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KastanDay / ML4Bio

LLMs to execute Bioinformatics workflows, esp. RNA-seq
MIT License
0 stars 1 forks source link

Navigate to https://programming-workshops.readthedocs.io/en/latest/workshops/02_R/Workshop_R.html, download the dataset using shell and replicate the entire workflow, commit the changes to a new branch and create a PR. #11

Open rohan-uiuc opened 1 year ago

lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

👉 Follow the bot's progress in real time on LangSmith.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: net::ERR_ABORTED at https://archive.ics.uci.edu/static/public/45/heart+disease.zip =========================== logs =========================== navigating to "https://archive.ics.uci.edu/static/public/45/heart+disease.zip", waiting until "load"

Traceback

Traceback (most recent call last):
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 91, in handle_issue_opened
    result = bot.run(prompt)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/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/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/agents/agent.py", line 991, in _take_next_step
    observation = tool.run(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/base.py", line 364, in run
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/base.py", line 336, in run
    self._run(*tool_args, run_manager=run_manager, **tool_kwargs)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/playwright/navigate.py", line 39, in _run
    response = page.goto(url)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/sync_api/_generated.py", line 9303, in goto
    self._sync(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_sync_base.py", line 109, in _sync
    return task.result()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_page.py", line 473, in goto
    return await self._main_frame.goto(**locals_to_params(locals()))
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_frame.py", line 138, in goto
    await self._channel.send("goto", locals_to_params(locals()))
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 61, in send
    return await self._connection.wrap_api_call(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 490, in wrap_api_call
    return await cb()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 99, in inner_send
    result = next(iter(done)).result()
playwright._impl._api_types.Error: net::ERR_ABORTED at https://archive.ics.uci.edu/static/public/45/heart+disease.zip
=========================== logs ===========================
navigating to "https://archive.ics.uci.edu/static/public/45/heart+disease.zip", waiting until "load"
============================================================
lil-jr-dev[bot] commented 1 year ago

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.

lil-jr-dev[bot] commented 1 year ago

👉 Follow the bot's progress in real time on LangSmith.

lil-jr-dev[bot] commented 1 year ago

Error in handle_issue_opened: net::ERR_ABORTED at https://archive.ics.uci.edu/static/public/45/heart+disease.zip =========================== logs =========================== navigating to "https://archive.ics.uci.edu/static/public/45/heart+disease.zip", waiting until "load"

Traceback

Traceback (most recent call last):
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/github_webhook_handlers.py", line 91, in handle_issue_opened
    result = bot.run(prompt)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/ai_ta_backend/agents/ml4bio_agent.py", line 34, in run
    result = self.agent.with_config({"run_name": "ML4BIO Plan & Execute Agent"}).invoke({"input":f"{input}"}, {"metadata": {"run_id_in_metadata": str(self.run_id_in_metadata)}})
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/schema/runnable/base.py", line 2316, in invoke
    return self.bound.invoke(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 84, in invoke
    return self(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain_experimental/plan_and_execute/agent_executor.py", line 56, in _call
    response = self.executor.step(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/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/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 506, in run
    return self(kwargs, callbacks=callbacks, tags=tags, metadata=metadata)[
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 306, in __call__
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/chains/base.py", line 300, in __call__
    self._call(inputs, run_manager=run_manager)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/agents/agent.py", line 1141, in _call
    next_step_output = self._take_next_step(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/agents/agent.py", line 991, in _take_next_step
    observation = tool.run(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/base.py", line 364, in run
    raise e
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/base.py", line 336, in run
    self._run(*tool_args, run_manager=run_manager, **tool_kwargs)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/langchain/tools/playwright/navigate.py", line 39, in _run
    response = page.goto(url)
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/sync_api/_generated.py", line 9303, in goto
    self._sync(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_sync_base.py", line 109, in _sync
    return task.result()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_page.py", line 473, in goto
    return await self._main_frame.goto(**locals_to_params(locals()))
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_frame.py", line 138, in goto
    await self._channel.send("goto", locals_to_params(locals()))
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 61, in send
    return await self._connection.wrap_api_call(
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 490, in wrap_api_call
    return await cb()
  File "/Users/rohanmarwaha/IdeaProjects/ai-ta-backend/env3.10/lib/python3.10/site-packages/playwright/_impl/_connection.py", line 99, in inner_send
    result = next(iter(done)).result()
playwright._impl._api_types.Error: net::ERR_ABORTED at https://archive.ics.uci.edu/static/public/45/heart+disease.zip
=========================== logs ===========================
navigating to "https://archive.ics.uci.edu/static/public/45/heart+disease.zip", waiting until "load"
============================================================