diff --git a/docs/app/flows/NodeEditor.mdx b/docs/app/flows/NodeEditor.mdx index 25a0070a..4861ba44 100644 --- a/docs/app/flows/NodeEditor.mdx +++ b/docs/app/flows/NodeEditor.mdx @@ -271,6 +271,6 @@ Flows can be configured to accept user inputs at the start of each run by select - File inputs (e.g. - FileAny, FileCSV, etc.) - Text (string) inputs (e.g. - string) -- Tag inputs (e.g. - TagBenchling) +- Tag inputs (e.g. - Input_Param) A list of available nodes and their associated categories can be found on the [table listing of node characteristics](../../nodes/Overview.mdx#list-of-available-nodes-and-key-characteristics) More detail can be found on the [Node documentation page](../../nodes/Overview.mdx). diff --git a/docs/nodes/App/Benchling_Read.md b/docs/nodes/App/Benchling_Read.md deleted file mode 100644 index 88913354..00000000 --- a/docs/nodes/App/Benchling_Read.md +++ /dev/null @@ -1,70 +0,0 @@ ---- -sidebar_label: Benchling_Read -title: Benchling_Read -displayed_sidebar: webUiSidebar ---- - -## Node - -### Node Description - -Reads Benchling data specified by Benchling run tag. - -Passes Benchling run tag to user-defined function and uploads tabular output -from user-defined function to Ganymede data lake. - -This node is used in conjunction with BenchlingTag; adding BenchlingTag to -a Flow enables a Benchling run tag to be specified in the Flow input box. -The user-defined function uses the Benchling ID associated with the run tag -to retrieve data and process data into table(s), which are uploaded to the Ganymede -data lake. - -### Node Attributes - -- **output_table_results** - - Table displayed on [Table Head](https://docs.ganymede.bio/app/intro/Concepts#table-head) in Ganymede UI. - -### Notes - -Usage requires configuration of a -[Benchling application](https://docs.benchling.com/docs/getting-started-benchling-apps#getting-started) -in the relevant Benchling tenant. - -Prior to usage, the secrets below must be configured in your Ganymede environment. More information -on acquiring these credentials can be found [here](https://docs.benchling.com/docs/authentication). -- **benchling_url**: URL for Benchling tenant; has form https://\.benchling.com -- **benchling_app_client_id**: Client ID for Benchling App -- **benchling_client_secret**: Client Secret for Benchling App - -Secrets can be configured by clicking on your username in the upper-right hand of the Ganymede -application, then selecting Environment Settings and navigating to the Secrets tab. If you need -assistance, please don't hesitate to reach out to Ganymede. - -In the execute function, returning NodeReturn(tables_to_upload=\{'results': df\}) would render the DataFrame df in the Flow Editor if Table Head visualization is enabled. - -## User-Defined Python - -Reads Benchling data based on run tag. This node should be used in -conjunction with the Benchling_Tag node. - -### Parameters - -- **benchling_context** : `BenchlingContext` - - Benchling context variable, which stores Benchling connection information -- **ganymede_context** : `GanymedeContext` - - Ganymede context variable, which stores flow run metadata - -### Returns - -`NodeReturn` - Object containing data to store in data lake and/or file storage - -### Notes - -This template shows how a target plate could be pulled via the Benchling object -Documentation for the Benchling API can be found here: https://benchling.com/api/reference - -benchling_context is an object of class BenchlingContext, consisting of -- **conn**: Benchling connection -- **run_tag**: Benchling ID associated with run tag -- **display_tag**: Displayed value of Benchling run tag diff --git a/docs/nodes/App/Benchling_Read_Object.md b/docs/nodes/App/Benchling_Read_Object.md deleted file mode 100644 index 66dc453b..00000000 --- a/docs/nodes/App/Benchling_Read_Object.