[AUR-395, AUR-415] Adopt Example1 Injury pipeline; add .flow() for enabling bottom-up pipeline execution (#32)

* add example1/injury pipeline example
* add dotenv
* update various api

.gitignore

@@ -453,7 +453,7 @@ $RECYCLE.BIN/
 logs/
 .gitsecret/keys/random_seed
 !*.secret
-credentials.txt
+.env
 
 S.gpg-agent*
 .vscode/settings.json

.gitsecret/paths/mapping.cfg

@@ -1 +1 @@
-credentials.txt:272c4eb7f422bebcc5d0f1da8bde47016b185ba8cb6ca06639bb2a3e88ea9bc5
+.env:272c4eb7f422bebcc5d0f1da8bde47016b185ba8cb6ca06639bb2a3e88ea9bc5

README.md

@@ -47,7 +47,12 @@ pip install kotaemon@git+ssh://git@github.com/Cinnamon/kotaemon.git
 
 ### Credential sharing
 
-This repo uses [git-secret](https://sobolevn.me/git-secret/) to share credentials, which internally uses `gpg` to encrypt and decrypt secret files.
+This repo uses [git-secret](https://sobolevn.me/git-secret/) to share credentials, which
+internally uses `gpg` to encrypt and decrypt secret files.
+
+This repo uses `python-dotenv` to manage credentials stored as enviroment variable.
+Please note that the use of `python-dotenv` and credentials are for development
+purposes only. Thus, it should not be used in the main source code (i.e. `kotaemon/` and `tests/`), but can be used in `examples/`.
 
 #### Install git-secret
 
@@ -63,13 +68,13 @@ In order to gain access to the secret files, you must provide your gpg public fi
 
 #### Decrypt the secret file
 
-The credentials are encrypted in the `credentials.txt.secret` file. To print the decrypted content to stdout, run
+The credentials are encrypted in the `.env.secret` file. To print the decrypted content to stdout, run
 
 ```shell
 git-secret cat [filename]
 ```
 
