diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 5fa51c9..8789242 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -3,37 +3,40 @@ name: Python package
 on:
   push:
     branches:
-    - main
+      - main
   pull_request:
     branches:
-    - main
+      - main
 
 jobs:
-
   build:
     name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: ['ubuntu-latest'] # ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.9'] # ['3.7', '3.8', '3.9', '3.10', '3.11']
+        os: ["ubuntu-latest"]
+        python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Python info
-        shell: bash -l {0}
+
+      # Installation
+      - name: Install dependencies
         run: |
-          which python3
-          python3 --version
-      - name: Upgrade pip and install dependencies
+          python -m pip install poetry
+          poetry install
+
+      # Testing
+      - name: Test with pytest
         run: |
-          python3 -m pip install --upgrade pip setuptools
-          python3 -m pip install .[test]
-      - name: Run unit tests
-        run: pytest -v
-      - name: Verify that we can build the package
-        run: python3 setup.py sdist bdist_wheel
\ No newline at end of file
+          poetry run pytest
+      # Type checking
+      # - name: Type check
+      #   run: |
+      #     poetry run pytype .
diff --git a/.github/workflows/publish-docker.yml b/.github/workflows/publish-docker.yml
new file mode 100644
index 0000000..f56219d
--- /dev/null
+++ b/.github/workflows/publish-docker.yml
@@ -0,0 +1,70 @@
+name: "Build and Publish docker image"
+
+on:
+  workflow_dispatch:  # This line adds the manual trigger
+  push:
+    branches: [ "main" ]
+  pull_request: # This should be removed once testing is complete
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          
+      - name: downcase REPO name
+        run: |
+          echo "REPO=${GITHUB_REPOSITORY,,}" >>${GITHUB_ENV}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.REPO }}
+          tags: |
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=sha,enable=true,priority=100,prefix=sha-,suffix=,format=short
+
+      - name: Install Arial font
+        run: |
+          sudo apt-get update
+          sudo apt install ttf-mscorefonts-installer
+          sudo apt-get install -y ttf-mscorefonts-installer
+          sudo fc-cache -f
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: false  # Do not push at this stage
+          tags: ${{ steps.meta.outputs.tags }}
+
+      - name: Push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: |
+            org.opencontainers.image.source=${{ github.event.repository.clone_url }}
+            org.opencontainers.image.created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')
+            org.opencontainers.image.revision=${{ github.sha }}
diff --git a/.gitignore b/.gitignore
index fc40ccc..bcae9da 100644
--- a/.gitignore
+++ b/.gitignore
@@ -309,4 +309,4 @@ tags
 
 # Output files
 
-out_*
+out/out_*
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d627aea..1440e11 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -13,13 +13,13 @@ The sections below outline the steps in each case.
 
 ## You have a question
 
-1. use the search functionality [here](git@github.com:Workflomics/workflomics-QCmetric/issues) to see if someone already filed the same issue;
+1. use the search functionality [here](git@github.com:Workflomics/pubmetric/issues) to see if someone already filed the same issue;
 2. if your issue search did not yield any relevant results, make a new issue;
 3. apply the "Question" label; apply other labels when relevant.
 
 ## You think you may have found a bug
 
-1. use the search functionality [here](git@github.com:Workflomics/workflomics-QCmetric/issues) to see if someone already filed the same issue;
+1. use the search functionality [here](git@github.com:Workflomics/pubmetric/issues) to see if someone already filed the same issue;
 1. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
     - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
     - some identifying information (name and version number) for dependencies you're using;
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..ef8a36b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,27 @@
+# Use an official Python runtime as a parent image
+FROM python:3.11-slim
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Install Poetry
+RUN pip install poetry
+
+# Copy the pyproject.toml and poetry.lock files
+COPY pyproject.toml poetry.lock /app/
+
+# Copy the application code before installing dependencies
+COPY . /app
+
+# Set the PYTHONPATH environment variable
+ENV PYTHONPATH=/app/src
+
+# Install the dependencies using Poetry without creating a virtual environment
+RUN poetry config virtualenvs.create false \
+    && poetry install --no-dev --no-interaction --no-ansi
+
+# Expose the port where the FastAPI app will run
+EXPOSE 8000
+
+# Command to run the FastAPI app using Uvicorn
+CMD ["poetry", "run", "uvicorn", "src.pubmetric.api_controller:app", "--host", "0.0.0.0", "--port", "8000"]
diff --git a/README.md b/README.md
index 2db2e9a..72cd48d 100644
--- a/README.md
+++ b/README.md
@@ -2,25 +2,46 @@
 
 This code is currently under development.
 
-
 ## Overview
 
 pubmetric is a library for benchmarking workflows based on the co-citation network connectivity of the publications describing the tools making up the workflow.
 
-
 ## Usage
 
 First start Cytoscape, then open your notebook environment and run the code.
 
-
 ## Dependencies
 
-Python packages listed in the `setup.py` file. You can install them using the following command: `pip install .`
-For the development, you can include the test dependencies by running `pip install .[test]`
+Python packages listed in the `pyproject.toml` file. You can install them using the following command:
+
+```bash
+    poetry install
+```
+
+If you're setting up the project for development and need the test dependencies, you can include them by running:
+
+```bash
+    poetry install --with dev
+```
 
 Cytoscape software, which can be downloaded from [https://cytoscape.org/](https://cytoscape.org/). Please make sure Cytoscape is open and running when executing the code.
 
+## For Developers
+
+Build the Docker image:
+
+```bash
+    sudo docker build -t pubmetric_v0.2 -f Dockerfile .
+```
+
+You can run the Docker image with the following command:
+
+```bash
+    sudo docker run -p 8000:8000 pubmetric_v0.2
+```
+
+This will start the FastAPI server on port 8000. For example you can access the OpenAPI specification (Swagger UI) at http://localhost:8000/docs.
 