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -sidebar_label: Benchling_Read_Object -title: Benchling_Read_Object -displayed_sidebar: webUiSidebar ---- - -## Node - -### Node Description - -Reads Benchling data specified by input Benchling ID string. - -Executes Benchling API call(s) based on user-defined function and upload results to data lake - -Passes Benchling ID to user-defined function for retrieving Benchling API data. -The user-defined function returns one or more DataFrames, which are uploaded as tables into -the Ganymede data lake. - -### Node Attributes - -- **input_string_id** - - Benchling API ID, specified on node -- **output_table_results** - - Table displayed on [Table Head](https://docs.ganymede.bio/app/intro/Concepts#table-head) in Ganymede UI. - -### Notes - -Usage requires configuration of a -[Benchling application](https://docs.benchling.com/docs/getting-started-benchling-apps#getting-started) -in the relevant Benchling tenant. - -Prior to usage, the secrets below must be configured in your Ganymede environment. More information -on acquiring these credentials can be found [here](https://docs.benchling.com/docs/authentication). -- **benchling_url**: URL for Benchling tenant; has form https://\.benchling.com -- **benchling_app_client_id**: Client ID for Benchling application -- **benchling_client_secret**: Client Secret for Benchling application - -Secrets can be configured by clicking on your username in the upper-right hand of the Ganymede -application, then selecting Environment Settings and navigating to the Secrets tab. If you need -assistance, please don't hesitate to reach out to Ganymede. - -In the execute function, returning NodeReturn(tables_to_upload=\{'results': df\}) would render the DataFrame df in the Flow Editor if Table Head visualization is enabled. - -## User-Defined Python - -Reads Benchling data based on input parameter. This node should be used in -conjunction with the Input_Param node. - -### Parameters - -- **benchling_context** : `BenchlingContext` - - Benchling context variable, which stores Benchling connection information -- **ganymede_context** : `GanymedeContext` - - Ganymede context variable, which stores flow run metadata - -### Returns - -`NodeReturn` - Object containing data to store in data lake and/or file storage - -### Notes - -This template shows how a Benchling entry could be accessed via the Benchling object -Documentation for the Benchling API can be found here: https://benchling.com/api/reference - -benchling_context is an object of class BenchlingContext, consisting of -- **conn**: Benchling connection -- **run_tag**: Benchling ID associated with run tag -- **display_tag**: Displayed value of Benchling run tag diff --git a/docs/nodes/App/sidebar.json b/docs/nodes/App/sidebar.json index 959fff8b..3e1c7f21 100644 --- a/docs/nodes/App/sidebar.json +++ b/docs/nodes/App/sidebar.json @@ -1 +1 @@ -{"type": "category", "label": "App", "items": ["nodes/App/APINode", "nodes/App/Airtable_Export", "nodes/App/Airtable_Import", "nodes/App/Azure_Query", "nodes/App/Azure_Read", "nodes/App/Azure_Read_Multi", "nodes/App/Azure_Write", "nodes/App/Benchling_Api", "nodes/App/Benchling_Event", "nodes/App/Benchling_Read", "nodes/App/Benchling_Read_Object", "nodes/App/Benchling_Warehouse_Query", "nodes/App/Benchling_Warehouse_Sync", "nodes/App/Benchling_Write", "nodes/App/Benchling_Write_Object", "nodes/App/Coda_Write", "nodes/App/ELabNext_Write", "nodes/App/Load_Parquet_to_Table", "nodes/App/S3_Event", "nodes/App/S3_Read", "nodes/App/S3_Write", "nodes/App/SciNote_API", "nodes/App/Smartsheet_Read", "nodes/App/Snowflake_Write", "nodes/App/Webhook_Event"]} \ No newline at end of file +{"type": "category", "label": "App", "items": ["nodes/App/APINode", "nodes/App/Airtable_Export", "nodes/App/Airtable_Import", "nodes/App/Azure_Query", "nodes/App/Azure_Read", "nodes/App/Azure_Read_Multi", "nodes/App/Azure_Write", "nodes/App/Benchling_Api", "nodes/App/Benchling_Event", "nodes/App/Benchling_Warehouse_Query", "nodes/App/Benchling_Warehouse_Sync", "nodes/App/Benchling_Write", "nodes/App/Benchling_Write_Object", "nodes/App/Coda_Write", "nodes/App/ELabNext_Write", "nodes/App/Load_Parquet_to_Table", "nodes/App/S3_Event", "nodes/App/S3_Read", "nodes/App/S3_Write", "nodes/App/SciNote_API", "nodes/App/Smartsheet_Read", "nodes/App/Snowflake_Write", "nodes/App/Webhook_Event"]} \ No newline at end of file diff --git a/docs/nodes/Overview.mdx b/docs/nodes/Overview.mdx index fc6227ab..0b417052 100644 --- a/docs/nodes/Overview.mdx +++ b/docs/nodes/Overview.mdx @@ -44,8 +44,6 @@ The table below