Concept linking (#28)

* Update README for concept-linking Change structure of requirements for entire project * Fully integrated prompt-engineering solution in concept linking to new shared repo. * Integrated UntrainedSpacy solution Changed gitignore Refactored some duplicate code for untrainedspacy and promptEng sol. * Integrated StringComparison solution * Update README for concept-linking Change structure of requirements for entire project * Fully integrated prompt-engineering solution in concept linking to new shared repo. * Integrated UntrainedSpacy solution Changed gitignore Refactored some duplicate code for untrainedspacy and promptEng sol. * Integrated StringComparison solution * Minor bugfixing * Fixed missing output.json * Test requirements fix * Test requirements fix 2 * Fix empty folders not being committed * Added support for outputting sentence when doing test_run * ML Solution refactor * ML Solution refactor * Deleted obsolete test files * Evaluation files * Fixed small label error * Fixed ont mapping mistakes * Evaluation Script * Generated output for Promptbased * Generated output for Promptbased * ML UnitTest * ML UnitTest * Minor fixes * String comparison test (#27) * String comparison test * Fixed requirements * Update test-and-build.yml * Added error handling for no triples generated. * Changed python 3.12 to 3.11 * Fixed test_server.py for concept_linking. --------- Co-authored-by: denBruneBarone <[email protected]> Co-authored-by: Vi Thien Le <[email protected]> Co-authored-by: Gamma <[email protected]> Co-authored-by: Mikkel Wissing <[email protected]>
Knox-AAU · Dec 12, 2023 · 140cff6 · 140cff6
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -15,7 +15,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v3
         with:
-          python-version: 3.12.0
+          python-version: 3.11.0
 
       - name: Install dependencies
         run: |

diff --git a/Dockerfile b/Dockerfile
@@ -2,9 +2,8 @@ FROM python:3.11-slim
 
 WORKDIR /code
 
-COPY requirements.txt ./
-RUN pip install --no-cache-dir -r requirements.txt
-
 COPY . .
+RUN pip install --no-cache-dir -r requirements_docker.txt
+
 
 CMD ["python", "-u", "-m", "server.server", "--host", "0.0.0.0", "--port", "4444", "--reload"]
diff --git a/concept_linking/.gitignore b/concept_linking/.gitignore
@@ -153,15 +153,12 @@ dmypy.json
 cython_debug/
 
 # PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  JetBrains specific template is maintained in a separate JetBrains..gitignore that can
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  and can be added to the global .gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 
-#Ignoring NDA classified files
-data/files/PromptEngineering/
-data/files/EvaluationData/output.json
 
 #Llama model
 tools/LlamaServer/llama-2-7b-chat.Q2_K.gguf

diff --git a/concept_linking/README.md b/concept_linking/README.md
@@ -1,61 +1,126 @@
-# D: Preproscessing Layer - Concept Linking
+# Concept Linking
 
-Repository of group D in KNOX pipeline.
+---
+## Background
+In group D, four different solutions have been implemented. These will be mentioned further in a later section.
+At default the solution that will be running is PromptEngineering.
 
-## Description
+To change which solution to run in the pipeline perform the following changes...
 
-This repository is for type classification of already provided sententes with given entity mentions. Several different solutions were created, in order to find the best one.
+First change directory to the 'server' folder in the root directory.
 
-### Dependencies
+Next, open the server.py file.
+On line 24, under the text "#Begin ConceptLinking"
+Change the code, to run the desired solution.
 
-- Python
-- PIP
-- Git
 
-### Installing
+## Requirements
+For any of the four solutions, it is necessary to install the requirements found
+in the requirements.txt file inside /{Solution_Name}/requirements.txt
+
+However since this is a joint codebase for both relation-extraction and concept-linking,
+there is a global requirements.txt file in the root directory.
+It follows a nested structure, meaning that installing only to one if the root folder, 
+will install all the rest.
+
+It will install both the necessary requirements for both groups' solutions.
+However since it is possible to change which of the four concept-linking solutions to run, 
+it is also necessary to the requirements to be installed accordingly.
+This is done by navigation to
 
 ```
-git clone https://github.com/Knox-AAU/PreprocessingLayer_Concept-Linking
+./concept_linking/requirements.txt
 ```
+In this file, there is listed a reference to the four different requirements.txt files.
+Remove the #(comment) from the one referencing the solution you want to run.
+
+### Example
+Install the requirements for the PromptEngineering solution
 
-### Initial Setup
+Navigate to the following directory
 
-- Navigate to root folder
-- Run the following command for installing all requirements:
+```
+../concept_linking/solutions/PromptEngineering/
+```
 
+And run the following command
 ```
 pip install -r requirements.txt
 ```
 
-### Adding modules
+## Solutions
 
-- Navigate to root folder.
-- Run the following command to add all installed modules:
+Following below is brief description of each of the four solutions and how to get started.
+
+---
 
-```
-pip freeze > requirements.txt
-```
 
-### Executing program
+### Machine Learning
+description WIP
 
-- Navigate to main.py in Program directory
-- Run main.py with Python
+### Prompt Engineering
+Uses the LLM Llama2. A prompt is given to the model. 
 
 ```
-python .\program\main.py
+ prompt_template = {
+                    "system_message": ("The input sentence is all your knowledge. \n"
+                                       "Do not answer if it can't be found in the sentence. \n"
+                                       "Do not use bullet points. \n"
+                                       "Do not identify entity mentions yourself, use the provided ones \n"
+                                       "Given the input in the form of the content from a file: \n"
+                                       "[Sentence]: {content_sentence} \n"
+                                       "[EntityMention]: {content_entity} \n"),
+
+                    "user_message": ("Classify the [EntityMention] in regards to ontology classes: {ontology_classes} \n"
+                                     "The output answer must be in JSON in the following format: \n"
+                                     "{{ \n"
+                                     "'Entity': 'Eiffel Tower', \n"
+                                     "'Class': 'ArchitecturalStructure' \n"
+                                     "}} \n"),
+
+                    "max_tokens": 4092
+                }
 ```
 
-or:
+The variables {content_sentence} and {content_entity} is found in a previous part of the KNOX pipeline.
+The variable {ontology_classes} fetched by the Ontology endpoint provided by group E(Database Layer)
 
+
+#### Using LocalLlama API server
+It is possible to use a local LlamaServer. It can be found in ../concept_linking/tools/LlamaServer.
+A README for setting up an instance of this server can be found in the directory given above.
+
+#### Using the Llama API server hosted in the KNOX pipeline
+WIP
+Go to the directory /concept_linking/PromptEngineering/main
+set the api_url accordingly
+``` 
+api_url={domain or ip+port of llama server hosted in the knox pipeline}
 ```
-cd .\program\
-python .\main.py
-```
+Refer to the <a href="https://docs.google.com/spreadsheets/d/1dvVQSEvw15ulNER8qvl1P8Ufq-p3vLU0PswUeahhThg/edit#gid=0" target="_blank">Server Distribution document</a>
+ for specific dns and ip+port information.
 
-## Report
+### String Comparison
+description WIP
 
-Description of the project can be found in the report on [Overleaf](https://www.overleaf.com/project/65000513b10b4521e8907099) (requires permission)
 
-## Authors
+### Untrained Spacy
+description WIP
+
+
+
+---
+
+## Tools
+
+### LlamaServer
 
-Lucas, Gamma, Vi, Mikkel, Caspar & Rune
+### OntologyGraphBuilder
+
+---
+
+## Report
+Description of the project can be found in the report on Overleaf (requires permission)
+
+## Authors
+Lucas, Gamma, Vi, Mikkel, Caspar & Rune