+
+List cell lines
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::CellLinesApi.new
+opts = {
+  cursor: 'cursor_example', # String | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it.
+  limit: 56, # Integer | Rows per page, up to 500 (default 50).
+  sort: 'sort_example', # String | Comma separated columns, a leading minus for descending: sort=a,-b.
+  group_by: 'group_by_example', # String | A dimension to group by; a date takes :year, :quarter or :month.
+  measure: 'measure_example' # String | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col).
+}
+
+begin
+  # List cell lines
+  result = api_instance.cell_lines_list(opts)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling CellLinesApi->cell_lines_list: #{e}"
+end
+```
+
+#### Using the cell_lines_list_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<CellLinesResponse>, Integer, Hash)> cell_lines_list_with_http_info(opts)
+
+```ruby
+begin
+  # List cell lines
+  data, status_code, headers = api_instance.cell_lines_list_with_http_info(opts)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <CellLinesResponse>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling CellLinesApi->cell_lines_list_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **cursor** | **String** | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it. | [optional] |
+| **limit** | **Integer** | Rows per page, up to 500 (default 50). | [optional] |
+| **sort** | **String** | Comma separated columns, a leading minus for descending: sort&#x3D;a,-b. | [optional] |
+| **group_by** | **String** | A dimension to group by; a date takes :year, :quarter or :month. | [optional] |
+| **measure** | **String** | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col). | [optional] |
+
+### Return type
+
+[**CellLinesResponse**](CellLinesResponse.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+

data/docs/CellLinesRecord.md

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+# PharmaObservatory::CellLinesRecord
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **object_type** | **String** |  |  |
+| **id** | **String** |  |  |
+| **record** | [**CellLinesRow**](CellLinesRow.md) |  |  |
+| **attributes** | **Object** |  | [optional] |
+| **datasets** | [**Array<DatasetListing>**](DatasetListing.md) |  |  |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::CellLinesRecord.new(
+  object_type: null,
+  id: null,
+  record: null,
+  attributes: null,
+  datasets: null,
+  attribution: null,
+  source_credit: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/CellLinesResponse.md

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+# PharmaObservatory::CellLinesResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<CellLinesRow>**](CellLinesRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::CellLinesResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/CellLinesRow.md

@@ -0,0 +1,54 @@
+# PharmaObservatory::CellLinesRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **cell_line_id** | **String** | The catalog listing's model id (scientist_model_id). | [optional] |
+| **alternate_cell_line_ids** | **String** | Other catalog model ids for the same line. | [optional] |
+| **model_lot_id** | **String** | The lot id. | [optional] |
+| **cell_type** | **String** | The cell line's name. | [optional] |
+| **provider_id** | **String** | The supplier's catalog id. | [optional] |
+| **supplier** | **String** | The supplier as listed. | [optional] |
+| **sample_species** | **String** | The species. | [optional] |
+| **storefront_enable** | **Boolean** | Whether the listing is enabled in the storefront. | [optional] |
+| **mutation_data** | **String** | Mutation data as listed. | [optional] |
+| **status** | **String** | The listing status. | [optional] |
+| **safety_status** | **String** | confirmed_problematic, review_candidate, no_problematic_match or missing_cell_type. | [optional] |
+| **resolution_status** | **String** | resolved, unresolved_review, no_match or missing_input. | [optional] |
+| **confirmed_problematic** | **Boolean** | Whether the line is confirmed problematic in Cellosaurus. | [optional] |
+| **cellosaurus_accession** | **String** | The displayed Cellosaurus accession. | [optional] |
+| **cellosaurus_url** | **String** | Link to the Cellosaurus entry. | [optional] |
+| **problem_category** | **String** | The problem category, for a problematic line. | [optional] |
+| **problematic_comment** | **String** | The Cellosaurus comment, for a problematic line. | [optional] |
+| **iclac_registration_ids** | **Array<String>** | ICLAC registration ids. | [optional] |
+| **release_version** | **String** | The Cellosaurus release the check ran against. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::CellLinesRow.new(
+  cell_line_id: null,
+  alternate_cell_line_ids: null,
+  model_lot_id: null,
+  cell_type: null,
+  provider_id: null,
+  supplier: null,
+  sample_species: null,
+  storefront_enable: null,
+  mutation_data: null,
+  status: null,
+  safety_status: null,
+  resolution_status: null,
+  confirmed_problematic: null,
+  cellosaurus_accession: null,
+  cellosaurus_url: null,
+  problem_category: null,
+  problematic_comment: null,
+  iclac_registration_ids: null,
+  release_version: null
+)
+```
+