update docs

RobokopU24 · Jul 22, 2024 · b4cc814 · b4cc814
1 parent 5822957
commit b4cc814
Show file tree

Hide file tree

Showing 256 changed files with 6,093 additions and 28,341 deletions.
diff --git a/api/openapi.json b/api/openapi.json
diff --git a/docs/automat/alliance-of-genome-resources.tag.mdx b/docs/automat/alliance-of-genome-resources.tag.mdx
@@ -10,31 +10,24 @@ custom_edit_url: null
 
 The Alliance of Genome Resources is a consortium of the owners of seven model organism databases (MODs) and the Gene Ontology (GO) Consortium, whose goal is to provide an integrated view of their data to all biologists, clinicians, and other interested parties. The Alliance provides the results of all methods that have been benchmarked by the Quest for Orthologs Consortium (QfO), as well as curated ortholog inferences from HGNC (human, mouse, rat genes).
 
-**Version:** 52b222baedc80328
+**Version:** 85a6ce01fb7d2cbe
 
 **URL:** [https://www.alliancegenome.org/](https://www.alliancegenome.org/)
 
-**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/GenomeAllianceOrthologs_Automat/52b222baedc80328](https://stars.renci.org/var/plater/bl-3.5.4/GenomeAllianceOrthologs_Automat/52b222baedc80328)
+**Files:** [https://stars.renci.org/var/plater/bl-4.1.6/GenomeAllianceOrthologs_Automat/85a6ce01fb7d2cbe](https://stars.renci.org/var/plater/bl-4.1.6/GenomeAllianceOrthologs_Automat/85a6ce01fb7d2cbe)
 
-**Nodes:** 94,336
+**Nodes:** 94,314
 
-**Edges:** 530,374
+**Edges:** 489,908
 
 
 
 
 
-
-## Query Endpoints
 ```mdx-code-block
 import DocCardList from '@theme/DocCardList';
 import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
 
-<DocCardList items={useCurrentSidebarCategory().items.slice(0, 6)}/>
-```
-
-## Metadata Endpoints    
-```mdx-code-block
-<DocCardList items={useCurrentSidebarCategory().items.slice(6)}/>
+<DocCardList items={useCurrentSidebarCategory().items}/>
 ```
 
diff --git a/docs/automat/binding.tag.mdx b/docs/automat/binding.tag.mdx
@@ -10,31 +10,24 @@ custom_edit_url: null
 
 Binding DataBase (BindingDB) openly exposes curated data on chemical entities and their molecular targets.
 
-**Version:** 711f33bcebbef313
+**Version:** 57e22a8a314b0df8
 
 **URL:** [https://www.bindingdb.org/](https://www.bindingdb.org/)
 
-**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/BINDING_Automat/711f33bcebbef313](https://stars.renci.org/var/plater/bl-3.5.4/BINDING_Automat/711f33bcebbef313)
+**Files:** [https://stars.renci.org/var/plater/bl-4.2.0/BINDING_Automat/57e22a8a314b0df8](https://stars.renci.org/var/plater/bl-4.2.0/BINDING_Automat/57e22a8a314b0df8)
 
-**Nodes:** 1,082,743
+**Nodes:** 1,114,169
 
-**Edges:** 2,168,353
+**Edges:** 2,230,910
 
 
 
 
 
-
-## Query Endpoints
 ```mdx-code-block
 import DocCardList from '@theme/DocCardList';
 import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
 
-<DocCardList items={useCurrentSidebarCategory().items.slice(0, 6)}/>
-```
-
-## Metadata Endpoints    
-```mdx-code-block
-<DocCardList items={useCurrentSidebarCategory().items.slice(6)}/>
+<DocCardList items={useCurrentSidebarCategory().items}/>
 ```
 
diff --git a/docs/automat/cam-kg.tag.mdx b/docs/automat/cam-kg.tag.mdx
@@ -10,31 +10,24 @@ custom_edit_url: null
 
 The CAM KG contains data on CAMs (Causal Activity Models), which are small knowledge graphs built using the Web Ontology Language (OWL). The CAM database combines many CAM graphs, along with a large merged bio-ontology containing the full vocabulary of concepts referenced within the individual CAMs. Each CAM describes an instantiation of some of those concepts in a particular context, modeling the interactions between those instances as an interlinked representation of a complex biological or environmental process.
 
