Fix Docker runtime issues, add CI checks, and refactor eFP schemas

.flake8

@@ -1,16 +1,12 @@
 [flake8]
-max-line-length = 120
-extend-ignore = E203, W503, E501
+ignore = E501, E203, E121, E123, E126, W503, W504
 exclude =
     .git,
-    __pycache__,
-    docs/source/conf.py,
-    old,
-    build,
-    dist,
-    venv,
-    env,
     .venv,
-    ./venv-docs,
+    __pycache__,
+    api/Archive,
+    data,
     docs,
-    .env
+    instance,
+    output,
+    venv

.github/workflows/bar-api.yml

@@ -12,6 +12,7 @@ jobs:
 
     runs-on: ubuntu-24.04
     strategy:
+      fail-fast: false
       matrix:
         python-version: [3.10.18, 3.11, 3.12, 3.13]
 

.github/workflows/codeql.yml

@@ -29,16 +29,16 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"

.gitignore

@@ -141,3 +141,6 @@ dmypy.json
 output/*
 !output
 !output/placeholder.txt
+
+# Local sqlite mirrors generated from MySQL dumps
+config/databases/*.db

README.md

@@ -4,4 +4,4 @@
 
 [![Website Status](https://img.shields.io/website?url=http%3A%2F%2Fbar.utoronto.ca%2Fapi%2F)](http://bar.utoronto.ca/api/) ![GitHub repo size](https://img.shields.io/github/repo-size/BioAnalyticResource/BAR_API) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/bar-api/badge/?version=latest)](https://bar-api.readthedocs.io/en/latest/?badge=latest)
 
-This is the official repository for the Bio-Analytic Resource API. The API documentation can be found [here](https://bar-api.readthedocs.io/en/latest/).
+This is the official repository for the Bio-Analytic Resource API. The API documentation can be found [here](https://bar-api.readthedocs.io/en/latest/).