-Or to get the decrypted `credentials.txt` file, run
+Or to get the decrypted `.env` file, run
 
 ```shell
 git-secret reveal [filename]

knowledgehub/base.py

@@ -16,6 +16,19 @@ class BaseComponent(Compose):
         - is_batch: check if input is batch
     """
 
+    inflow = None
+
+    def flow(self):
+        if self.inflow is None:
+            raise ValueError("No inflow provided.")
+
+        if not isinstance(self.inflow, BaseComponent):
+            raise ValueError(
+                f"inflow must be a BaseComponent, found {type(self.inflow)}"
+            )
+
+        return self.__call__(self.inflow.flow())
+
     @abstractmethod
     def run_raw(self, *args, **kwargs):
         ...

knowledgehub/llms/base.py

@@ -1,25 +1,13 @@
-from dataclasses import dataclass, field
 from typing import List
 
-from ..base import BaseComponent
+from pydantic import Field
+
+from kotaemon.documents.base import Document
 
 
-@dataclass
+class LLMInterface(Document):
-class LLMInterface:
+    candidates: List[str]
-    text: List[str]
     completion_tokens: int = -1
     total_tokens: int = -1
     prompt_tokens: int = -1
-    logits: List[List[float]] = field(default_factory=list)
+    logits: List[List[float]] = Field(default_factory=list)
-
-
-class PromptTemplate(BaseComponent):
-    pass
-
-
-class Extract(BaseComponent):
-    pass
-
-
-class PromptNode(BaseComponent):
-    pass

knowledgehub/llms/chats/base.py

@@ -11,7 +11,17 @@ Message = TypeVar("Message", bound=BaseMessage)
 
 
 class ChatLLM(BaseComponent):
-    ...
+    def flow(self):
+        if self.inflow is None:
+            raise ValueError("No inflow provided.")
+
+        if not isinstance(self.inflow, BaseComponent):
+            raise ValueError(
+                f"inflow must be a BaseComponent, found {type(self.inflow)}"
+            )
+
+        text = self.inflow.flow().text
+        return self.__call__(text)
 
 
 class LangchainChatLLM(ChatLLM):
@@ -44,8 +54,10 @@ class LangchainChatLLM(ChatLLM):
 
     def run_document(self, text: List[Message], **kwargs) -> LLMInterface:
         pred = self.agent.generate([text], **kwargs)  # type: ignore
+        all_text = [each.text for each in pred.generations[0]]
         return LLMInterface(
-            text=[each.text for each in pred.generations[0]],
+            text=all_text[0] if len(all_text) > 0 else "",
+            candidates=all_text,
             completion_tokens=pred.llm_output["token_usage"]["completion_tokens"],
             total_tokens=pred.llm_output["token_usage"]["total_tokens"],
             prompt_tokens=pred.llm_output["token_usage"]["prompt_tokens"],

knowledgehub/llms/completions/base.py

@@ -33,8 +33,10 @@ class LangchainLLM(LLM):
 
     def run_raw(self, text: str) -> LLMInterface:
         pred = self.agent.generate([text])
+        all_text = [each.text for each in pred.generations[0]]
         return LLMInterface(
-            text=[each.text for each in pred.generations[0]],
+            text=all_text[0] if len(all_text) > 0 else "",
+            candidates=all_text,
             completion_tokens=pred.llm_output["token_usage"]["completion_tokens"],
             total_tokens=pred.llm_output["token_usage"]["total_tokens"],
             prompt_tokens=pred.llm_output["token_usage"]["prompt_tokens"],

knowledgehub/pipelines/agents/react/agent.py

@@ -162,7 +162,7 @@ class ReactAgent(BaseAgent):
             prompt = self._compose_prompt(instruction)
             logging.info(f"Prompt: {prompt}")
             response = self.llm(prompt, stop=["Observation:"])  # type: ignore
-            response_text = response.text[0]
+            response_text = response.text
             logging.info(f"Response: {response_text}")
             action_step = self._parse_output(response_text)
             if action_step is None:

knowledgehub/pipelines/agents/rewoo/agent.py

@@ -245,7 +245,7 @@ class RewooAgent(BaseAgent):
 
         # Plan
         planner_output = planner(instruction)
-        plannner_text_output = planner_output.text[0]
+        plannner_text_output = planner_output.text
         plan_to_es, plans = self._parse_plan_map(plannner_text_output)
         planner_evidences, evidence_level = self._parse_planner_evidences(
             plannner_text_output
@@ -263,7 +263,7 @@ class RewooAgent(BaseAgent):
 
         # Solve
         solver_output = solver(instruction, worker_log)
-        solver_output_text = solver_output.text[0]
+        solver_output_text = solver_output.text
 
         return AgentOutput(
             output=solver_output_text, cost=total_cost, token_usage=total_token

knowledgehub/post_processing/extractor.py

@@ -50,9 +50,9 @@ class RegexExtractor(BaseComponent):
         if not output_map:
             return text
 
-        return output_map.get(text, text)
+        return str(output_map.get(text, text))
 
-    def run_raw(self, text: str) -> List[str]:
+    def run_raw(self, text: str) -> List[Document]:
         """
         Runs the raw text through the static pattern and output mapping, returning a
             list of strings.
@@ -66,9 +66,12 @@ class RegexExtractor(BaseComponent):
         output = self.run_raw_static(self.pattern, text)
         output = [self.map_output(text, self.output_map) for text in output]
 
-        return output
+        return [
+            Document(text=text, metadata={"origin": "RegexExtractor"})
+            for text in output
+        ]
 
-    def run_batch_raw(self, text_batch: List[str]) -> List[List[str]]:
+    def run_batch_raw(self, text_batch: List[str]) -> List[List[Document]]:
         """
         Runs a batch of raw text inputs through the `run_raw()` method and returns the
             output for each input.
@@ -95,13 +98,7 @@ class RegexExtractor(BaseComponent):
         Returns:
             List[Document]: A list of extracted documents.
         """
-        texts = self.run_raw(document.text)
+        return self.run_raw(document.text)
-        output = [
-            Document(text=text, metadata={**document.metadata, "RegexExtractor": True})
-            for text in texts
-        ]
-
-        return output
 
     def run_batch_document(
         self, document_batch: List[Document]

knowledgehub/prompt/base.py

@@ -1,3 +1,4 @@
+import warnings
 from typing import Union
 
 from kotaemon.base import BaseComponent
@@ -5,7 +6,7 @@ from kotaemon.documents.base import Document
 from kotaemon.prompt.template import PromptTemplate
 
 
-class BasePrompt(BaseComponent):