 ## License
 
-This project is licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0). 
+This project is licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).
diff --git a/data/out_default/doi_pmid_library.json b/data/out_default/doi_pmid_library.json
new file mode 100644
index 0000000..8d3f661
--- /dev/null
+++ b/data/out_default/doi_pmid_library.json
@@ -0,0 +1 @@
+{"10.1002/pmic.201200439": "23148064", "10.1038/nbt.2377": "23051804", "10.1093/nar/gkz369": "31066453", "10.1093/bioinformatics/bth092": "14976030", "10.1038/nmeth.4256": "28394336"}
\ No newline at end of file
diff --git a/data/out_default/graph.pkl b/data/out_default/graph.pkl
new file mode 100644
index 0000000..d2d003c
Binary files /dev/null and b/data/out_default/graph.pkl differ
diff --git a/data/out_default/tool_metadata.json b/data/out_default/tool_metadata.json
new file mode 100644
index 0000000..5873634
--- /dev/null
+++ b/data/out_default/tool_metadata.json
@@ -0,0 +1 @@
+{"creation_date": "2024-10-16 06:14:52.344396", "topic": "", "total_nr_tools": 15, "biotools_wo_pmid": 5, "pmid_from_doi": 5, "tools": [{"name": "PeptideProphet", "doi": null, "topics": ["Proteomics", "Proteomics experiment", "Statistics and probability"], "nr_publications": 1, "all_publications": ["12403597"], "publication_date": 2002, "pmid": "12403597"}, {"name": "ProteinProphet", "doi": null, "topics": ["Proteomics", "Proteomics experiment", "Statistics and probability"], "nr_publications": 1, "all_publications": ["14632076"], "publication_date": 2003, "pmid": "14632076"}, {"name": "StPeter", "doi": "10.1021/acs.jproteome.7b00786", "topics": ["Proteomics", "Proteomics experiment"], "nr_publications": 1, "all_publications": ["29400476"], "publication_date": 2018, "pmid": "29400476"}, {"name": "mzRecal", "doi": "10.1093/bioinformatics/btab056", "topics": ["Proteomics"], "nr_publications": 1, "all_publications": ["33538780"], "publication_date": 2021, "pmid": "33538780"}, {"name": "MS Amanda", "doi": "10.1021/pr500202e", "topics": ["Proteomics", "Protein modifications"], "nr_publications": 3, "all_publications": ["24909410", "33759252", "29863353"], "publication_date": 2014, "pmid": "24909410"}, {"name": "Comet", "doi": "10.1002/pmic.201200439", "topics": ["Proteomics", "Protein modifications"], "nr_publications": 2, "all_publications": [null, null], "publication_date": 2013, "pmid": "23148064"}, {"name": "idconvert", "doi": "10.1038/nbt.2377", "topics": ["Proteomics", "Proteomics experiment"], "nr_publications": 1, "all_publications": [null], "publication_date": 2012, "pmid": "23051804"}, {"name": "XTandem", "doi": "10.1093/bioinformatics/bth092", "topics": ["Proteomics", "Proteomics experiment"], "nr_publications": 1, "all_publications": [null], "publication_date": 2004, "pmid": "14976030"}, {"name": "MSFragger", "doi": "10.1038/nmeth.4256", "topics": ["Proteomics experiment", "Proteomics", "Protein modifications"], "nr_publications": 1, "all_publications": [null], "publication_date": 2017, "pmid": "28394336"}]}
\ No newline at end of file
diff --git a/dev-viz-notebooks/ML_metric_eval.ipynb b/dev-viz-notebooks/ML_metric_eval.ipynb
index 5c55df6..719d295 100644
--- a/dev-viz-notebooks/ML_metric_eval.ipynb
+++ b/dev-viz-notebooks/ML_metric_eval.ipynb
@@ -20,7 +20,7 @@
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import seaborn as sns\n",
-    "import wfqc.network as nw\n",
+    "import pumetric.network as nw\n",
     "from scipy.stats import ttest_rel, spearmanr\n",
     "from sklearn.metrics import confusion_matrix, mean_squared_error\n",
     "from sklearn.model_selection import train_test_split\n",
@@ -30,7 +30,7 @@
     "from sklearn.svm import SVR\n",
     "from sklearn.preprocessing import KBinsDiscretizer\n",
     "from sklearn import tree\n",
-    "from wfqc.metrics import *\n",
+    "from pumetric.metrics import *\n",
     "from datetime import datetime"
    ]
   },
diff --git a/dev-viz-notebooks/TTP_data.ipynb b/dev-viz-notebooks/TTP_data.ipynb
index 1517d51..d16a72e 100644
--- a/dev-viz-notebooks/TTP_data.ipynb
+++ b/dev-viz-notebooks/TTP_data.ipynb
@@ -22,8 +22,8 @@
     "\n",
     "sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '../src')))\n",
     "\n",
-    "from wfqc.metrics import *\n",
-    "from wfqc.network import create_network\n"
+    "from pumetric.metrics import *\n",
+    "from pumetric.network import create_network\n"
    ]
   },
   {
@@ -471,7 +471,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/broken_dataset_gen.ipynb b/dev-viz-notebooks/broken_dataset_gen.ipynb
index c39a175..84d8994 100644
--- a/dev-viz-notebooks/broken_dataset_gen.ipynb
+++ b/dev-viz-notebooks/broken_dataset_gen.ipynb
@@ -953,7 +953,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/graph_statistics.ipynb b/dev-viz-notebooks/graph_statistics.ipynb
index d39913f..d9b2545 100644
--- a/dev-viz-notebooks/graph_statistics.ipynb
+++ b/dev-viz-notebooks/graph_statistics.ipynb
@@ -869,7 +869,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/metric_dev.ipynb b/dev-viz-notebooks/metric_dev.ipynb
index b1e1ea2..1200e46 100644
--- a/dev-viz-notebooks/metric_dev.ipynb
+++ b/dev-viz-notebooks/metric_dev.ipynb
@@ -1344,7 +1344,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/network_dev.ipynb b/dev-viz-notebooks/network_dev.ipynb
index ed656c8..b7679cd 100644
--- a/dev-viz-notebooks/network_dev.ipynb
+++ b/dev-viz-notebooks/network_dev.ipynb
@@ -412,7 +412,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/random_dataset_gen.ipynb b/dev-viz-notebooks/random_dataset_gen.ipynb
index 5cfe2d0..8418331 100644
--- a/dev-viz-notebooks/random_dataset_gen.ipynb
+++ b/dev-viz-notebooks/random_dataset_gen.ipynb
@@ -535,7 +535,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/rated_dataset_expanded.ipynb b/dev-viz-notebooks/rated_dataset_expanded.ipynb
index 3666b5c..18e213b 100644
--- a/dev-viz-notebooks/rated_dataset_expanded.ipynb
+++ b/dev-viz-notebooks/rated_dataset_expanded.ipynb
@@ -298,7 +298,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/rated_dataset_parsing.ipynb b/dev-viz-notebooks/rated_dataset_parsing.ipynb
index afc8b14..615ef12 100644
--- a/dev-viz-notebooks/rated_dataset_parsing.ipynb
+++ b/dev-viz-notebooks/rated_dataset_parsing.ipynb
@@ -420,7 +420,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/thresholding.ipynb b/dev-viz-notebooks/thresholding.ipynb
index 1aa2738..83c43e8 100644
--- a/dev-viz-notebooks/thresholding.ipynb
+++ b/dev-viz-notebooks/thresholding.ipynb
@@ -238,7 +238,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/workflow_length_stats.ipynb b/dev-viz-notebooks/workflow_length_stats.ipynb
index ffc6079..daca98c 100644
--- a/dev-viz-notebooks/workflow_length_stats.ipynb
+++ b/dev-viz-notebooks/workflow_length_stats.ipynb
@@ -22,8 +22,8 @@
     "\n",
     "sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '../src')))\n",
     "\n",
-    "from wfqc.metrics import *\n",
-    "from wfqc.network import create_network\n"
+    "from pumetric.metrics import *\n",
+    "from pumetric.network import create_network\n"
    ]
   },
   {
@@ -125,7 +125,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": "pumetric",
    "language": "python",
    "name": "python3"
   },
diff --git a/dev-viz-notebooks/workflow_parsing.ipynb b/dev-viz-notebooks/workflow_parsing.ipynb
index a7ed11c..d7c5835 100644
--- a/dev-viz-notebooks/workflow_parsing.ipynb
+++ b/dev-viz-notebooks/workflow_parsing.ipynb
@@ -9,13 +9,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "import sys\n",
     "import os\n",
     "import json\n",
+    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
     "import igraph\n",
     "sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '../src')))\n",
@@ -25,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 70,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -41,7 +42,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -49,9 +50,18 @@
      "output_type": "stream",
      "text": [
       "doc: A workflow including the tool(s) XTandem, ProteinProphet, PeptideProphet, StPeter.\n",
-      "\n",
-      "[('12403597', '29400476'), ('14632076', '29400476'), ('14976030', '12403597'), ('14976030', '14632076')]\n",
-      "[('12403597', '29400476'), ('14632076', '29400476'), ('14976030', '12403597'), ('14976030', '14632076')]\n"
+      "\n"
+     ]
+    },
+    {
+     "ename": "NameError",
+     "evalue": "name 'parse_workflows' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[7], line 10\u001b[0m\n\u001b[1;32m      7\u001b[0m expected_tuple_workflow \u001b[38;5;241m=\u001b[39m [(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m14976030\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m14632076\u001b[39m\u001b[38;5;124m'\u001b[39m )  , (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m14976030\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m12403597\u001b[39m\u001b[38;5;124m'\u001b[39m)  , (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m14632076\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m29400476\u001b[39m\u001b[38;5;124m'\u001b[39m)  , (\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m12403597\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124m29400476\u001b[39m\u001b[38;5;124m'\u001b[39m)  ]\n\u001b[1;32m      8\u001b[0m                         \u001b[38;5;66;03m# [ (XTandem, ProteinProphet), (XTandem, PeptideProphet), (ProteinProphet, StPeter), (PeptideProphet, StPeter) ]\u001b[39;00m\n\u001b[0;32m---> 10\u001b[0m tuple_workflow \u001b[38;5;241m=\u001b[39m \u001b[43mparse_workflows\u001b[49m(cwl_filename\u001b[38;5;241m=\u001b[39mcwl_filename, metadata_filename\u001b[38;5;241m=\u001b[39mmetadata_filename)\n\u001b[1;32m     11\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;28msorted\u001b[39m(tuple_workflow))\n\u001b[1;32m     12\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;28msorted\u001b[39m(expected_tuple_workflow))\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'parse_workflows' is not defined"
      ]
     }
    ],
@@ -377,7 +387,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "WFQC",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -391,7 +401,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,
diff --git a/github_workflomics_stats.ipynb b/github_workflomics_stats.ipynb
new file mode 100644
index 0000000..e88ff6e
--- /dev/null
+++ b/github_workflomics_stats.ipynb
@@ -0,0 +1,156 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Issues"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Total open Issues: 78\n",
+      "Total closed Issues: 69\n",
+      "Total open Issues: 24\n",
+      "Total closed Issues: 6\n"
+     ]
+    }
+   ],
+   "source": [
+    "\n",
+    "w_issues_open = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"Internal_documenation\", \"issues\": { \"totalCount\": 6 } }, { \"name\": \"workflomics-frontend\", \"issues\": { \"totalCount\": 23 } }, { \"name\": \"tools-and-domains\", \"issues\": { \"totalCount\": 28 } }, { \"name\": \"domain-annotations\", \"issues\": { \"totalCount\": 3 } }, { \"name\": \"WOMBAT-Pipelines\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"DemoKit\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"designtime-bench-service\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"biohackathon_2023\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"workflomics-benchmarker\", \"issues\": { \"totalCount\": 3 } }, { \"name\": \"workflomics-readthedocs\", \"issues\": { \"totalCount\": 9 } }, { \"name\": \"IEEE-eScience-2024\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"pubmetric\", \"issues\": { \"totalCount\": 6 } }, { \"name\": \"pubmetric-develipment\", \"issues\": { \"totalCount\": 0 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOMqb6gg==\" } } } } }\n",
+    "\n",
+    "w_issues_closed = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"Internal_documenation\", \"issues\": { \"totalCount\": 12 } }, { \"name\": \"workflomics-frontend\", \"issues\": { \"totalCount\": 9 } }, { \"name\": \"tools-and-domains\", \"issues\": { \"totalCount\": 17 } }, { \"name\": \"domain-annotations\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"WOMBAT-Pipelines\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"DemoKit\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"designtime-bench-service\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"biohackathon_2023\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"workflomics-benchmarker\", \"issues\": { \"totalCount\": 8 } }, { \"name\": \"workflomics-readthedocs\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"IEEE-eScience-2024\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"pubmetric\", \"issues\": { \"totalCount\": 23 } }, { \"name\": \"pubmetric-develipment\", \"issues\": { \"totalCount\": 0 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOMqb6gg==\" } } } } }\n",
+    "\n",
+    "\n",
+    "\n",
+    "w_pr_counts_open = [repo[\"issues\"][\"totalCount\"] for repo in w_issues_open[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "total_prs = sum(w_pr_counts_open)\n",
+    "print(f\"Total open Issues: {total_prs}\")\n",
+    "\n",
+    "w_pr_counts_closed = [repo[\"issues\"][\"totalCount\"] for repo in w_issues_closed[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "total_prs = sum(w_pr_counts_closed)\n",
+    "print(f\"Total closed Issues: {total_prs}\")\n",
+    "\n",
+    "\n",
+    "a_issues_open = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"APE\", \"issues\": { \"totalCount\": 9 } }, { \"name\": \"APE_UseCases\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"Burke_Docker\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"APE_readthedocs\", \"issues\": { \"totalCount\": 2 } }, { \"name\": \"Proteomics_domain_setup\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"APE-Web\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"Automated_Cascabel_Pipeline\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"SLTLx-ANTLR-to-JavaScript\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"restape\", \"issues\": { \"totalCount\": 13 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOJGjdug==\" } } } } }\n",
+    "\n",
+    "a_issues_closed = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"APE\", \"issues\": { \"totalCount\": 5 } }, { \"name\": \"APE_UseCases\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"Burke_Docker\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"APE_readthedocs\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"Proteomics_domain_setup\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"APE-Web\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"Automated_Cascabel_Pipeline\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"SLTLx-ANTLR-to-JavaScript\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"issues\": { \"totalCount\": 0 } }, { \"name\": \"restape\", \"issues\": { \"totalCount\": 1 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOJGjdug==\" } } } } }\n",
+    "\n",
+    "\n",
+    "a_pr_counts_open = [repo[\"issues\"][\"totalCount\"] for repo in a_issues_open[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "total_prs = sum(a_pr_counts_open)\n",
+    "print(f\"Total open Issues: {total_prs}\")\n",
+    "\n",
+    "a_pr_counts_closed = [repo[\"issues\"][\"totalCount\"] for repo in a_issues_closed[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "total_prs = sum(a_pr_counts_closed)\n",
+    "print(f\"Total closed Issues: {total_prs}\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## PRs"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Total PRs: 120\n",
+      "Total PRs: 215\n"
+     ]
+    }
+   ],
+   "source": [
+    "w_pr = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"Internal_documenation\", \"pullRequests\": { \"totalCount\": 1 } }, { \"name\": \"workflomics-frontend\", \"pullRequests\": { \"totalCount\": 45 } }, { \"name\": \"tools-and-domains\", \"pullRequests\": { \"totalCount\": 34 } }, { \"name\": \"domain-annotations\", \"pullRequests\": { \"totalCount\": 5 } }, { \"name\": \"WOMBAT-Pipelines\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"DemoKit\", \"pullRequests\": { \"totalCount\": 1 } }, { \"name\": \"designtime-bench-service\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"biohackathon_2023\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"workflomics-benchmarker\", \"pullRequests\": { \"totalCount\": 9 } }, { \"name\": \"workflomics-readthedocs\", \"pullRequests\": { \"totalCount\": 13 } }, { \"name\": \"IEEE-eScience-2024\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"pubmetric\", \"pullRequests\": { \"totalCount\": 12 } }, { \"name\": \"pubmetric-develipment\", \"pullRequests\": { \"totalCount\": 0 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOMqb6gg==\" } } } } }\n",