api/Archive/analyze_efp_schemas.py

@@ -0,0 +1,269 @@
+"""
+Analyze eFP database structures to find the most compact schema representation.
+
+Since we only need 3 columns (data_probeset_id, data_signal, data_bot_id),
+this script groups databases by their column signatures to identify
+shared patterns and enable a table-driven schema definition.
+
+Usage:
+    python api/Archive/analyze_efp_schemas.py
+"""
+
+import csv
+from collections import defaultdict
+
+STRUCTURE_CSV = "api/Archive/efp_tables_structure_sample_data_dump_01_28_25.csv"
+SAMPLE_DATA_CSV = "api/Archive/sample_data_export_feb_4.csv"
+
+# Only these 3 columns matter for the API
+NEEDED_COLUMNS = {"data_probeset_id", "data_signal", "data_bot_id"}
+
+# Extra columns that some databases have (we want to know which ones)
+EXTRA_COLUMNS = {
+    "channel", "data_call", "data_num", "data_p_val", "data_p_value",
+    "genome", "genome_id", "log", "orthogroup", "p_val", "project_id",
+    "qvalue", "sample_file_name", "sample_tissue", "version",
+}
+
+
+def parse_structure_csv():
+    """Parse the structure CSV into per-database column definitions."""
+    db_columns = defaultdict(dict)  # {db_name: {col_name: {type, nullable, default}}}
+
+    with open(STRUCTURE_CSV, newline="") as f:
+        reader = csv.DictReader(f)
+        for row in reader:
+            db = row["database_name"]
+            col = row["COLUMN_NAME"]
+            db_columns[db][col] = {
+                "type": row["COLUMN_TYPE"],
+                "nullable": row["IS_NULLABLE"] == "YES",
+                "default": row["COLUMN_DEFAULT"],
+            }
+    return db_columns
+
+
+def extract_signature(db_cols):
+    """
+    Extract a signature tuple for the 3 needed columns.
+    Returns (probeset_type, probeset_nullable, signal_nullable, signal_default, bot_type, bot_nullable)
+    """
+    p = db_cols.get("data_probeset_id", {})
+    s = db_cols.get("data_signal", {})
+    b = db_cols.get("data_bot_id", {})
+    return (
+        p.get("type", "?"),
+        p.get("nullable", False),
+        s.get("nullable", False),
+        s.get("default", "NULL"),
+        b.get("type", "?"),
+        b.get("nullable", False),
+    )
+
+
+def parse_varchar_length(col_type):
+    """Extract length from varchar(N) or return None for tinytext/text."""
+    if col_type.startswith("varchar("):
+        return int(col_type[8:-1])
+    return None  # tinytext, text, etc.
+
+
+def main():
+    db_columns = parse_structure_csv()
+
+    print("=" * 80)
+    print("EFP SCHEMA ANALYSIS - Only 3 columns needed")
+    print("=" * 80)
+    print(f"\nTotal databases: {len(db_columns)}")
+    print(f"Needed columns: {', '.join(sorted(NEEDED_COLUMNS))}")
+
+    # ---- 1. Check which databases have extra columns beyond the 3 ----
+    print("\n" + "=" * 80)
+    print("DATABASES WITH EXTRA COLUMNS (beyond the 3 needed + proj_id + sample_id)")
+    print("=" * 80)
+    dbs_with_extras = {}
+    for db, cols in sorted(db_columns.items()):
+        extras = set(cols.keys()) - NEEDED_COLUMNS - {"proj_id", "sample_id"}
+        if extras:
+            dbs_with_extras[db] = extras
+            print(f"  {db}: {', '.join(sorted(extras))}")
+
+    dbs_simple = set(db_columns.keys()) - set(dbs_with_extras.keys())
+    print(f"\n  -> {len(dbs_simple)} databases have ONLY the 5 standard columns")
+    print(f"  -> {len(dbs_with_extras)} databases have extra columns")
+
+    # ---- 2. Group databases by their 3-column signature ----
+    print("\n" + "=" * 80)
+    print("GROUPING BY SIGNATURE (probeset_type, probeset_nullable, signal_nullable, signal_default, bot_type, bot_nullable)")
+    print("=" * 80)
+
+    sig_groups = defaultdict(list)
+    for db, cols in sorted(db_columns.items()):
+        sig = extract_signature(cols)
+        sig_groups[sig].append(db)
+
+    for sig, dbs in sorted(sig_groups.items(), key=lambda x: -len(x[1])):
+        print(f"\n  Signature: probeset={sig[0]}(nullable={sig[1]}) signal(nullable={sig[2]}, default={sig[3]}) bot={sig[4]}(nullable={sig[5]})")
+        print(f"  Count: {len(dbs)}")
+        print(f"  DBs: {', '.join(dbs[:10])}{'...' if len(dbs) > 10 else ''}")
+
+    # ---- 3. Group by (probeset_len, bot_len) - the key variable dimensions ----
+    print("\n" + "=" * 80)
+    print("DATA-DRIVEN COMPACT FORMAT: Group by (probeset_type, bot_type)")
+    print("Only considering the 3 needed columns")
+    print("=" * 80)
+
+    # For the compact representation, what varies per database is:
+    # - data_probeset_id: type (varchar(N) or tinytext) and length
+    # - data_bot_id: type (varchar(N) or tinytext) and length
+    # - data_signal: nullable and default (always float)
+    # We can represent this as a tuple per database
+
+    compact_entries = []
+    for db, cols in sorted(db_columns.items()):
+        p = cols.get("data_probeset_id", {})
+        s = cols.get("data_signal", {})
+        b = cols.get("data_bot_id", {})
+
+        probeset_type = p.get("type", "varchar(24)")
+        bot_type = b.get("type", "varchar(16)")
+        signal_nullable = s.get("nullable", False)
+
+        probeset_len = parse_varchar_length(probeset_type)
+        bot_len = parse_varchar_length(bot_type)
+
+        # Determine extra columns this DB needs
+        extras = set(cols.keys()) - NEEDED_COLUMNS - {"proj_id", "sample_id"}
+
+        compact_entries.append({
+            "db": db,
+            "probeset_len": probeset_len,  # None = tinytext