-**Version:** e553a5174c60a698
+**Version:** dfdb15b2ecef5629
 
 
 
-**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/CAMKP_Automat/e553a5174c60a698](https://stars.renci.org/var/plater/bl-3.5.4/CAMKP_Automat/e553a5174c60a698)
+**Files:** [https://stars.renci.org/var/plater/bl-4.2.0/CAMKP_Automat/dfdb15b2ecef5629](https://stars.renci.org/var/plater/bl-4.2.0/CAMKP_Automat/dfdb15b2ecef5629)
 
-**Nodes:** 119,464
+**Nodes:** 119,931
 
-**Edges:** 2,199,905
+**Edges:** 2,222,643
 
 
 
 
 
-
-## Query Endpoints
 ```mdx-code-block
 import DocCardList from '@theme/DocCardList';
 import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
 
-<DocCardList items={useCurrentSidebarCategory().items.slice(0, 6)}/>
-```
-
-## Metadata Endpoints    
-```mdx-code-block
-<DocCardList items={useCurrentSidebarCategory().items.slice(6)}/>
+<DocCardList items={useCurrentSidebarCategory().items}/>
 ```
 
diff --git a/docs/automat/ctd.tag.mdx b/docs/automat/ctd.tag.mdx
@@ -10,31 +10,24 @@ custom_edit_url: null
 
 The Comparative Toxicogenomics Database (CTD) is an open-source database that provides manually curated information about chemical-gene/protein, chemical-disease, and gene/protein-disease relationships, with additional support for the curated relationships provided by function and pathway data.
 
-**Version:** c471321e4404efde
+**Version:** 8b5f74462c4179ca
 
 **URL:** [http://ctdbase.org/about/](http://ctdbase.org/about/)
 
-**Files:** [https://stars.renci.org/var/plater/bl-3.5.4/CTD_Automat/c471321e4404efde](https://stars.renci.org/var/plater/bl-3.5.4/CTD_Automat/c471321e4404efde)
+**Files:** [https://stars.renci.org/var/plater/bl-4.2.0/CTD_Automat/8b5f74462c4179ca](https://stars.renci.org/var/plater/bl-4.2.0/CTD_Automat/8b5f74462c4179ca)
 
-**Nodes:** 446,233
+**Nodes:** 504,315
 
-**Edges:** 1,467,233
+**Edges:** 1,602,508
 
 
 
 
 
-
-## Query Endpoints
 ```mdx-code-block
 import DocCardList from '@theme/DocCardList';
 import {useCurrentSidebarCategory} from '@docusaurus/theme-common';
 
-<DocCardList items={useCurrentSidebarCategory().items.slice(0, 6)}/>
-```
-
-## Metadata Endpoints    
-```mdx-code-block
-<DocCardList items={useCurrentSidebarCategory().items.slice(6)}/>
+<DocCardList items={useCurrentSidebarCategory().items}/>
 ```
 
diff --git a/docs/automat/cypher-cypher-post-binding-db.api.mdx b/docs/automat/cypher-cypher-post-binding-db.api.mdx
@@ -1,11 +1,11 @@
 ---
 id: cypher-cypher-post-binding-db
-title: "Run cypher query"
-description: "Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/)."
-sidebar_label: "Run cypher query"
+title: "Run a Neo4j cypher query."
+description: "Runs a cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/)."
+sidebar_label: "Run a Neo4j cypher query."
 hide_title: true
 hide_table_of_contents: true
-api: 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
+api: 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
 sidebar_class_name: "post api-method"
 info_path: docs/automat/automat
 custom_edit_url: null
@@ -22,23 +22,21 @@ import SchemaItem from "@theme/SchemaItem";
 import SchemaTabs from "@theme/SchemaTabs";
 import TabItem from "@theme/TabItem";
 
-<h1 className={"openapi__heading"}>Run cypher query</h1>
+<h1 className={"openapi__heading"}>Run a Neo4j cypher query.</h1>
 
 <MethodEndpoint method={"post"} path={"/binding-db/cypher"}></MethodEndpoint>
 
 
 
-Runs cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).
-
-<details><summary>Schema</summary>
+Runs a cypher query against the Neo4j instance, and returns an equivalent response expected from a Neo4j HTTP endpoint (https://neo4j.com/docs/rest-docs/current/).
 
 ## Request
 
 <MimeTabs className={"openapi-tabs__mime"}><TabItem label={"application/json"} value={"application/json-schema"}><details style={{}} className={"openapi-markdown__details mime"} data-collapsed={false} open={true}><summary style={{}} className={"openapi-markdown__details-summary-mime"}><h3 className={"openapi-markdown__details-summary-header-body"}>Body</h3><strong className={"openapi-schema__required"}>required</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}><SchemaItem collapsible={false} name={"query"} required={true} schemaName={"Query"} qualifierMessage={undefined} schema={{"title":"Query","type":"string"}}></SchemaItem></ul></details></TabItem></MimeTabs><div><div><ApiTabs><TabItem label={"200"} value={"200"}><div>
 