+    "\n",
+    "w_pr_count = [repo[\"pullRequests\"][\"totalCount\"] for repo in w_pr[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "\n",
+    "total_prs = sum(w_pr_count)\n",
+    "print(f\"Total PRs: {total_prs}\")\n",
+    "\n",
+    "a_pr = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"APE\", \"pullRequests\": { \"totalCount\": 80 } }, { \"name\": \"APE_UseCases\", \"pullRequests\": { \"totalCount\": 7 } }, { \"name\": \"Burke_Docker\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"APE_readthedocs\", \"pullRequests\": { \"totalCount\": 8 } }, { \"name\": \"Proteomics_domain_setup\", \"pullRequests\": { \"totalCount\": 3 } }, { \"name\": \"APE-Web\", \"pullRequests\": { \"totalCount\": 60 } }, { \"name\": \"Automated_Cascabel_Pipeline\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"SLTLx-ANTLR-to-JavaScript\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \".github\", \"pullRequests\": { \"totalCount\": 0 } }, { \"name\": \"restape\", \"pullRequests\": { \"totalCount\": 57 } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOJGjdug==\" } } } } }\n",
+    "\n",
+    "a_pr_count = [repo[\"pullRequests\"][\"totalCount\"] for repo in a_pr[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "\n",
+    "total_prs = sum(a_pr_count)\n",
+    "print(f\"Total PRs: {total_prs}\")\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Commits"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Total PRs: 1069\n",
+      "Total PRs: 481\n"
+     ]
+    }
+   ],
+   "source": [
+    "w_commits = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"Internal_documenation\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 45 } } } }, { \"name\": \"workflomics-frontend\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 225 } } } }, { \"name\": \"tools-and-domains\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 252 } } } }, { \"name\": \"domain-annotations\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 58 } } } }, { \"name\": \"WOMBAT-Pipelines\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 117 } } } }, { \"name\": \"DemoKit\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 21 } } } }, { \"name\": \"designtime-bench-service\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 4 } } } }, { \"name\": \".github\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 34 } } } }, { \"name\": \"biohackathon_2023\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 13 } } } }, { \"name\": \"workflomics-benchmarker\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 56 } } } }, { \"name\": \"workflomics-readthedocs\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 107 } } } }, { \"name\": \"IEEE-eScience-2024\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 19 } } } }, { \"name\": \"pubmetric\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 116 } } } }, { \"name\": \"pubmetric-develipment\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 2 } } } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOMqb6gg==\" } } } } }\n",
+    "\n",
+    "a_commits = { \"data\": { \"organization\": { \"repositories\": { \"nodes\": [ { \"name\": \"APE\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 162 } } } }, { \"name\": \"APE_UseCases\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 10 } } } }, { \"name\": \"Burke_Docker\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 0 } } } }, { \"name\": \"APE_readthedocs\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 56 } } } }, { \"name\": \"Proteomics_domain_setup\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 0 } } } }, { \"name\": \"APE-Web\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 11 } } } }, { \"name\": \"Automated_Cascabel_Pipeline\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 0 } } } }, { \"name\": \"SLTLx-ANTLR-to-JavaScript\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 0 } } } }, { \"name\": \".github\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 9 } } } }, { \"name\": \"restape\", \"defaultBranchRef\": { \"target\": { \"history\": { \"totalCount\": 233 } } } } ], \"pageInfo\": { \"hasNextPage\": 0, \"endCursor\": \"Y3Vyc29yOnYyOpHOJGjdug==\" } } } } }\n",
+    "\n",
+    "w_pr_counts = [repo[\"defaultBranchRef\"][\"target\"][\"history\"][\"totalCount\"] for repo in w_commits[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "\n",
+    "# summarise\n",
+    "w_total_prs = sum(w_pr_counts)\n",
+    "print(f\"Total PRs: {w_total_prs}\")\n",
+    "\n",
+    "a_pr_counts = [repo[\"defaultBranchRef\"][\"target\"][\"history\"][\"totalCount\"] for repo in a_commits[\"data\"][\"organization\"][\"repositories\"][\"nodes\"]]\n",
+    "\n",
+    "# summarise\n",
+    "a_total_prs = sum(a_pr_counts)\n",
+    "print(f\"Total PRs: {a_total_prs}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..e29eec7
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,2927 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "aiohappyeyeballs"
+version = "2.4.3"
+description = "Happy Eyeballs for asyncio"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[[package]]
+name = "aiohttp"
+version = "3.10.10"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "yarl-1.15.3.tar.gz", hash = "sha256:fbcff47f8ba82467f203037f7a30decf5c724211b224682f7236edb0dcbb5b95"},
+]
+
+[package.dependencies]
+idna = ">=2.0"
+multidict = ">=4.0"
+propcache = ">=0.2.0"
+
+[metadata]
+lock-version = "2.0"
+python-versions = ">=3.10,<4.0"
+content-hash = "b923fbd8647e5cd77daaa781d7c318da775a04b5707c94f74dac629b9ab3eb0a"
diff --git a/pubmetric_demo.ipynb b/pubmetric_demo.ipynb
index 1cc6acb..2baf49c 100644
--- a/pubmetric_demo.ipynb
+++ b/pubmetric_demo.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "metadata": {}
    },
@@ -75,23 +75,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "metadata": {}
    },
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "2024-08-29 10:56:39 - Loading graph from out_202407041439/graph.pkl.\n",
-      "2024-08-29 10:56:39 - Graph loaded from out_202407041439/graph.pkl.\n",
-      "2024-08-29 10:56:39 - Complete data download and graph creation took 0:00:00.025578\n"
+     "ename": "FileNotFoundError",
+     "evalue": "File not found: out/out_default/graph.pkl.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[3], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m path_to_data \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mout/out_default\u001b[39m\u001b[38;5;124m'\u001b[39m \n\u001b[0;32m----> 3\u001b[0m loaded_graph \u001b[38;5;241m=\u001b[39m \u001b[43masyncio\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcreate_network\u001b[49m\u001b[43m(\u001b[49m\u001b[43minpath\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpath_to_data\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mload_graph\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m# TODO: if no data then make data or ask if make data?\u001b[39;00m\n",
+      "File \u001b[0;32m~/git/Workflomics_repo/pubmetric/.venv/lib/python3.11/site-packages/nest_asyncio.py:30\u001b[0m, in \u001b[0;36m_patch_asyncio.<locals>.run\u001b[0;34m(main, debug)\u001b[0m\n\u001b[1;32m     28\u001b[0m task \u001b[38;5;241m=\u001b[39m asyncio\u001b[38;5;241m.\u001b[39mensure_future(main)\n\u001b[1;32m     29\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m---> 30\u001b[0m     \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mloop\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrun_until_complete\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtask\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     31\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m     32\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m task\u001b[38;5;241m.\u001b[39mdone():\n",
+      "File \u001b[0;32m~/git/Workflomics_repo/pubmetric/.venv/lib/python3.11/site-packages/nest_asyncio.py:98\u001b[0m, in \u001b[0;36m_patch_loop.<locals>.run_until_complete\u001b[0;34m(self, future)\u001b[0m\n\u001b[1;32m     95\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m f\u001b[38;5;241m.\u001b[39mdone():\n\u001b[1;32m     96\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\n\u001b[1;32m     97\u001b[0m         \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mEvent loop stopped before Future completed.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[0;32m---> 98\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+      "File \u001b[0;32m/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/futures.py:203\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    201\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m__log_traceback \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m    202\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m--> 203\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\u001b[38;5;241m.\u001b[39mwith_traceback(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception_tb)\n\u001b[1;32m    204\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_result\n",
+      "File \u001b[0;32m/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/asyncio/tasks.py:267\u001b[0m, in \u001b[0;36mTask.__step\u001b[0;34m(***failed resolving arguments***)\u001b[0m\n\u001b[1;32m    263\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m    264\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m exc \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m    265\u001b[0m         \u001b[38;5;66;03m# We use the `send` method directly, because coroutines\u001b[39;00m\n\u001b[1;32m    266\u001b[0m         \u001b[38;5;66;03m# don't have `__iter__` and `__next__` methods.\u001b[39;00m\n\u001b[0;32m--> 267\u001b[0m         result \u001b[38;5;241m=\u001b[39m \u001b[43mcoro\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m    268\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    269\u001b[0m         result \u001b[38;5;241m=\u001b[39m coro\u001b[38;5;241m.\u001b[39mthrow(exc)\n",
+      "File \u001b[0;32m~/git/Workflomics_repo/pubmetric/src/pubmetric/network.py:216\u001b[0m, in \u001b[0;36mcreate_network\u001b[0;34m(outpath, test_size, topic_id, random_seed, load_graph, inpath, save_files, tool_selection)\u001b[0m\n\u001b[1;32m    214\u001b[0m         pubmetric\u001b[38;5;241m.\u001b[39mlog\u001b[38;5;241m.\u001b[39mlog_with_timestamp(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mGraph loaded from \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mgraph_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    215\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 216\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mFileNotFoundError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mFile not found: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mgraph_path\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    218\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m    219\u001b[0m     \u001b[38;5;66;03m# Create output directory\u001b[39;00m\n\u001b[1;32m    220\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m outpath:\n",
+      "\u001b[0;31mFileNotFoundError\u001b[0m: File not found: out/out_default/graph.pkl."
      ]
     }
    ],
    "source": [
-    "path_to_data = 'out_202407041439' \n",
+    "path_to_data = 'out/out_default' \n",
     "\n",
     "loaded_graph = asyncio.run(create_network(inpath=path_to_data, load_graph=True)) # TODO: if no data then make data or ask if make data?\n"
    ]
@@ -187,7 +194,7 @@
     }
    ],
    "source": [
-    "testsize_graph = asyncio.run(create_network(load_graph=False, test_size=20))#, inpath='tests/data'))\n",
+    "testsize_graph = asyncio.run(create_network(load_graph=False, test_size=2000))#, inpath='tests/data'))\n",
     "print(testsize_graph.vs['age'])"
    ]
   },
@@ -536,9 +543,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'parse_cwl' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m cwl_file_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m./workflows/workflomics/candidate_workflow_23.cwl\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;66;03m# loading one of the APE generated workflows \u001b[39;00m\n\u001b[1;32m      2\u001b[0m metadate_file_path \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mout_202407041439/tool_metadata.json\u001b[39m\u001b[38;5;124m'\u001b[39m\n\u001b[0;32m----> 3\u001b[0m workflow \u001b[38;5;241m=\u001b[39m \u001b[43mparse_cwl\u001b[49m(cwl_file_path, metadate_file_path)\n",
+      "\u001b[0;31mNameError\u001b[0m: name 'parse_cwl' is not defined"
+     ]
+    }
+   ],
    "source": [
     "cwl_file_path = \"./workflows/workflomics/candidate_workflow_23.cwl\" # loading one of the APE generated workflows \n",
     "metadate_file_path = 'out_202407041439/tool_metadata.json'\n",
@@ -912,7 +931,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "workflomics",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -926,7 +945,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.19"
+   "version": "3.11.2"
   }
  },
  "nbformat": 4,
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..6a5ad9f
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,51 @@
+[tool.poetry]
+name = "pubmetric"
+version = "0.2.0"
+description = "Cocitation based metric for workflow evaluation"
+authors = ["Alma Nilsson <alma.as.nilsson@gmail.com>", "Vedran Kasalica", "Magnus Palmblad"]
+license = "Apache-2.0"
+readme = "README.md"
+packages = [
+    { include = "pubmetric", from = "src" }]
+homepage = "https://github.com/Workflomics/pubmetric"
+repository = "https://github.com/Workflomics/pubmetric"
+documentation = "https://workflomics.readthedocs.io/en/latest/developer-guide/pubmetric.html"
+keywords = []
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent"
+]
+
+[tool.poetry.dependencies]
+python = ">=3.10,<4.0"
+asyncio = "^3.4.3"
+igraph = "^0.11.6"
+requests = "^2.32"
+py4cytoscape = "^1.9.0"
+pandas = "^2.2.3"
+tqdm = "^4.66.2"
+numpy = "^2.1.2"
+matplotlib = "^3.9.2"
+cwl_utils = "^0.15"
+fastapi = "^0.115.2"
+scikit-learn = "^1.5.2"
+apscheduler = "^3.10"
+uvicorn = "^0.31.1"
+httpx = "^0.27.2"
+python-multipart = "^0.0.12"
+pytype = "^2024.10.11"
+certifi = "^2024.8.30"
+aiohttp = "^3.10.10"
+
+[tool.poetry.dev-dependencies]
+pytest = "^8.3.3"
+pytest-datadir = "^1.3.1"
+pytest-asyncio = "^0.24.0"
+
+[tool.poetry.scripts]
+pubmetric-api = "uvicorn src.pubmetric.api_controller:app --reload"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index eee129e..0000000
--- a/setup.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from setuptools import setup, find_packages
-
-setup(
-    name='pubmetric',
-    version='0.1.0',
-    description='Cocitation based metric for workflow evaluation',
-    author='Alma Nilsson, Vedran Kasalica, Magnus Palmblad ',
-    author_email='alma.as.nilsson@gmail.com',
-    license='Apache License 2.0',
-    packages=find_packages(),
-    install_requires=[
-        'aiohttp==3.9.5',
-        'asyncio==3.4.3',
-        'igraph',
-        'requests',
-        'py4cytoscape==1.9.0',
-        'pandas',
-        'tqdm==4.66.2',
-        'numpy',
-        'matplotlib',
-        'jsonpath-ng',
-        'ruamel.yaml',
-        'cwl_utils',
-        'fastapi',
-        'scikit-learn',
-        'apscheduler'
-    ],
-    extras_require={
-        'test': [
-            'pytest',
-            'pytest-datadir',
-            'pytest-asyncio'
-        ]
-    },
-    classifiers=[
-        'Programming Language :: Python :: 3',
-        'License :: OSI Approved :: Apache Software License',
-        'Operating System :: OS Independent',
-    ],
-    python_requires='>=3.6',
-)
diff --git a/src/pubmetric/api_controller.py b/src/pubmetric/api_controller.py
index f43ba3d..32170fb 100644
--- a/src/pubmetric/api_controller.py
+++ b/src/pubmetric/api_controller.py
@@ -1,27 +1,23 @@
 import os
 import tempfile
 from contextlib import asynccontextmanager
+from typing import List, Optional
 