+class BasePromptComponent(BaseComponent):
     """
     Base class for prompt components.
 
@@ -15,6 +16,16 @@ class BasePrompt(BaseComponent):
             given template.
     """
 
+    def __init__(self, template: Union[str, PromptTemplate], **kwargs):
+        super().__init__()
+        self.template = (
+            template
+            if isinstance(template, PromptTemplate)
+            else PromptTemplate(template)
+        )
+
+        self.__set(**kwargs)
+
     def __check_redundant_kwargs(self, **kwargs):
         """
         Check for redundant keyword arguments.
@@ -33,7 +44,9 @@ class BasePrompt(BaseComponent):
 
         redundant_keys = provided_keys - expected_keys
         if redundant_keys:
-            raise ValueError(f"\nKeys provided but not in template: {redundant_keys}")
+            warnings.warn(
+                f"Keys provided but not in template: {redundant_keys}", UserWarning
+            )
 
     def __check_unset_placeholders(self):
         """
@@ -111,27 +124,34 @@ class BasePrompt(BaseComponent):
         Returns:
             dict: A dictionary of keyword arguments.
         """
+
+        def __prepare(key, value):
+            if isinstance(value, str):
+                return value
+            if isinstance(value, (int, Document)):
+                return str(value)
+
+            raise ValueError(
+                f"Unsupported type {type(value)} for template value of key {key}"
+            )
+
         kwargs = {}
         for k in self.template.placeholders:
             v = getattr(self, k)
-            if isinstance(v, (int, Document)):
+            if isinstance(v, BaseComponent):
-                v = str(v)
+                v = v()
-            elif isinstance(v, BaseComponent):
+            if isinstance(v, list):
-                v = str(v())
+                v = str([__prepare(k, each) for each in v])
+            elif isinstance(v, (str, int, Document)):
+                v = __prepare(k, v)
+            else:
+                raise ValueError(
+                    f"Unsupported type {type(v)} for template value of key {k}"
+                )
             kwargs[k] = v
 
         return kwargs
 
-    def __init__(self, template: Union[str, PromptTemplate], **kwargs):
-        super().__init__()
-        self.template = (
-            template
-            if isinstance(template, PromptTemplate)
-            else PromptTemplate(template)
-        )
-
-        self.__set(**kwargs)
-
     def set(self, **kwargs):
         """
         Similar to `__set` but for external use.
@@ -163,7 +183,8 @@ class BasePrompt(BaseComponent):
         self.__check_unset_placeholders()
         prepared_kwargs = self.__prepare_value()
 
-        return self.template.populate(**prepared_kwargs)
+        text = self.template.populate(**prepared_kwargs)
+        return Document(text=text, metadata={"origin": "PromptComponent"})
 
     def run_raw(self, *args, **kwargs):
         pass
@@ -182,3 +203,6 @@ class BasePrompt(BaseComponent):
 
     def is_batch(self, *args, **kwargs):
         pass
+
+    def flow(self):
+        return self.__call__()

setup.py

@@ -56,6 +56,8 @@ setuptools.setup(
             "chromadb",
             "wikipedia",
             "googlesearch-python",
+            "python-dotenv",
+            "pytest-mock",
         ],
     },
     entry_points={"console_scripts": ["kh=kotaemon.cli:main"]},

tests/test_post_processing.py

@@ -30,9 +30,11 @@ def test_is_batch(regex_extractor):
 
 def test_run_raw(regex_extractor):
     output = regex_extractor("This is a test. 123")
+    output = [each.text for each in output]
     assert output == ["123"]
 
 
 def test_run_batch_raw(regex_extractor):
     output = regex_extractor(["This is a test. 123", "456"])
+    output = [[each.text for each in batch] for batch in output]
     assert output == [["123"], ["456"]]

tests/test_prompt.py

@@ -2,7 +2,7 @@ import pytest
 
 from kotaemon.documents.base import Document
 from kotaemon.post_processing.extractor import RegexExtractor
-from kotaemon.prompt.base import BasePrompt
+from kotaemon.prompt.base import BasePromptComponent
 from kotaemon.prompt.template import PromptTemplate
 
 
@@ -14,7 +14,7 @@ def test_set_attributes():
     )
     comp.set_run(kwargs={"text": "This is a test. 1 2 3"}, temp=True)
 
-    prompt = BasePrompt(template=template, s="Alice", i=30, doc=doc, comp=comp)
+    prompt = BasePromptComponent(template=template, s="Alice", i=30, doc=doc, comp=comp)
     assert prompt.s == "Alice"
     assert prompt.i == 30
     assert prompt.doc == doc
@@ -23,23 +23,23 @@ def test_set_attributes():
 
 def test_check_redundant_kwargs():
     template = PromptTemplate("Hello, {name}!")
-    prompt = BasePrompt(template, name="Alice")
+    prompt = BasePromptComponent(template, name="Alice")
-    with pytest.raises(ValueError):
+    with pytest.warns(UserWarning, match="Keys provided but not in template: {'age'}"):
-        prompt._BasePrompt__check_redundant_kwargs(name="Alice", age=30)
+        prompt._BasePromptComponent__check_redundant_kwargs(name="Alice", age=30)
 
 
 def test_check_unset_placeholders():
     template = PromptTemplate("Hello, {name}! I'm {age} years old.")
-    prompt = BasePrompt(template, name="Alice")
+    prompt = BasePromptComponent(template, name="Alice")
     with pytest.raises(ValueError):
-        prompt._BasePrompt__check_unset_placeholders()
+        prompt._BasePromptComponent__check_unset_placeholders()
 
 
 def test_validate_value_type():
     template = PromptTemplate("Hello, {name}!")
-    prompt = BasePrompt(template)
+    prompt = BasePromptComponent(template)
     with pytest.raises(ValueError):
-        prompt._BasePrompt__validate_value_type(name={})
+        prompt._BasePromptComponent__validate_value_type(name={})
 
 
 def test_run():
@@ -50,18 +50,18 @@ def test_run():
     )
     comp.set_run(kwargs={"text": "This is a test. 1 2 3"}, temp=True)
 
-    prompt = BasePrompt(template=template, s="Alice", i=30, doc=doc, comp=comp)
+    prompt = BasePromptComponent(template=template, s="Alice", i=30, doc=doc, comp=comp)
 
     result = prompt()
 
     assert (
-        result
+        result.text
         == "str = Alice, int = 30, doc = Helloo, Alice!, comp = ['One', 'Two', 'Three']"
     )
 
 
 def test_set_method():
     template = PromptTemplate("Hello, {name}!")
-    prompt = BasePrompt(template)
+    prompt = BasePromptComponent(template)
     prompt.set(name="Alice")
     assert prompt.name == "Alice"