 Successful Response
 
-</div><div><MimeTabs className={"openapi-tabs__mime"} schemaType={"response"}><TabItem label={"application/json"} value={"application/json"}><SchemaTabs className={"openapi-tabs__schema"}><TabItem label={"Schema"} value={"Schema"}><details style={{}} className={"openapi-markdown__details response"} data-collapsed={false} open={true}><summary style={{}} className={"openapi-markdown__details-summary-response"}><strong>Schema</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}} className={"openapi-markdown__details"}><summary style={{}}><span className={"openapi-schema__container"}><strong className={"openapi-schema__property"}>results</strong><span className={"openapi-schema__name"}> object[]</span><span className={"openapi-schema__divider"}></span><span className={"openapi-schema__required"}>required</span></span></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"columns"} required={true} schemaName={"string[]"} qualifierMessage={undefined} schema={{"title":"Columns","type":"array","items":{"type":"string"}}}></SchemaItem><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}} className={"openapi-markdown__details"}><summary style={{}}><span className={"openapi-schema__container"}><strong className={"openapi-schema__property"}>data</strong><span className={"openapi-schema__name"}> object[]</span><span className={"openapi-schema__divider"}></span><span className={"openapi-schema__required"}>required</span></span></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"row"} required={true} schemaName={"undefined[]"} qualifierMessage={undefined} schema={{"title":"Row","type":"array","items":{}}}></SchemaItem><SchemaItem collapsible={false} name={"meta"} required={true} schemaName={"undefined[]"} qualifierMessage={undefined} schema={{"title":"Meta","type":"array","items":{}}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><SchemaItem collapsible={true} className={"schemaItem"}><details style={{}} className={"openapi-markdown__details"}><summary style={{}}><span className={"openapi-schema__container"}><strong className={"openapi-schema__property"}>errors</strong><span className={"openapi-schema__name"}> object[]</span><span className={"openapi-schema__divider"}></span><span className={"openapi-schema__required"}>required</span></span></summary><div style={{"marginLeft":"1rem"}}><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem","paddingBottom":".5rem"}}>Array [</div></li><SchemaItem collapsible={false} name={"code"} required={true} schemaName={"Code"} qualifierMessage={undefined} schema={{"title":"Code","type":"string"}}></SchemaItem><SchemaItem collapsible={false} name={"message"} required={true} schemaName={"Message"} qualifierMessage={undefined} schema={{"title":"Message","type":"string"}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem></ul></details></TabItem><TabItem label={"Example (from schema)"} value={"Example (from schema)"}><ResponseSamples responseExample={"{\n  \"results\": [\n    {\n      \"columns\": [\n        \"string\"\n      ],\n      \"data\": [\n        {\n          \"row\": [\n            null\n          ],\n          \"meta\": [\n            null\n          ]\n        }\n      ]\n    }\n  ],\n  \"errors\": [\n    {\n      \"code\": \"string\",\n      \"message\": \"string\"\n    }\n  ]\n}"} language={"json"}></ResponseSamples></TabItem></SchemaTabs></TabItem></MimeTabs></div></TabItem><TabItem label={"422"} value={"422"}><div>
+</div><div><MimeTabs className={"openapi-tabs__mime"} schemaType={"response"}><TabItem label={"application/json"} value={"application/json"}><SchemaTabs className={"openapi-tabs__schema"}><TabItem label={"Schema"} value={"Schema"}><details style={{}} className={"openapi-markdown__details response"} data-collapsed={false} open={true}><summary style={{}} className={"openapi-markdown__details-summary-response"}><strong>Schema</strong></summary><div style={{"textAlign":"left","marginLeft":"1rem"}}></div><ul style={{"marginLeft":"1rem"}}>any</ul></details></TabItem></SchemaTabs></TabItem></MimeTabs></div></TabItem><TabItem label={"422"} value={"422"}><div>
 
 Validation Error
 
@@ -51,5 +49,4 @@ string
 integer
 
 </div></TabItem></SchemaTabs></div><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem><SchemaItem collapsible={false} name={"msg"} required={true} schemaName={"Message"} qualifierMessage={undefined} schema={{"title":"Message","type":"string"}}></SchemaItem><SchemaItem collapsible={false} name={"type"} required={true} schemaName={"Error Type"} qualifierMessage={undefined} schema={{"title":"Error Type","type":"string"}}></SchemaItem><li><div style={{"fontSize":"var(--ifm-code-font-size)","opacity":"0.6","marginLeft":"-.5rem"}}>]</div></li></div></details></SchemaItem></ul></details></TabItem><TabItem label={"Example (from schema)"} value={"Example (from schema)"}><ResponseSamples responseExample={"{\n  \"detail\": [\n    {\n      \"loc\": [\n        \"string\",\n        0\n      ],\n      \"msg\": \"string\",\n      \"type\": \"string\"\n    }\n  ]\n}"} language={"json"}></ResponseSamples></TabItem></SchemaTabs></TabItem></MimeTabs></div></TabItem></ApiTabs></div></div>
-
-</details>
+