+            "probeset_type": probeset_type,
+            "bot_len": bot_len,  # None = tinytext
+            "bot_type": bot_type,
+            "signal_nullable": signal_nullable,
+            "extras": extras,
+        })
+
+    # ---- 4. Show the most compact table-driven representation ----
+    print("\n" + "=" * 80)
+    print("PROPOSED COMPACT TUPLE FORMAT")
+    print("Each DB needs: (name, probeset_len_or_None, bot_len_or_None, signal_nullable)")
+    print("None = tinytext (TEXT in our schema)")
+    print("=" * 80)
+
+    # Group by shared properties to find patterns
+    pattern_groups = defaultdict(list)
+    for e in compact_entries:
+        key = (e["probeset_len"], e["bot_len"], e["signal_nullable"], tuple(sorted(e["extras"])))
+        pattern_groups[key].append(e["db"])
+
+    print(f"\nUnique (probeset_len, bot_len, signal_nullable, extras) combinations: {len(pattern_groups)}")
+    print("\nTop patterns (most databases sharing the same column spec):")
+    for (pl, bl, sn, ex), dbs in sorted(pattern_groups.items(), key=lambda x: -len(x[1]))[:20]:
+        extras_str = f", extras={list(ex)}" if ex else ""
+        print(f"  probeset={pl}, bot={bl}, signal_nullable={sn}{extras_str}")
+        print(f"    Count: {len(dbs)}, DBs: {', '.join(dbs[:5])}{'...' if len(dbs) > 5 else ''}")
+
+    # ---- 5. Generate the most compact code ----
+    print("\n" + "=" * 80)
+    print("GENERATED COMPACT TABLE (for efp_schemas.py)")
+    print("Format: (db_name, probeset_len, bot_len)")
+    print("  - probeset_len: int for varchar(N), 0 for tinytext")
+    print("  - bot_len: int for varchar(N), 0 for tinytext")
+    print("  - signal is always float, nullable is always True (safe default)")
+    print("=" * 80)
+
+    # Simple databases (only 3 needed columns, no extras of concern)
+    simple_dbs = []
+    complex_dbs = []
+    for e in compact_entries:
+        # Filter out databases that ONLY have unneeded extras
+        # (sample_file_name, data_call, data_p_val etc. are not needed)
+        has_important_extras = e["extras"] - {
+            "sample_file_name", "data_call", "data_p_val", "data_p_value", "data_num"
+        }
+        if has_important_extras:
+            complex_dbs.append(e)
+        else:
+            simple_dbs.append(e)
+
+    print(f"\nSimple databases (only need 3 columns): {len(simple_dbs)}")
+    print(f"Complex databases (have unique extra columns): {len(complex_dbs)}")
+
+    print("\n# ---- SIMPLE DATABASES (table-driven) ----")
+    print("# (db_name, probeset_len, bot_len)")
+    print("# probeset_len/bot_len: positive int = varchar(N), 0 = tinytext")
+    print("_SIMPLE_EFP_SPECS = [")
+    for e in sorted(simple_dbs, key=lambda x: x["db"]):
+        pl = e["probeset_len"] if e["probeset_len"] is not None else 0
+        bl = e["bot_len"] if e["bot_len"] is not None else 0
+        print(f'    ("{e["db"]}", {pl}, {bl}),')
+    print("]")
+
+    print(f"\n# ---- COMPLEX DATABASES (need manual definition) ----")
+    for e in sorted(complex_dbs, key=lambda x: x["db"]):
+        pl = e["probeset_len"] if e["probeset_len"] is not None else "tinytext"
+        bl = e["bot_len"] if e["bot_len"] is not None else "tinytext"
+        print(f'# {e["db"]}: probeset={pl}, bot={bl}, extras={sorted(e["extras"])}')
+
+    # ---- 6. Analyze sample data for testing ----
+    print("\n" + "=" * 80)
+    print("SAMPLE DATA SUMMARY (for test verification)")
+    print("=" * 80)
+
+    try:
+        db_samples = defaultdict(list)
+        with open(SAMPLE_DATA_CSV, newline="") as f:
+            reader = csv.DictReader(f)
+            for row in reader:
+                db_samples[row["source_database"]].append({
+                    "data_bot_id": row["data_bot_id"],
+                    "data_probeset_id": row["data_probeset_id"],
+                    "data_signal": row["data_signal"],
+                })
+
+        print(f"Total databases with sample data: {len(db_samples)}")
+        print(f"Total sample rows: {sum(len(v) for v in db_samples.values())}")
+
+        # Verify sample data matches structure
+        for db in sorted(db_samples.keys()):
+            if db not in db_columns:
+                print(f"  WARNING: {db} has sample data but no structure definition!")
+        for db in sorted(db_columns.keys()):
+            if db not in db_samples:
+                print(f"  WARNING: {db} has structure but no sample data!")
+
+    except FileNotFoundError:
+        print("  Sample data file not found, skipping.")
+
+    # ---- 7. Final recommendation ----
+    print("\n" + "=" * 80)
+    print("RECOMMENDATION")
+    print("=" * 80)
+    print(f"""
+Since you only need 3 columns (data_probeset_id, data_signal, data_bot_id),
+the entire schema can be reduced to a simple lookup table.
+
+Current efp_schemas.py: ~1984 lines
+Proposed compact version: ~{len(simple_dbs) + 50} lines (table + builder)
+
+Each database only differs in:
+  1. data_probeset_id length (varchar(N) or tinytext)
+  2. data_bot_id length (varchar(N) or tinytext)
+
+data_signal is always float.
+
+The compact format uses a list of tuples:
+  (db_name, probeset_len, bot_len)
+
+A single builder function converts these tuples into full schema dicts.
+
+Complex databases ({len(complex_dbs)}) that have unique extra columns
+(channel, genome, genome_id, orthogroup, version, log, p_val, qvalue,
+sample_tissue) need individual definitions.
+""")
+
+
+if __name__ == "__main__":
+    main()