 from apscheduler.jobstores.memory import MemoryJobStore
 from apscheduler.schedulers.asyncio import AsyncIOScheduler
 from fastapi import FastAPI, File, UploadFile
 from pydantic import BaseModel
-from typing import List, Optional
 
 import pubmetric.metrics
 import pubmetric.network
 import pubmetric.workflow
 
 
-app = FastAPI()
-
-jobstores = {
-    'default': MemoryJobStore()
-}
+jobstores = {"default": MemoryJobStore()}
 
-scheduler = AsyncIOScheduler(jobstores=jobstores, timezone='Europe/Berlin')
+scheduler = AsyncIOScheduler(jobstores=jobstores, timezone="Europe/Berlin")
 
-latest_output_path = "out_20240801231111"
+latest_output_path = "data/out_default"
 
 
 @asynccontextmanager
@@ -34,40 +30,57 @@ async def lifespan(application: FastAPI):
 
 app = FastAPI(lifespan=lifespan)
 
+
+@app.get("/")
+async def read_main():
+    return {"msg": "Welcome to Pubmetric!"}
+
+
 class ScoreResponse(BaseModel):
-    workflow_scores: List
+    benchmarks: List
+
 
 class GraphRequest(BaseModel):
     topic_id: str
     test_size: str
     tool_list: Optional[list]
 
-@scheduler.scheduled_job('interval', days=30)
+
+@scheduler.scheduled_job("interval", days=30)
 async def periodic_graph_generation():
     """Periodically generates a new citation network graph every 30 days and updates
-        the global path if the graph is successfully created. 
+        the global path if the graph is successfully created.
         If the graph file is not found, it logs an error message.
 
     :return: Dict
-        A dictionary containing a message with the new graph path if successful 
+        A dictionary containing a message with the new graph path if successful
         or an error message if the graph file is not found.
 
     """
     global latest_output_path
     try:
-        new_output_path = await pubmetric.network.create_network(topic_id="default",
-                                                                 test_size=20,
-                                                                 return_path = True) # TODO: rm test size
+        new_output_path = await pubmetric.network.create_network(
+            topic_id="default", test_size=50
+        )  # TODO: rm test size
         if os.path.exists(new_output_path + "/graph.pkl"):
             latest_output_path = new_output_path
-            return {"message": f"Graph and metadata file recreated "
-                    f"successfully New graph path: {latest_output_path}."}
+            return {
+                "message": f"Graph and metadata file recreated "
+                f"successfully New graph path: {latest_output_path}."
+            }
         else:
-            return {"error": "Error: Generated graph file not found."} #TODO error type 
+            return {
+                "error": "Error: Generated graph file not found."
+            }  # TODO error type
     except Exception as e:
-        return {"error": f"An error occurred while recreating the graph: {e}." 
-                "The previous graph will continue to be used."}
-scheduler.add_job(periodic_graph_generation, 'interval', days=30)
+        return {
+            "error": f"An error occurred while recreating the graph: {e}."
+            "The previous graph will continue to be used."
+        }
+
+
+scheduler.add_job(periodic_graph_generation, "interval", days=30)
+
 
 @app.post("/score_workflow/", response_model=ScoreResponse)
 async def score_workflow(cwl_file: UploadFile = File(None)):
@@ -82,41 +95,47 @@ async def score_workflow(cwl_file: UploadFile = File(None)):
         metric and age benchmarks accoring to the Workflomics JSON Schema for Benchmarks.
     """
 
-    graph = await pubmetric.network.create_network(inpath=latest_output_path, load_graph=True) 
+    graph = await pubmetric.network.create_network(
+        inpath=latest_output_path, load_graph=True
+    )
     with tempfile.TemporaryDirectory() as temp_dir:
 
         cwl_file_path = os.path.join(temp_dir, cwl_file.filename)
-        with open(cwl_file_path, "wb") as f: # Slightly dumb to open and save and then just 
-                                                # open again within the parse workflows function. 
-                                                # Shoudl I update parse wf to work with open files?
+        with open(
+            cwl_file_path, "wb"
+        ) as f:  # Slightly dumb to open and save and then just
+            # open again within the parse workflows function.
+            # Shoudl I update parse wf to work with open files?
             f.write(cwl_file.file.read())
 
-        
-        workflow = pubmetric.workflow.parse_cwl(cwl_filename=cwl_file_path, 
-                                                graph=graph)  
-        pmid_workflow = workflow['pmid_edges']
+        workflow = pubmetric.workflow.parse_cwl(cwl_filename=cwl_file_path, graph=graph)
+        pmid_workflow = workflow["pmid_edges"]
 
         # Metrics
-        workflow_level_score =  pubmetric.metrics.workflow_average(graph=graph,
-                                                                   workflow=pmid_workflow)
-        workflow_desirability = pubmetric.metrics.calculate_desirability(score=workflow_level_score,
-                                                                         thresholds= [0, 400])
+        workflow_level_score = pubmetric.metrics.workflow_average(
+            graph=graph, workflow=pmid_workflow
+        )
+        workflow_desirability = pubmetric.metrics.calculate_desirability(
+            score=workflow_level_score, thresholds=[0, 400]
+        )
         tool_level_scores = pubmetric.metrics.tool_average_sum(graph, workflow)
 
-
         tool_level_output = []
         for tool_name, score in tool_level_scores.items():
             # lower since they are multiplied by the desirability of workflows
-            desirability = pubmetric.metrics.calculate_desirability(score=score,
-                                                                    thresholds= [0,200])
+            desirability = pubmetric.metrics.calculate_desirability(
+                score=score, thresholds=[0, 200]
+            )
 
             if not score or score == 0:
-                score = 'Unknown'
-            tool_level_output.append({
+                score = "Unknown"
+            tool_level_output.append(
+                {
                     "desirability": desirability,
                     "label": f'{tool_name.split("_")[0]}: {score}',
-                    "value": str(score)
-                })
+                    "value": str(score),
+                }
+            )
 
         ages_output = []
         ages = []
@@ -126,48 +145,53 @@ async def score_workflow(cwl_file: UploadFile = File(None)):
                 age = "Unknown"
                 desirability = 0
             else:
-                # capped by putting the upper threshold above maximum 
-                desirability = pubmetric.metrics.calculate_desirability(score=age,
-                                                                        thresholds= [0, 45],
-                                                                        inverted=True,
-                                                                        transform = False) 
+                # capped by putting the upper threshold above maximum
+                desirability = pubmetric.metrics.calculate_desirability(
+                    score=age, thresholds=[0, 45], inverted=True, transform=False
+                )
             ages.append(age)
-            ages_output.append({
-                    "desirability": desirability, # Because green == new?  
-                    "label":  f'{tool_name.split("_")[0]}: {age}',
-                    "value": str(age)
-                })
-            
-        
+            ages_output.append(
+                {
+                    "desirability": desirability,  # Because green == new?
+                    "label": f'{tool_name.split("_")[0]}: {age}',
+                    "value": str(age),
+                }
+            )
+
         metric_benchmark = {
             "unit": "metric",
-            "description": "The tool- and workflow-level metric",
-            "title": "Pubmetric",
+            "category": "Bibliometrics",
+            "description": "The tool- and workflow-level co-citation metric",
+            "title": "Co-citation score",
             "steps": tool_level_output,
             "aggregate_value": {
-                "desirability": workflow_desirability, 
-                "value": str(workflow_level_score)
-            }
+                "desirability": workflow_desirability,
+                "value": str(workflow_level_score),
+            },
         }
         age_benchmark = {
             "unit": "age",
-            "description": "Time since release of primary publications",
-            "title": "Age",
+            "category": "Bibliometrics",
+            "description": "Time since release of primary publication",
+            "title": "Tool age",
             "steps": ages_output,
             "aggregate_value": {
-                "desirability": 1.0, # unclear what to put here
-                "value": f'{len([age for age in ages_output if age["value"] != "Unknown"])}/{len(ages_output)}'
-            }
+                "desirability": 1.0,  # unclear what to put here
+                "value": f'{len([age for age in ages_output if age["value"] != "Unknown"])}/{len(ages_output)}',
+            },
         }
 
     benchmarks = [metric_benchmark, age_benchmark]
 
-    return ScoreResponse(workflow_scores=benchmarks)
+    return ScoreResponse(benchmarks=benchmarks)
+
 
 @app.post("/recreate_graph/")
-async def recreate_graph(graph_request: GraphRequest): # if you want to recreate it with a request
+async def recreate_graph(
+    graph_request: GraphRequest,
+):  # if you want to recreate it with a request
     """
-    Recreates the citation network graph based on the provided topic ID and test size. 
+    Recreates the citation network graph based on the provided topic ID and test size.
     Updates the global graph path if the graph is successfully generated.
 
