Create a full command line executable workflow for RNA-Seq on PBMC Samples. Open a PR on different branch once finished.

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Error in handle_issue_opened: 1 validation error for PromptTemplate root Invalid prompt schema; check for mismatched or missing input parameters. '\\n \"action\"' (type=value_error) Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 98, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id, image_name=image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 88, in __init__
    self.agent = self.make_agent()
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 147, in make_agent
    executor = self.custom_load_agent_executor(self.llm, tools, verbose=True, callbacks=[self.callback_handler], handle_parsing_errors=True)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 127, in custom_load_agent_executor
    agent = StructuredChatAgent.from_llm_and_tools(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 130, in from_llm_and_tools
    prompt = cls.create_prompt(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 109, in create_prompt
    HumanMessagePromptTemplate.from_template(human_message_template),
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/chat.py", line 151, in from_template
    prompt = PromptTemplate.from_template(template, template_format=template_format)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/prompt.py", line 217, in from_template
    return cls(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/load/serializable.py", line 97, in __init__
    super().__init__(**kwargs)
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for PromptTemplate
__root__
  Invalid prompt schema; check for mismatched or missing input parameters. '\\\\n  \\"action\\"' (type=value_error)

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

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Error in handle_issue_opened: 1 validation error for PromptTemplate root Invalid prompt schema; check for mismatched or missing input parameters. ' \"action\"' (type=value_error) Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 98, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id, image_name=image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 88, in __init__
    self.agent = self.make_agent()
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 147, in make_agent
    executor = self.custom_load_agent_executor(self.llm, tools, verbose=True, callbacks=[self.callback_handler], handle_parsing_errors=True)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 127, in custom_load_agent_executor
    agent = StructuredChatAgent.from_llm_and_tools(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 130, in from_llm_and_tools
    prompt = cls.create_prompt(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 109, in create_prompt
    HumanMessagePromptTemplate.from_template(human_message_template),
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/chat.py", line 151, in from_template
    prompt = PromptTemplate.from_template(template, template_format=template_format)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/prompt.py", line 217, in from_template
    return cls(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/load/serializable.py", line 97, in __init__
    super().__init__(**kwargs)
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for PromptTemplate
__root__
  Invalid prompt schema; check for mismatched or missing input parameters. '  \\"action\\"' (type=value_error)

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Error in handle_issue_opened: 1 validation error for PromptTemplate root Invalid prompt schema; check for mismatched or missing input parameters. ' \"action\"' (type=value_error) Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 98, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id, image_name=image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 88, in __init__
    self.agent = self.make_agent()
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 147, in make_agent
    executor = self.custom_load_agent_executor(self.llm, tools, verbose=True, callbacks=[self.callback_handler], handle_parsing_errors=True)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 127, in custom_load_agent_executor
    agent = StructuredChatAgent.from_llm_and_tools(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 130, in from_llm_and_tools
    prompt = cls.create_prompt(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 109, in create_prompt
    HumanMessagePromptTemplate.from_template(human_message_template),
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/chat.py", line 151, in from_template
    prompt = PromptTemplate.from_template(template, template_format=template_format)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/prompt.py", line 217, in from_template
    return cls(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/load/serializable.py", line 97, in __init__
    super().__init__(**kwargs)
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for PromptTemplate
__root__
  Invalid prompt schema; check for mismatched or missing input parameters. '  \\"action\\"' (type=value_error)

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Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

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Error in handle_issue_opened: 1 validation error for PromptTemplate root Invalid format specifier (type=value_error) Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 98, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id, image_name=image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 88, in __init__
    self.agent = self.make_agent()
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 147, in make_agent
    executor = self.custom_load_agent_executor(self.llm, tools, verbose=True, callbacks=[self.callback_handler], handle_parsing_errors=True)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 127, in custom_load_agent_executor
    agent = StructuredChatAgent.from_llm_and_tools(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 130, in from_llm_and_tools
    prompt = cls.create_prompt(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/structured_chat/base.py", line 109, in create_prompt
    HumanMessagePromptTemplate.from_template(human_message_template),
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/chat.py", line 151, in from_template
    prompt = PromptTemplate.from_template(template, template_format=template_format)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/prompts/prompt.py", line 217, in from_template
    return cls(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/load/serializable.py", line 97, in __init__
    super().__init__(**kwargs)
  File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for PromptTemplate
__root__
  Invalid format specifier (type=value_error)

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[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

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Error in handle_issue_opened: string indices must be integers Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 98, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id, image_name=image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 88, in __init__
    self.agent = self.make_agent()
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 147, in make_agent
    executor = self.custom_load_agent_executor(self.llm, tools, verbose=True, callbacks=[self.callback_handler], handle_parsing_errors=True)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 117, in custom_load_agent_executor
    memory_context = get_memory_context(table_name="docker_images", image_name=self.image_name)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 64, in get_memory_context
    action_data_string = [item['log'] for item in action_data]
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 64, in <listcomp>
    action_data_string = [item['log'] for item in action_data]
TypeError: string indices must be integers

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[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

Feel free to comment in this thread to give me additional instructions, or I'll tag you in a comment if I get stuck. If I think I'm successful I'll 'request your review' on the resulting PR. Just watch for emails while I work.

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Error in handle_issue_opened: GitHubAction._run() missing 1 required positional argument: 'instructions' Traceback

Traceback (most recent call last):
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 99, in handle_issue_opened
    result = bot.run(prompt)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 91, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input": f"{input}"}, {
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/executors/base.py", line 37, in step
    response = self.chain.run(**inputs, callbacks=callbacks)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/agents/agent.py", line 991, in _take_next_step
    observation = tool.run(
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/tools/base.py", line 364, in run
    raise e
  File "/Users/minum/Documents/NCSA/UIUC-Chatbot/ai-ta-backend/.venv310/src/langchain/libs/langchain/langchain/tools/base.py", line 336, in run
    self._run(*tool_args, run_manager=run_manager, **tool_kwargs)
TypeError: GitHubAction._run() missing 1 required positional argument: 'instructions'

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