Add Journal preset, update funder aliases, and UI improvements

- Add Journal Preset dropdown (Top 10 by count, Top 10 by percent)
- Update funder aliases from v3 to v4
- Add percent sign to mouseover text for percent metrics
- Add page title and description with links to repos
- Disable Country filtering (temporarily, ~25% coverage)
- Update Aggregation menu labels for clarity
- Sort Journal/Funder dropdowns by Data Sharing %
- Display Data Sharing % in dropdown labels
- Update README to describe dashboard with link to opensciencemetrics.org
- Update parquet file to dashboard_20251211-1738.parquet

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: agt24

README.md

@@ -2,59 +2,70 @@
 
 OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.
 
-# Running the app
+## Dashboard
 
-N.B. pdf parsing does not work on Apple silicon...
+The Open Science Metrics Dashboard visualizes data sharing and code sharing trends across biomedical research funders and journals, based on analysis of PubMed Central publications.
 
-- With docker-compose and python >=3.11 installed, run the following from the project's root directory:
+**Live Dashboard:** [https://www.opensciencemetrics.org](https://www.opensciencemetrics.org)
 
-```
-pip install .
-osm -f path/to/pdf-or-xml -u uuid
-```
+### Features
 
-If you have many files to upload you may with to start up the docker-compose  dependencies in a separate terminal window:
+- **Splitting Variables:** View trends by Journal or Funder
+- **Presets:** Quick selection of top journals/funders by data sharing count or percent
+- **Aggregation Metrics:** Data Sharing %, Code Sharing %, article counts
+- **Interactive Charts:** Toggle individual lines, hover for details
+- **Year Range Filter:** Focus on specific time periods (default: 2010-2024)
 
-```
-docker compose up # docker-compose on some systems
-```
+## CLI Tool (Legacy)
 
-And then tell the osm tool that this has been handled:
+The repository also contains a command line tool for processing individual PDFs and XMLs. Note: This tool is not currently being actively maintained.
 
-```
-osm -f path/to/pdf-or-xml -u uuid --user-managed-compose
-osm -f path/to/pdf-or-xml2 -u uuid2 --user-managed-compose
-```
+With docker-compose and python >=3.11 installed:
 
-# Contributing
+```bash
+pip install .
+osm -f path/to/pdf-or-xml -u uuid
+```
 
-N.B. On Apple silicon you must use emulation and download the mongo container in advance:
+For processing many files, start docker-compose dependencies separately:
 
-```
-export DOCKER_DEFAULT_PLATFORM=linux/amd64
-docker pull mongo:4.4.6
+```bash
+docker compose up  # In one terminal
+osm -f path/to/pdf-or-xml -u uuid --user-managed-compose  # In another terminal
 ```
 
-To contribute to the project please run the following commands to set up a development environment:
+## Contributing
 
-```
+To set up a development environment:
+
+```bash
 pip install -e .
 docker compose -f compose.yaml -f compose.development.override.yaml up --build
 ```
-And in another terminal:
 
-```
+In another terminal:
+
+```bash
 export OSM_API="http://localhost:80"
 osm -f path/to/pdf-or-xml -u uuid --user-managed-compose
 ```
 
+### Pre-commit Hooks
 
-## Using pre-commit for commit checks
-
-Pre-commit will run all of its hooks on every commit you make. To install
-pre-commit and its hooks, run the following commands:
+Pre-commit runs checks on every commit. To install:
 
-```
+```bash
 pip install pre-commit
 pre-commit install
 ```
+
+### Apple Silicon Notes
+
+On Apple silicon, you must use emulation:
+
+```bash
+export DOCKER_DEFAULT_PLATFORM=linux/amd64
+docker pull mongo:4.4.6
+```
+
+Note: PDF parsing does not work on Apple silicon.

web/dashboard/streamlit_app.py

@@ -289,7 +289,6 @@ def get_journal_labels(journal_list: list[str]) -> list[str]:
 
 # Preset to journal list mapping
 JOURNAL_PRESETS = {
-    "Top 5 by count + Top 5 by percent": top_5_journals_combined,
     "Top 10 by data sharing count": top_10_journals_by_count,
     "Top 10 by data sharing percent": top_10_journals_by_percent,
 }
@@ -303,9 +302,9 @@ def on_journal_preset_change() -> None:
 
 
 if splitting_variable == "journal":
-    # Initialize journal selection if not set
+    # Initialize journal selection if not set (use first preset)
     if "journal" not in st.session_state:
-        st.session_state["journal"] = get_journal_labels(top_5_journals_combined)
+        st.session_state["journal"] = get_journal_labels(top_10_journals_by_count)
 
     journal_preset = st.selectbox(
         "Journals preset",
@@ -314,19 +313,24 @@ def on_journal_preset_change() -> None:
         key="journal_preset_select",
         on_change=on_journal_preset_change,
     )
-    default_journal_labels: list[str] = st.session_state.get(
-        "journal", get_journal_labels(top_5_journals_combined)
-    )
-else:
-    default_journal_labels = []
 
 with row_2_col_1:
-    selected_journal_labels = st.multiselect(
-        "Journal (sorted by Data Sharing %)",
-        options=unique_journal_labels,
-        default=default_journal_labels,
-        key="journal",
-    )
+    # When using session state (splitting_variable == "journal"), don't pass default
+    # to avoid "widget with key was created with default but also had value set via
+    # Session State API" warning
+    if splitting_variable == "journal":
+        selected_journal_labels = st.multiselect(
+            "Journal (sorted by Data Sharing %)",
+            options=unique_journal_labels,
+            key="journal",
+        )
+    else:
+        selected_journal_labels = st.multiselect(
+            "Journal (sorted by Data Sharing %)",
+            options=unique_journal_labels,
+            default=[],
+            key="journal",
+        )
     # Map back to actual journal names for filtering
     journals = [journal_display_map[label] for label in selected_journal_labels]
 
@@ -416,19 +420,24 @@ def on_funder_preset_change() -> None:
         key="funder_preset_select",
         on_change=on_funder_preset_change,
     )
-    default_funder_labels: list[str] = st.session_state.get(
-        "funder", get_funder_labels(top_5_combined)
-    )
-else:
-    default_funder_labels = []
 
 with row_2_col_3:
-    selected_funder_labels = st.multiselect(
-        "Funder (sorted by Data Sharing %)",
-        options=unique_funder_labels,
-        default=default_funder_labels,
-        key="funder",
-    )
+    # When using session state (splitting_variable == "funder"), don't pass default
+    # to avoid "widget with key was created with default but also had value set via
+    # Session State API" warning
+    if splitting_variable == "funder":
+        selected_funder_labels = st.multiselect(
+            "Funder (sorted by Data Sharing %)",
+            options=unique_funder_labels,
+            key="funder",
+        )
+    else:
+        selected_funder_labels = st.multiselect(
+            "Funder (sorted by Data Sharing %)",
+            options=unique_funder_labels,
+            default=[],
+            key="funder",
+        )
     # Map back to actual funder names for filtering
     funders = [funder_display_map[label] for label in selected_funder_labels]