     :param graph_request: GraphRequest
@@ -181,18 +205,18 @@ async def recreate_graph(graph_request: GraphRequest): # if you want to recreate
     """
     global latest_output_path
     try:
-        new_output_path = await pubmetric.network.create_network(topic_id=graph_request.topic_id,
-                                                                 test_size=20,
-                                                                 return_path=True)
+        new_output_path = await pubmetric.network.create_network(
+            topic_id=graph_request.topic_id, test_size=50
+        )
         if os.path.exists(os.path.join(new_output_path, "graph.pkl")):
             latest_output_path = new_output_path
-            return {"message": 
-                    f"Graph and metadata file recreated successfully New graph path: {latest_output_path}."}
+            return {
+                "message": f"Graph and metadata file recreated successfully New graph path: {latest_output_path}."
+            }
         else:
             return {"error": "Error: Generated graph file not found."}
     except Exception as e:
-        return {"error": f"An error occurred while recreating the graph: {e}." 
-                "The previous graph will continue to be used."}
-    
-    
-
+        return {
+            "error": f"An error occurred while recreating the graph: {e}."
+            "The previous graph will continue to be used."
+        }
diff --git a/src/pubmetric/data.py b/src/pubmetric/data.py
index 4b91d79..395adea 100644
--- a/src/pubmetric/data.py
+++ b/src/pubmetric/data.py
@@ -1,11 +1,12 @@
 """
 Module to download meta data about software in bio.tools
 """
+
 import os
 import json
 from datetime import datetime
 from collections import defaultdict, Counter
-from typing import Optional
+from typing import Optional, Tuple
 
 import numpy as np
 import asyncio
@@ -18,7 +19,9 @@
 import pubmetric.log
 
 
-def download_domain_annotations(tools: list, annotations: str = "full") -> list:
+def download_domain_annotations(
+    tools: list | None = None, annotations: str = "workflomics"
+) -> list:
     """
     Downloads a JSON file containing domain annotations from workflomics repository.
 
@@ -30,25 +33,29 @@ def download_domain_annotations(tools: list, annotations: str = "full") -> list:
              Returns None if the file could not be retrieved.
     """
     if annotations == "full":
-        url = "https://raw.githubusercontent.com/Workflomics/domain-annotations/main/genomics/bio.tools.json" # TODO move this into won repo 
+        url = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/bio.tools/tools.json"  # TODO move this into won repo
     elif annotations == "workflomics":
-        url = "path/to/workflomicstools"
+        url = "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/domains/proteomics/tools.json"
     else:
-        raise TypeError("Invalid type for tool_selection string, expected 'full' or 'workflomics'.")    
+        raise TypeError(
+            "Invalid type for tool_selection string, expected 'full' or 'workflomics'."
+        )
 
     response = requests.get(url)
 
     if response.status_code == 200:
         biotools = response.json()
-        tool_selection = list({tool['label'] for tool in biotools["functions"]})
-        return [tool for tool in tools if tool['name'] in tool_selection]
+        tool_selection = list({tool["label"] for tool in biotools["functions"]})
+        if tools:
+            return [tool for tool in tools if tool["name"] in tool_selection]
+        return tool_selection
     else:
         print(f"Failed to retrieve file: {response.status_code}")
 
-async def aggregate_requests(session: aiohttp.ClientSession,
-                             url: str,
-                             retries: int = 3,
-                             backoff: float = 2.0) -> dict:
+
+async def aggregate_requests(
+    session: aiohttp.ClientSession, url: str, retries: int = 3, backoff: float = 2.0
+) -> dict:
     """
     Sync requests so they are all made in a single session
 
@@ -63,32 +70,35 @@ async def aggregate_requests(session: aiohttp.ClientSession,
     attempt = 0
     while attempt < retries:
         try:
-            async with session.get(url) as response:
+            async with session.get(url, ssl=False) as response:
                 response.raise_for_status()
                 return await response.json()
-        except aiohttp.ClientError: # as e:
+        except aiohttp.ClientError:  # as e:
             attempt += 1
-            wait_time = backoff ** attempt
-            #might be good to print, but it does so so many times 
-            #pubmetric.log.log_with_timestamp(
-                #f"Request failed: {e}. Retrying in {wait_time:.1f} seconds...")
+            wait_time = backoff**attempt
+            # might be good to print, but it does so so many times
+            # pubmetric.log.log_with_timestamp(
+            # f"Request failed: {e}. Retrying in {wait_time:.1f} seconds...")
             await asyncio.sleep(wait_time)
     raise Exception(f"Failed to fetch data from {url} after {retries} attempts.")
 
-async def get_pmid_from_doi(doi_tools: dict,
-                            outpath: str,
-                            inpath: str = None,
-                            doi_library_filename: str = 'doi_pmid_library.json',
-                            save_interval: int = 10) -> dict:
+
+async def get_pmid_from_doi(
+    doi_tools: dict,
+    outpath: str,
+    inpath: str = None,
+    doi_library_filename: str = "doi_pmid_library.json",
+    save_interval: int = 10,
+) -> dict:
     """
-    Given a list of dictionaries with data about (tool) publications, 
+    Given a list of dictionaries with data about (tool) publications,
     this function uses their DOIs to retrieve their PMIDs from NCBI eutils API.
 
     :param doi_tools: list of dicts
-    :param outpath: str path to the directory where you want the file to be 
+    :param outpath: str path to the directory where you want the file to be
     :param inpath: str path to the directory where an old file is
     :param doi_library_filename: str, default 'doi_pmid_library.json'.
-        To load this is assumed to be in main directory. 
+        To load this is assumed to be in main directory.
     :param save_interval: int, default 10, Save progress after this many updates
 
     :return: Updated list of dicts with PMIDs included.
@@ -99,13 +109,14 @@ async def get_pmid_from_doi(doi_tools: dict,
 
     if inpath and os.path.isfile(os.path.join(inpath, doi_library_filename)):
         pubmetric.log.log_with_timestamp("Loading doi-pmid library")
-        with open(os.path.join(inpath, doi_library_filename), 'r', encoding='utf-8') as f:
+        with open(
+            os.path.join(inpath, doi_library_filename), "r", encoding="utf-8"
+        ) as f:
             doi_library = json.load(f)
-    else: 
-        pubmetric.log.log_with_timestamp('Creating a new doi-pmid library')
+    else:
+        pubmetric.log.log_with_timestamp("Creating a new doi-pmid library")
         doi_library = {}
 
-
     library_updates = 0
     async with aiohttp.ClientSession() as session:
         for tool in tqdm(doi_tools, desc="Downloading pmids from dois."):
@@ -117,10 +128,10 @@ async def get_pmid_from_doi(doi_tools: dict,
 
             url = f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=PubMed&retmode=json&term={doi}"
             result = await aggregate_requests(session, url)
-            id_list = result.get('esearchresult', {}).get('idlist', [])
+            id_list = result.get("esearchresult", {}).get("idlist", [])
             doi_pmid = next(iter(id_list), None)
 
-            if doi_pmid and doi_pmid != '39073865': # what is this cursed paper?
+            if doi_pmid and doi_pmid != "39073865":  # what is this cursed paper?
                 tool["pmid"] = doi_pmid
                 doi_library[doi] = doi_pmid
                 library_updates += 1
@@ -128,28 +139,34 @@ async def get_pmid_from_doi(doi_tools: dict,
                 continue
 
             if library_updates >= save_interval:
-                with open(os.path.join(outpath, doi_library_filename), 'w', encoding='utf-8') as f:
+                with open(
+                    os.path.join(outpath, doi_library_filename), "w", encoding="utf-8"
+                ) as f:
                     json.dump(doi_library, f)
                 library_updates = 0  # Reset update counter
 
     if library_updates > 0:
-        with open(os.path.join(outpath, doi_library_filename), 'w', encoding='utf-8') as f:
+        with open(
+            os.path.join(outpath, doi_library_filename), "w", encoding="utf-8"
+        ) as f:
             json.dump(doi_library, f)
 
-    updated_doi_tools = [tool for tool in doi_tools if tool.get('pmid')]
+    updated_doi_tools = [tool for tool in doi_tools if tool.get("pmid")]
     pubmetric.log.log_with_timestamp(
-        f"Found {len(updated_doi_tools)} tools with PMIDs using their DOIs")
+        f"Found {len(updated_doi_tools)} tools with PMIDs using their DOIs"
+    )
 
     return updated_doi_tools
 
+
 async def get_pmids(topic_id: Optional[str], test_size: Optional[int]) -> tuple:
-    """ 
+    """
     Downloads all (or a specified amount) of the bio.tools tools for a specific
     topic and returns metadata about the tools.
 
     :param topic_id: str
         The ID to which the tools downloaded belong,
-        e.g., "Proteomics" or "DNA" as defined by EDAM ontology. 
+        e.g., "Proteomics" or "DNA" as defined by EDAM ontology.
     :param test_size: int, default None
         Determines the number of tools downloaded
 
@@ -158,12 +175,12 @@ async def get_pmids(topic_id: Optional[str], test_size: Optional[int]) -> tuple:
         a list of tools without PMIDs, and the total number of tools.
     """
     pmid_tools = []
-    doi_tools = [] # collect tools without pmid
+    doi_tools = []  # collect tools without pmid
 
     if topic_id:
-        base_url = f'https://bio.tools/api/t?topicID=%22{topic_id}%22&format=json&page='
+        base_url = f"https://bio.tools/api/t?topicID=%22{topic_id}%22&format=json&page="
     else:
-        base_url = 'https://bio.tools/api/t?%22&format=json&page=' # Full bio.tools
+        base_url = "https://bio.tools/api/t?%22&format=json&page="  # Full bio.tools
 
     page = 1
     # graph stats:
@@ -172,85 +189,222 @@ async def get_pmids(topic_id: Optional[str], test_size: Optional[int]) -> tuple:
 
     async with aiohttp.ClientSession() as session:
         while page:
-            # Sends request for tools on the page, 
+            # Sends request for tools on the page,
             # await further requests and return resonse in json format
             biotools_url = base_url + str(page)
             biotool_data = await aggregate_requests(session, biotools_url)
 
-            if 'list' in biotool_data: 
-                biotools_list = biotool_data['list']
-                
+            if "list" in biotool_data:
+                biotools_list = biotool_data["list"]
+
                 for tool in biotools_list:
-                    publications = tool.get('publication')
-                    if not publications: # Graph needs tools with pmids
+                    publications = tool.get("publication")
+                    if not publications:  # Graph needs tools with pmids
                         no_publication_stat += 1
                         continue
-                    name = tool.get('name')
-                    topic = tool.get('topic')
+                    name = tool.get("name")
+                    topic = tool.get("topic")
                     nr_publications = len(publications)
-                    primary_publication = next((pub 
-                                                for pub in publications 
-                                                if 'Primary' in pub.get('type')), 
-                                                None)
+                    primary_publication = next(
+                        (pub for pub in publications if "Primary" in pub.get("type")),
+                        None,
+                    )
                     if primary_publication is None:
                         primary_publication = publications[0]
-                        primary_stat +=1
+                        primary_stat += 1
 
-                    all_publications = [pub.get('pmid') for pub in publications]
+                    all_publications = [pub.get("pmid") for pub in publications]
 