provides a list of available Nodes, along with details on whethe | App | Azure_Write | FileAny | API | False | False | | App | Benchling_Api | API | NodeReturn | True | False | | App | Benchling_Event | Event | FlowInputs or NodeReturn | True | False | -| App | Benchling_Read | API | NodeReturn | True | False | -| App | Benchling_Read_Object | API | NodeReturn | True | False | | App | Benchling_Warehouse_Query | Table | NodeReturn | True | False | | App | Benchling_Warehouse_Sync | API | NodeReturn | True | False | | App | Benchling_Write | Table | NodeReturn | True | False | @@ -88,7 +86,6 @@ The table below provides a list of available Nodes, along with details on whethe | Instrument | Synergy_Read | FileTxt | NodeReturn | True | False | | Instrument | Synergy_Read_Multi | Set[FileTxt] | NodeReturn | True | True | | Instrument | WSP_Read | FileWSP | NodeReturn | True | False | -| Tag | Benchling_Tag | TagBenchling | string | False | False | | Tag | Input_Param | | string | False | False | #### Node Categories @@ -186,11 +183,6 @@ To initialize a `FlowInputs` object, use the following parameters from `ganymede - _param_ **param_name**: str - Node parameter in the triggered Flow Node that is used to specify the string pattern that the parameter must match (e.g., "param" for the Input_Param Node). - _param_ **param_value**: str - Value to pass into Node. -`Tag` is a dataclass used to pass Benchling Tags into a node, and is used exclusively with the [Benchling_Tag Node](./Tag/Benchling_Tag.md). It has the following attributes: - - _param_ **node_name**: str - Name of the node within triggered Flow to pass tag(s) into. - - _param_ **display_tag**: str - Value displayed in the dropdown in the Ganymede UI. For Benchling_Tag Nodes, this is the name of the tag displayed in the dropdown in Flow View / Flow Editor. - - _param_ **run_tag**: str - Underlying value of the tag. For Benchling_Tag Nodes, this is the Benchling ID associated with the value selected in the dropdown. - #### Other input/output types Some other input and output types characteristic to Nodes are: @@ -206,7 +198,6 @@ Some other input and output types characteristic to Nodes are: - **FileXML**: XML file - **FileZip**: Zip file - **FileAny**: generic data file, which may be unstructured -- **TagBenchling**: Benchling run tag - **string**: String parameter Python sets, lists, and dictionaries are denoted as Set, List, and Dict, respectively. diff --git a/docs/nodes/Tag/Benchling_Tag.md b/docs/nodes/Tag/Benchling_Tag.md deleted file mode 100644 index f286653a..00000000 --- a/docs/nodes/Tag/Benchling_Tag.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -sidebar_label: Benchling_Tag -title: Benchling_Tag -displayed_sidebar: webUiSidebar ---- - -## Node - -### Node Description - -Associates a Benchling run tag with a Flow run - -### Node Attributes - -- **input_tag_benchling** - - Benchling run tag to associate with flow run - -### Notes - -Usage requires configuration of a -[Benchling application](https://docs.benchling.com/docs/getting-started-benchling-apps#getting-started) -in the relevant Benchling tenant. - -Prior to usage, the secrets below must be configured in your Ganymede environment. More information -on acquiring these credentials can be found [here](https://docs.benchling.com/docs/authentication). -- **benchling_url**: URL for Benchling tenant; has form https://\.benchling.com -- **benchling_app_client_id**: Client ID for Benchling Application -- **benchling_client_secret**: Client Secret for Benchling Application - -Secrets can be configured by clicking on your username in the upper-right hand of the Ganymede -application, then selecting Environment Settings and navigating to the Secrets tab. If you need -assistance, please don't hesitate to reach out to Ganymede. diff --git a/docs/nodes/Tag/sidebar.json b/docs/nodes/Tag/sidebar.json index 65c00c17..a6169b81 100644 --- a/docs/nodes/Tag/sidebar.json +++ b/docs/nodes/Tag/sidebar.json @@ -1 +1 @@ -{"type": "category", "label": "Tag", "items": ["nodes/Tag/Benchling_Tag", "nodes/Tag/Input_Param"]} \ No newline at end of file +{"type": "category", "label": "Tag", "items": ["nodes/Tag/Input_Param"]} \ No newline at end of file