-                    if primary_publication.get('metadata'):
-                        pub_date = primary_publication['metadata'].get('date')
+                    if primary_publication.get("metadata"):
+                        pub_date = primary_publication["metadata"].get("date")
                         if pub_date:
-                            pub_date = int(pub_date.split('-')[0])
-                    else: 
+                            pub_date = int(pub_date.split("-")[0])
+                    else:
                         pub_date = None
-                    if primary_publication.get('pmid'):
-                        pmid_tools.append({
-                            'name': name,
-                            'doi': primary_publication.get('doi'), # adding doi here too 
-                            'topics': [t.get('term') for t in topic] if topic else None,
-                            'nr_publications':  nr_publications,
-                            'all_publications': all_publications,
-                            'publication_date': pub_date,
-                            'pmid': str(primary_publication['pmid'])
-
-                        })
+                    if primary_publication.get("pmid"):
+                        pmid_tools.append(
+                            {
+                                "name": name,
+                                "doi": primary_publication.get(
+                                    "doi"
+                                ),  # adding doi here too
+                                "topics": (
+                                    [t.get("term") for t in topic] if topic else None
+                                ),
+                                "nr_publications": nr_publications,
+                                "all_publications": all_publications,
+                                "publication_date": pub_date,
+                                "pmid": str(primary_publication["pmid"]),
+                            }
+                        )
                     else:
-                        
-                        doi_tools.append({
-                            'name': name,
-                            'doi': primary_publication.get('doi'),
-                            'topics': [t.get('term') for t in topic] if topic else None,
-                            'nr_publications':  nr_publications,
-                            'all_publications': all_publications,
-                            'publication_date': pub_date
-                        })
-
-                if test_size and len(pmid_tools) + len(doi_tools) >= test_size: # this is not exaxt 
-                                                                    #since dois might not give pmid
+
+                        doi_tools.append(
+                            {
+                                "name": name,
+                                "doi": primary_publication.get("doi"),
+                                "topics": (
+                                    [t.get("term") for t in topic] if topic else None
+                                ),
+                                "nr_publications": nr_publications,
+                                "all_publications": all_publications,
+                                "publication_date": pub_date,
+                            }
+                        )
+
+                if (
+                    test_size and len(pmid_tools) + len(doi_tools) >= test_size
+                ):  # this is not exaxt
+                    # since dois might not give pmid
                     break
 
-                page = biotool_data.get('next')
-                if page: # else page will be None and loop will stop
-                    page = page.split('=')[-1] # only want the page number
+                page = biotool_data.get("next")
+                if page:  # else page will be None and loop will stop
+                    page = page.split("=")[-1]  # only want the page number
             else:
                 pubmetric.log.log_with_timestamp(
-                    f'Error while fetching tool names from page {page}')
+                    f"Error while fetching tool names from page {page}"
+                )
                 break
     pubmetric.log.log_with_timestamp(
-        f"Primary publications count: {primary_stat}," 
-        f"missing publication count: {no_publication_stat}")
-    total_nr_tools = int(biotool_data['count']) if biotool_data and 'count' in biotool_data else 0
+        f"Primary publications count: {primary_stat},"
+        f"missing publication count: {no_publication_stat}"
+    )
+    total_nr_tools = (
+        int(biotool_data["count"]) if biotool_data and "count" in biotool_data else 0
+    )
 
     return (pmid_tools, doi_tools, total_nr_tools)
 
+
+def get_tool_by_id(biotools_id) -> dict:
+    base_url = f"https://bio.tools/api/tool/{biotools_id}"
+    params = {"format": "json"}
+
+    response = requests.get(base_url, params=params)
+    response.raise_for_status()  # Check for request errors
+    return response.json()
+
+
+def get_specific_tools_by_id(biotools_ids) -> list:
+    tools = []
+    for biotools_id in biotools_ids:
+        try:
+            tool = get_tool_by_id(biotools_id)
+            tools.append(tool)
+            print(f"Found tool: {tool['name']} with biotoolsID: {biotools_id}")
+        except requests.HTTPError:
+            print(f"Tool with biotoolsID '{biotools_id}' not found.")
+    return tools
+
+
+def get_pmids_workflomics() -> Tuple[list, list, int]:
+    """
+    Downloads all (or a specified amount) of the bio.tools tools for a specific
+    topic and returns metadata about the tools.
+
+    :return: tuple
+        Tuple containing a list of tools (dictionaries) with PMIDs,
+        a list of tools without PMIDs, and the total number of tools.
+    """
+    pmid_tools = []
+    doi_tools = []  # collect tools without pmid
+
+    biotools_ids = [
+        "comet",
+        "peptideprophet",
+        "proteinprophet",
+        "stpeter",
+        "mzrecal",
+        "idconvert",
+        "msconvert",
+        "GOEnrichment",
+        "gprofiler",
+        "xtandem",
+        "MS_Amanda",
+        "msfragger",
+        "protXml2IdList",
+        "MetaMorpheus",
+        "Sage-proteomics",
+        "wcloud",
+    ]
+
+    # Fetch details for the specified tools using biotoolsID
+    specific_tools = get_specific_tools_by_id(biotools_ids)
+
+    # graph stats:
+    primary_stat = 0
+    no_publication_stat = 0
+
+    if len(specific_tools) > 0:
+
+        for tool in specific_tools:
+            publications = tool.get("publication")
+            if not publications:  # Graph needs tools with pmids
+                no_publication_stat += 1
+                continue
+            name = tool.get("name")
+            topic = tool.get("topic")
+            nr_publications = len(publications)
+            primary_publication = next(
+                (pub for pub in publications if "Primary" in pub.get("type")),
+                None,
+            )
+            if primary_publication is None:
+                primary_publication = publications[0]
+                primary_stat += 1
+
+            all_publications = [pub.get("pmid") for pub in publications]
+
+            if primary_publication.get("metadata"):
+                pub_date = primary_publication["metadata"].get("date")
+                if pub_date:
+                    pub_date = int(pub_date.split("-")[0])
+            else:
+                pub_date = None
+            if primary_publication.get("pmid"):
+                pmid_tools.append(
+                    {
+                        "name": name,
+                        "doi": primary_publication.get("doi"),  # adding doi here too
+                        "topics": ([t.get("term") for t in topic] if topic else None),
+                        "nr_publications": nr_publications,
+                        "all_publications": all_publications,
+                        "publication_date": pub_date,
+                        "pmid": str(primary_publication["pmid"]),
+                    }
+                )
+            else:
+
+                doi_tools.append(
+                    {
+                        "name": name,
+                        "doi": primary_publication.get("doi"),
+                        "topics": ([t.get("term") for t in topic] if topic else None),
+                        "nr_publications": nr_publications,
+                        "all_publications": all_publications,
+                        "publication_date": pub_date,
+                    }
+                )
+
+    else:
+        pubmetric.log.log_with_timestamp("Error while fetching tools")
+    pubmetric.log.log_with_timestamp(
+        f"Primary publications count: {primary_stat},"
+        f"missing publication count: {no_publication_stat}"
+    )
+
+    return (pmid_tools, doi_tools, len(specific_tools))
+
+
 async def fetch_publication_dates(session: aiohttp.ClientSession, pmids: list):
     """Fetches publication dates for a list of PMIDs from NCBI."""
-    pmid_str = ','.join(pmids)
+    pmid_str = ",".join(pmids)
     url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={pmid_str}&retmode=json"
-    async with session.get(url) as response:
+    async with session.get(url, ssl=False) as response:
         return await response.json()
 
+
 async def process_publication_dates(tool_metadata: list) -> list:
     """
     Downloads the publication date from NCBI using the PMID of the file
@@ -264,12 +418,12 @@ async def process_publication_dates(tool_metadata: list) -> list:
     """
 
     pmid_to_tool = {
-        tool['pmid']: tool
+        tool["pmid"]: tool
         for tool in tool_metadata
-        if 'publication_date' not in tool
-        or not tool['publication_date']
-        or tool['publication_date'] == 'null'
-        }
+        if "publication_date" not in tool
+        or not tool["publication_date"]
+        or tool["publication_date"] == "null"
+    }
     pmids = list(pmid_to_tool.keys())
 
     # If no pmids need updates return the original list
@@ -279,14 +433,14 @@ async def process_publication_dates(tool_metadata: list) -> list:
     async with aiohttp.ClientSession() as session:
         data = await fetch_publication_dates(session, pmids)
 
-    results = data.get('result', {})
+    results = data.get("result", {})
     tools_without_pubdate = 0
 
     for pmid in pmids:
         tool = pmid_to_tool.get(pmid)
-        pub_date = results.get(pmid, {}).get('pubdate', None)
+        pub_date = results.get(pmid, {}).get("pubdate", None)
         if pub_date:
-            tool['publication_date'] = int(str(pub_date).split()[0])
+            tool["publication_date"] = int(str(pub_date).split()[0])
         else:
             tools_without_pubdate += 1
 
@@ -295,11 +449,14 @@ async def process_publication_dates(tool_metadata: list) -> list:
     )
     return tool_metadata
 
-async def get_tool_metadata(outpath: str,
-                            topic_id: str ,
-                            inpath: Optional[str] = None,
-                            test_size: Optional[int] = None,
-                            random_seed: int = 42) -> dict:
+
+async def get_tool_metadata(
+    outpath: str,
+    topic_id: str,
+    inpath: Optional[str] = None,
+    test_size: Optional[int] = None,
+    random_seed: int = 42,
+) -> dict:
     """
     Fetches metadata about tools from bio.tools, belonging to a given topic_id
     and returns as a dictionary.
@@ -307,8 +464,8 @@ async def get_tool_metadata(outpath: str,
     :param outpath: str
         Path to directory where a newly created file should be placed.
     :param topic_id: str
-        The ID to which the tools downloaded belong 
-    :param inpath: The path to an already existing file which will be loaded. 
+        The ID to which the tools downloaded belong
+    :param inpath: The path to an already existing file which will be loaded.
     :param update: bool, default False
         Determines whether or not to force the retrieval of a new data file.
     :param test_size: int, default None
@@ -319,51 +476,56 @@ async def get_tool_metadata(outpath: str,
         Dictionary containing metadata about the tools.
     """
     if test_size:
-        metadata_file_name = f'tool_metadata_test{test_size}.json'
+        metadata_file_name = f"tool_metadata_test{test_size}.json"
     else:
-        metadata_file_name = 'tool_metadata.json'
+        metadata_file_name = "tool_metadata.json"
 
-    if inpath: # Indicates we want to load a file
+    if inpath:  # Indicates we want to load a file
         metadata_path = os.path.join(inpath, metadata_file_name)
-        if os.path.isfile(metadata_path): 
-            with open(metadata_path, "r", encoding='utf-8') as f:
+        if os.path.isfile(metadata_path):
+            with open(metadata_path, "r", encoding="utf-8") as f:
                 metadata_file = json.load(f)
         else:
-            raise FileNotFoundError(f"Can not find {os.path.join(inpath, metadata_file_name)} ")
-        if (not isinstance(metadata_file['tools'], list) or
-                not isinstance(metadata_file['tools'][0], dict)):
+            raise FileNotFoundError(
+                f"Can not find {os.path.join(inpath, metadata_file_name)} "
+            )
+        if not isinstance(metadata_file["tools"], list) or not isinstance(
+            metadata_file["tools"][0], dict
+        ):
 
             raise SchemaValidationError(
-                "Metadata file does not have the required structure." 
-                "Please refer to metadata file schema.")
+                "Metadata file does not have the required structure."
+                "Please refer to metadata file schema."
+            )
 
-        if test_size: # Takes a random selection of the specified size from the file
+        if test_size:  # Takes a random selection of the specified size from the file
             np.random.seed(random_seed)
-            test_tools = list(np.random.choice(metadata_file['tools'], size = test_size))
-            metadata_file['tools'] = test_tools
+            test_size = min(
+                test_size, len(metadata_file["tools"])
+            )  # to avoid index error
+            test_tools = list(np.random.choice(metadata_file["tools"], size=test_size))
+            metadata_file["tools"] = test_tools
 
         return metadata_file
 
     # If no inpath is specified we recreate the metadatafile
     # Creating json file
-    metadata_file = {
-        "creation_date": str(datetime.now()),
-        "topic": topic_id
-    }
+    metadata_file = {"creation_date": str(datetime.now()), "topic": topic_id}
 
     get_pmids_time = datetime.now()
 
-    pmid_tools, doi_tools, tot_nr_tools = await get_pmids(topic_id=topic_id,
-                                                          test_size=test_size)
+    pmid_tools, doi_tools, tot_nr_tools = get_pmids_workflomics()
 
     pubmetric.log.step_timer(get_pmids_time, "Downloading pmids")
 
-    metadata_file['total_nr_tools'] = tot_nr_tools  
-    metadata_file['biotools_wo_pmid'] = len(doi_tools)
+    metadata_file["total_nr_tools"] = tot_nr_tools
+    metadata_file["biotools_wo_pmid"] = len(doi_tools)
 
     # Update list of doi_tools to include pmid
     get_pmid_from_doi_time = datetime.now()
-    doi_tools = await get_pmid_from_doi(outpath=outpath, inpath=inpath, doi_tools=doi_tools)
+    doi_tools = await get_pmid_from_doi(
+        outpath=outpath, inpath=inpath, doi_tools=doi_tools
+    )
 
     pubmetric.log.step_timer(get_pmid_from_doi_time, "Downloading pmids from doi's")
     metadata_file["pmid_from_doi"] = len(doi_tools)
@@ -377,47 +539,59 @@ async def get_tool_metadata(outpath: str,
     metadata_file["tools"] = all_tools_with_age
 
     pubmetric.log.log_with_timestamp(
-        f'Found {len(all_tools_with_age)} out of a total of {tot_nr_tools} tools with PMIDS.')
+        f"Found {len(all_tools_with_age)} out of a total of {tot_nr_tools} tools with PMIDS."
+    )
 
     return metadata_file
 
-async def fetch_citations(article_id: str,
-                          session: aiohttp.ClientSession,
-                          source: str = 'MED',
-                          batch_size: int = 1000,
-                          page: int = 1) -> list:
+
+async def fetch_citations(
+    article_id: str,
+    session: aiohttp.ClientSession,
+    source: str = "MED",
+    batch_size: int = 1000,
+    page: int = 1,
+) -> list:
     """
     Recursively fetches all citation PMIDs for a given article ID, handling pagination.
-    
+
     :param article_id: PubMed ID for the article.
     :param session: An aiohttp.ClientSession object used for making HTTP requests.
     :param source: The source from which citations are fetched. Default is 'MED'.
     :param batch_size: Number of citations to fetch per request. Default is 1000.
     :param page: The page number for pagination. Defaults to 1.
-    
+
     :return: A list of citation PMIDs.
     """
-    url = f'https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{article_id}/citations?page={page}&pageSize={batch_size}&format=json'
-    async with session.get(url) as response:
+    url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/{source}/{article_id}/citations?page={page}&pageSize={batch_size}&format=json"
+    async with session.get(url, ssl=False) as response:
         if response.ok:
             result = await response.json()
-            citations = result.get('citationList', {}).get('citation', [])
-            citation_ids = [citation['id'] for citation in citations]
-            total_hits = result.get('hitCount')
-
-            if len(citation_ids) < (total_hits - batch_size*( page-1 )):
-                next_page_citations = await fetch_citations(article_id=article_id,
-                                                            session=session,
-                                                            source=source,
-                                                            batch_size=batch_size,
-                                                            page=page + 1)
+            citations = result.get("citationList", {}).get("citation", [])
+            citation_ids = [citation["id"] for citation in citations]
+            total_hits = result.get("hitCount")
+
+            if len(citation_ids) < (total_hits - batch_size * (page - 1)):
+                next_page_citations = await fetch_citations(
+                    article_id=article_id,
+                    session=session,
+                    source=source,
+                    batch_size=batch_size,
+                    page=page + 1,
+                )
                 return citation_ids + next_page_citations
             return citation_ids
         else:
-            pubmetric.log.log_with_timestamp(f'Something went wrong with request {url}')
+            pubmetric.log.log_with_timestamp(f"Something went wrong with request {url}")
             return []
 
-async def fetch_citations_batch(article_ids:list, session: aiohttp.ClientSession, source: str = 'MED', batch_size: int = 1000) -> dict:
+
+async def fetch_citations_batch(
+    article_ids: list,
+    session: aiohttp.ClientSession,
+    source: str = "MED",
+    batch_size: int = 1000,
+) -> dict:
     """
     Asynchronously fetches all citation PMIDs for a batch of article PMIDs from EuropePMC,
     handling pagination recursively.
@@ -426,28 +600,36 @@ async def fetch_citations_batch(article_ids:list, session: aiohttp.ClientSession
     :param session: An aiohttp.ClientSession object used for making HTTP requests.
     :param source: The source from which citations are fetched. Default is 'MED'.
     :param batch_size: Number of citations to fetch per request. Default is 1000.
-    
+
     :return: A dictionary where each key is an article PMID and the value is a list of citation
              PMIDs for that article. If an error occurs while fetching citations for an article,
              the value for that article is an empty list.
     """
     results = {}
-    for article_id in tqdm_asyncio(article_ids, desc="Fetching Citations", unit="article"):
+    for article_id in tqdm_asyncio(
+        article_ids, desc="Fetching Citations", unit="article"
+    ):
         try:
             citations = await fetch_citations(article_id, session, source, batch_size)
             results[article_id] = citations
         except Exception as e:
             pubmetric.log.log_with_timestamp(
-                f"Failed to fetch citations for {article_id}: {str(e)}")
-            results[article_id] = []  # TODO do I want to continue processing other articles even if one fails?
+                f"Failed to fetch citations for {article_id}: {str(e)}"
+            )
+            results[article_id] = (
+                []
+            )  # TODO do I want to continue processing other articles even if one fails?
 
     return results
 
-async def process_citation_data(metadata_file: list,
-                                inpath: Optional[str]='', # default main dir temporarily
-                                outpath: Optional[str]='',
-                                threshold: int = 20,
-                                batch_size: int = 1000) -> dict:
+
+async def process_citation_data(
+    metadata_file: list,
+    inpath: Optional[str] = "",  # default main dir temporarily
+    outpath: Optional[str] = "",
+    threshold: int = 20,
+    batch_size: int = 1000,
+) -> dict:
     """
     Processes citation data by fetching citations for tools listed in the metadata file
     and filtering them based on a citation threshold.
@@ -470,16 +652,22 @@ async def process_citation_data(metadata_file: list,
     citation_counts = Counter()
     paper_citations = defaultdict(set)
 
-    if os.path.exists(os.path.join(inpath, 'paper_citations.json')):
-        with open(os.path.join(inpath, 'paper_citations.json'), 'r', encoding='utf-8') as f:
+    if os.path.exists(os.path.join(inpath, "paper_citations.json")):
+        with open(
+            os.path.join(inpath, "paper_citations.json"), "r", encoding="utf-8"
+        ) as f:
             saved_data = json.load(f)
     else:
         saved_data = {}
-    pending_tools = [tool['pmid']
-                     for tool in metadata_file['tools']
-                     if tool['pmid'] not in saved_data]
-    
-    async with aiohttp.ClientSession(timeout=aiohttp.ClientTimeout(total=60)) as session:
+    pending_tools = [
+        tool["pmid"]
+        for tool in metadata_file["tools"]
+        if tool["pmid"] not in saved_data
+    ]
+
+    async with aiohttp.ClientSession(
+        timeout=aiohttp.ClientTimeout(total=60)
+    ) as session:
         while pending_tools:
             current_batch = pending_tools[:batch_size]
             pending_tools = pending_tools[batch_size:]
@@ -488,14 +676,16 @@ async def process_citation_data(metadata_file: list,
 
             # Saving data incrementally
             saved_data.update(batch_results)
-            with open(os.path.join(outpath, 'paper_citations.json'), 'w', encoding='utf-8') as f:
+            with open(
+                os.path.join(outpath, "paper_citations.json"), "w", encoding="utf-8"
+            ) as f:
                 json.dump(saved_data, f)
             await asyncio.sleep(60)
 
-    for tool in tqdm(metadata_file['tools'], desc="Processing citations", unit="tool"):
-        paper_pmid = tool['pmid']
+    for tool in tqdm(metadata_file["tools"], desc="Processing citations", unit="tool"):
+        paper_pmid = tool["pmid"]
         citations = saved_data.get(paper_pmid, [])
-        tool['nr_citations'] = len(citations)
+        tool["nr_citations"] = len(citations)
         if citations:
             for citation_pmid in citations:
                 if citation_pmid == paper_pmid:
@@ -503,14 +693,20 @@ async def process_citation_data(metadata_file: list,
                 paper_citations[citation_pmid].add(paper_pmid)
                 citation_counts[citation_pmid] += 1
 
-    paper_citations = {citation: papers for citation, papers in paper_citations.items()
-                       if 1 < citation_counts[citation] <= threshold}
+    paper_citations = {
+        citation: papers
+        for citation, papers in paper_citations.items()
+        if 1 < citation_counts[citation] <= threshold
+    }
     removed_citations = len(citation_counts) - len(paper_citations)
     pubmetric.log.log_with_timestamp(
         f"Number of citations removed due to exceeding threshold {threshold} "
-        f"or referencing only one paper: {removed_citations}")
+        f"or referencing only one paper: {removed_citations}"
+    )
 
-    if os.path.exists(os.path.join(outpath, 'paper_citations.json')): # rm file after completion
-        os.remove(os.path.join(outpath, 'paper_citations.json'))
+    if os.path.exists(
+        os.path.join(outpath, "paper_citations.json")
+    ):  # rm file after completion
+        os.remove(os.path.join(outpath, "paper_citations.json"))
 
     return paper_citations
diff --git a/src/pubmetric/fetch_tools.py b/src/pubmetric/fetch_tools.py
new file mode 100644
index 0000000..692126f
--- /dev/null
+++ b/src/pubmetric/fetch_tools.py
@@ -0,0 +1,34 @@
+import json
+import requests
+
+def get_tool_by_id(biotools_id):
+    base_url = f"https://bio.tools/api/tool/{biotools_id}"
+    params = {
+        "format": "json"
+    }
+    
+    response = requests.get(base_url, params=params)
+    response.raise_for_status()  # Check for request errors
+    return response.json()
+
+def get_specific_tools_by_id(biotools_ids):
+    tools = []
+    for biotools_id in biotools_ids:
+        try:
+            tool = get_tool_by_id(biotools_id)
+            tools.append(tool)
+            print(f"Found tool: {tool['name']} with biotoolsID: {biotools_id}")
+        except requests.HTTPError:
+            print(f"Tool with biotoolsID '{biotools_id}' not found.")
+    return tools
+
+# List of biotoolsIDs for the specific tools you want to get
+biotools_ids = [
+    "comet", "peptideprophet", "proteinprophet", "stpeter",
+    "mzrecal", "idconvert", "msconvert", "GOEnrichment",
+    "gprofiler", "xtandem", "MS_Amanda", "msfragger", 
+    "protXml2IdList"
+]
+
+# Fetch details for the specified tools using biotoolsID
+specific_tools = get_specific_tools_by_id(biotools_ids)
\ No newline at end of file
diff --git a/src/pubmetric/metrics.py b/src/pubmetric/metrics.py
index aef56d9..0cabd21 100644
--- a/src/pubmetric/metrics.py
+++ b/src/pubmetric/metrics.py
@@ -346,6 +346,8 @@ def complete_average(graph: igraph.Graph,
     elif isinstance(workflow, list):
         step_names = list(set(element for tup in workflow for element in tup))
         edges = workflow
+    else:
+        raise TypeError("Workflow must be a list or a dictionary")
 
     nr_steps = len(step_names)
     nr_edges = len(edges)
diff --git a/src/pubmetric/network.py b/src/pubmetric/network.py
index 2ba1cad..30762a7 100644
--- a/src/pubmetric/network.py
+++ b/src/pubmetric/network.py
@@ -168,7 +168,7 @@ def process_chunk(chunk: dict):
 
 async def create_network(outpath: Optional[str] = None,
                         test_size: Optional[int] = None,
-                        topic_id: Optional[str] = "topic_0121",
+                        topic_id: Optional[str] = "",
                         random_seed: int = 42,
                         load_graph: bool = False,
                         inpath: str = '',
@@ -180,7 +180,7 @@ async def create_network(outpath: Optional[str] = None,
 
     :param topic_id: The ID to which the downloaded tools belong,
         e.g., "Proteomics" or "DNA" as defined by EDAM ontology.
-    :param test_size: Determines the minimum number of tools downloaded.
+    :param test_size: Determines the maximum number of tools downloaded.
     :param random_seed: Specifies the seed used to randomly pick tools in a test run.
         Default is 42.
     :param load_graph: Determines if an already generated graph is loaded or if it
@@ -243,9 +243,10 @@ async def create_network(outpath: Optional[str] = None,
                 if not selected_tools:
                     raise ValueError("No tools were downloaded; please check the download source.")
             elif isinstance(tool_selection, (list, set)):
+                tool_selection_set = set(tool_selection)
                 selected_tools = [tool
                                   for tool in metadata_file['tools']
-                                  if tool['name'] in tool_selection]
+                                  if tool['name'] in tool_selection_set]
                 if not selected_tools:
                     raise ValueError(
                         "No matching tools found; check the tool names in tool_selection.")
diff --git a/tests/schemas.py b/tests/schemas.py
index e29953c..9799761 100644
--- a/tests/schemas.py
+++ b/tests/schemas.py
@@ -29,7 +29,7 @@ def metafile_schema_validation(metadata_file):
     if not all(key in metadata_file and isinstance(metadata_file[key], required_meta_keys[key]) for key in required_meta_keys):
         raise SchemaValidationError("The schema of the top layer of the metadata file is incorrect.")
     
-    tool = metadata_file["tools"][0] # check only first cause otherwise it takes too much time 
+    tool = metadata_file["tools"][0] # check only first cause otherwise it takes too much time
     print(tool)
     if not all(key in tool and isinstance(tool[key], required_meta_tool_keys[key]) for key in required_meta_tool_keys):
         print([(tool[key], required_meta_tool_keys[key]) for key in required_meta_tool_keys])
diff --git a/tests/test_api_controller.py b/tests/test_api_controller.py
new file mode 100644
index 0000000..022740b
--- /dev/null
+++ b/tests/test_api_controller.py
@@ -0,0 +1,21 @@
+import os
+import pytest
+from fastapi.testclient import TestClient
+from pubmetric.api_controller import app, periodic_graph_generation, recreate_graph
+
+
+from fastapi import FastAPI
+from fastapi.testclient import TestClient
+
+
+client = TestClient(app)
+
+
+def test_read_main():
+    response = client.get("/")
+    assert response.status_code == 200
+    assert response.json() == {"msg": "Welcome to Pubmetric!"}
+
+
+def test_graph_generation():
+    periodic_graph_generation()
diff --git a/tests/test_data.py b/tests/test_data.py
index bc599eb..da65c4d 100644
--- a/tests/test_data.py
+++ b/tests/test_data.py
@@ -1,9 +1,12 @@
+import json
 import os
 import pytest
 import asyncio
 import aiohttp
 import pubmetric.data as data
 from schemas import metafile_schema_validation
+from pubmetric.data import download_domain_annotations, get_tool_metadata
+from pubmetric.network import create_network
 
 def test_get_tool_metadata_from_file(shared_datadir):
     """ Testing that loading a metadata file works"""
@@ -19,7 +22,7 @@ def test_get_tool_metadata_schema():
     """Testing that the generated medatata file has the right format"""
     metadata_file = asyncio.run(data.get_tool_metadata(outpath='',
                                                        topic_id="topic_0121",
-                                                       test_size=20))
+                                                       test_size=100))
     assert metafile_schema_validation(metadata_file)
 
 @pytest.mark.asyncio
@@ -61,7 +64,7 @@ def test_get_pmid_from_doi_from_file_with_updates(shared_datadir):
     assert str(pmid_list[0]["pmid"]) == '23051804'
 
 def test_get_pmids():
-    test_size = 10
+    test_size = 100
     pmid_tools, doi_tools, total_nr_tools  = asyncio.run(data.get_pmids(topic_id="topic_0121", test_size=test_size))
     print(pmid_tools, doi_tools, total_nr_tools)
     # TODO: just checking some format things right now, could improve
@@ -90,4 +93,45 @@ def test_get_ages():
         },
      ]
      tool_metadata_inc_ages = asyncio.run(data.process_publication_dates(tool_metadata))
-     assert tool_metadata_inc_ages[0]['publication_date'] == 2002
\ No newline at end of file
+     assert tool_metadata_inc_ages[0]['publication_date'] == 2002
+
+
+def test_download_domain_annotations():
+    """Tests downloading the domain annotations for one tool"""
+    tools = download_domain_annotations(annotations="workflomics")
+    assert len(tools) > 10
+    assert len(tools) < 30
+
+
+def test_create_network():
+    asyncio.run(create_network(tool_selection="workflomics", outpath="out/out_default", inpath="out/out_default"))
+
+def test_create_network_2():
+    asyncio.run(create_network(tool_selection=["Comet",
+    "PeptideProphet",
+    "ProteinProphet",
+    "StPeter",
+    "mzRecal",
+    "idconvert",
+    "msconvert",
+    "GOEnrichment",
+    "gProfiler",
+    "XTandem",
+    "MS Amanda",
+    "MSFragger",
+    "protXml2IdList","wcloud"], outpath="out/out_default", inpath="out/out_default"))
+
+
+def test_get_tool_metadata():
+    file :dict = asyncio.run(get_tool_metadata(outpath="out/out_default", topic_id=""))
+
+    # now write to the file system the dict as a json file
+    with open("out/out_default/tool_metadata.json", "w") as f:
+        f.write(json.dumps(file,indent=4,
+    separators=(',', ': ')))
+
+def test_get_pmids_workflomics():
+    _, _, no_tools = data.get_pmids_workflomics()
+    assert no_tools > 10
+    assert no_tools < 30
+    
\ No newline at end of file
diff --git a/tests/test_network.py b/tests/test_network.py
index af39f7c..73a0a0a 100644
--- a/tests/test_network.py
+++ b/tests/test_network.py
@@ -56,4 +56,4 @@ def test_add_attributes():
     assert 'age' in attribute_graph.vs.attributes()
     assert 'pmid' in attribute_graph.vs.attributes()
     assert 'nr_citations' in attribute_graph.vs.attributes()
-    assert 'degree' in attribute_graph.vs.attributes()
\ No newline at end of file
+    assert 'degree' in attribute_graph.vs.attributes()
diff --git a/tests/test_pckg_dev.py b/tests/test_pckg_dev.py
index 88a105b..b349d62 100644
--- a/tests/test_pckg_dev.py
+++ b/tests/test_pckg_dev.py
@@ -1,8 +1,11 @@
-from pubmetric.pckg_dev import *
+import os
+import igraph
 from pubmetric import data
 import asyncio
 import pickle
 
+from pubmetric.pckg_dev import generate_random_workflow
+
 def get_pmids_from_file(shared_datadir): # TODO why is this here?
     filename = os.path.join(shared_datadir, "doi_pmid_library.json")
     doi_list = [{"name": "mzRecal", "doi": "10.1093/bioinformatics/btab056"}, {"name": "DIAgui", "doi": "10.1093/bioadv/vbae001"}]
diff --git a/tests/test_workflow.py b/tests/test_workflow.py
index f2fa7b5..b0907b9 100644
--- a/tests/test_workflow.py
+++ b/tests/test_workflow.py
@@ -1,6 +1,5 @@
 import os 
-import igraph 
-from pubmetric.workflow import *
+from pubmetric.workflow import parse_cwl, parse_undocumented_workflows
 import pickle
 
 
@@ -26,25 +25,3 @@ def test_parse_undocumented_workflows(shared_datadir):
     assert workflow['edges'] == [('XTandem_01', 'ProteinProphet_02'), ('ProteinProphet_02', 'StPeter_04'), ('XTandem_03', 'StPeter_04')]
     assert workflow == undoc_workflow
 
-
-
-
-# def test_generate_pmid_edges(shared_datadir): # This is outdated now, dont know If i want to recreate it. TODO
-#     metadata_filename = os.path.join(shared_datadir, "tool_metadata_test20_topic_0121_20250705.json")
-
-#     name_workflow = [ ('XTandem', 'ProteinProphet'), ('XTandem', 'PeptideProphet'), ('ProteinProphet', 'StPeter'), ('PeptideProphet', 'StPeter') ]
-#     expected_tuple_workflow = [('14976030','14632076' )  , ('14976030','12403597')  , ('14632076','29400476')  , ('12403597', '29400476')  ]
-#                             # [ (XTandem, ProteinProphet), (XTandem, PeptideProphet), (ProteinProphet, StPeter), (PeptideProphet, StPeter) ]
-
-#     faulty_name_workflow = [ ('XTandem', 'ProteinProphet'), ('XTandem', 'NotATOOL'), ('ProteinProphet', 'StPeter'), ('NotATOOL', 'StPeter') ]
-
-#     reconnected_workflow = generate_pmid_edges(metadata_filename, name_workflow)
-#     reconnected_faulty_workflow = generate_pmid_edges(metadata_filename, faulty_name_workflow, handle_missing='reconnect')
-#     removed_faulty_workflow = generate_pmid_edges(metadata_filename, faulty_name_workflow, handle_missing='remove')
-#     kept_faulty_workflow = generate_pmid_edges(metadata_filename, faulty_name_workflow, handle_missing='keep')
-
-#     assert sorted(reconnected_workflow) == sorted(expected_tuple_workflow) # A wofklow where all PmIDs are in the metadatafile should not be changed
-#     assert len(reconnected_faulty_workflow) == 3 # the two edges containing 'NotATOOL' should be turned into a single edge ('XTandem', 'StPeter')
-#     assert len(removed_faulty_workflow) == 2 # the two edges containing 'NotATOOL' are removed
-#     assert len(kept_faulty_workflow) == 4 and 'None' in kept_faulty_workflow[1] # the two edges containing 'NotATOOL' will contain a None 
-#                                                 #TODO this should not be a string none but a none none
\ No newline at end of file