@gen3/workspaces 0.12.62 → 0.12.64

package/dist/index.d.ts

@@ -40,6 +40,7 @@ interface TierToolbarConfiguration extends LabelAndDescription {
     tierLabel?: string;
 }
 interface SettingsPanelConfiguration {
+    enabled?: boolean;
     showKernels: boolean;
     width?: number;
 }
@@ -59,6 +60,7 @@ interface FreeWorkspaceTierConfiguration extends WorkspaceTierInformation {
 }
 interface RemoteComputeWorkspaceTierConfiguration extends WorkspaceTierInformation {
     baseUrl?: string;
+    enableOptions?: boolean;
     type: Extract<WorkspaceTier, 'remote'>;
     startTimeLimit?: number;
 }

package/dist/jupyterlite-builds/free-private/overrides.json

@@ -0,0 +1 @@
+{}

package/dist/jupyterlite-builds/remote-private/overrides.json

@@ -0,0 +1,26 @@
+{
+  "@jupyterlab/mainmenu-extension:plugin": {
+    "menus": [
+      {
+        "id": "jp-mainmenu-file",
+        "items": [
+          {
+            "command": "docmanager:download",
+            "args": { "isMenu": true },
+            "disabled": true
+          }
+        ]
+      }
+    ]
+  },
+  "@jupyterlab/shortcuts-extension:shortcuts": {
+    "shortcuts": [
+      {
+        "command": "docmanager:download",
+        "keys": ["Accel Shift S"],
+        "selector": "body",
+        "disabled": true
+      }
+    ]
+  }
+}

package/dist/jupyterlite-builds/scripts/build-gen3sdk-lite_v2.sh

@@ -0,0 +1,310 @@
+#!/usr/bin/env bash
+# =============================================================================
+# build-gen3sdk-lite.sh — Build Gen3 SDK and dependencies as WASM wheels
+#
+# Prerequisites:
+#   - uv  (https://docs.astral.sh/uv/getting-started/installation/)
+#   - git
+#   - cmake, make, and a C compiler (for emsdk bootstrap)
+#
+# Usage:
+#   ./build-gen3sdk-lite.sh            # full build (setup + all packages)
+#   ./build-gen3sdk-lite.sh --setup    # environment setup only
+#   ./build-gen3sdk-lite.sh --build    # build wheels only (assumes setup done)
+#   ./build-gen3sdk-lite.sh --clean    # remove cloned repos, build artifacts
+# =============================================================================
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+# ── Configuration ────────────────────────────────────────────────────────────
+# Repositories to build (order matters — independent packages first)
+# Format: "name|git_url|subdir"  (subdir is optional)
+REPOS=(
+  "cdislogging|https://github.com/uc-cdis/cdislogging.git"
+  "python-json-logger|https://github.com/nhairs/python-json-logger.git"
+  "fastavro|https://github.com/fastavro/fastavro.git"
+  "drsclient|https://github.com/uc-cdis/drsclient.git"
+  "indexd|https://github.com/uc-cdis/indexd.git|indexclient"
+  "dictionaryutils|https://github.com/uc-cdis/dictionaryutils.git"
+  "pypfb|https://github.com/uc-cdis/pypfb.git"
+  "gen3sdk-python|https://github.com/uc-cdis/gen3sdk-python.git"
+  "gen3users|git@github.com:uc-cdis/gen3users.git"
+)
+
+# ── Source shared environment ────────────────────────────────────────────────
+# setup-env.sh exports: ROOT_DIR, SRC_DIR, BUILD_DIR, VENV_DIR, WORK_DIR,
+# EMSDK_DIR, SOURCES_DIR, OUTPUT_DIR, LOG_DIR and helper functions.
+# It also creates + activates the venv and installs core tooling.
+source_shared_env() {
+  # shellcheck disable=SC1091
+  source "${SCRIPT_DIR}/setup-env.sh"
+}
+
+# ── Emscripten SDK ───────────────────────────────────────────────────────────
+setup_emsdk() {
+  info "Setting up Emscripten SDK …"
+
+  if [[ ! -d "${EMSDK_DIR}" ]]; then
+    git clone https://github.com/emscripten-core/emsdk.git "${EMSDK_DIR}"
+  fi
+
+  local em_version
+  em_version="$(pyodide config get emscripten_version)"
+  info "Pyodide requires Emscripten ${em_version}"
+
+  pushd "${EMSDK_DIR}" > /dev/null
+  ./emsdk install "${em_version}"
+  ./emsdk activate "${em_version}"
+  # shellcheck disable=SC1091
+  source emsdk_env.sh
+  popd > /dev/null
+
+  success "Emscripten $(emcc --version | head -1) activated"
+}
+
+# ── Full environment setup ───────────────────────────────────────────────────
+setup_environment() {
+  source_shared_env
+  mkdir -p "${WORK_DIR}" "${SOURCES_DIR}" "${OUTPUT_DIR}" "${LOG_DIR}"
+
+  # WASM-specific tooling (on top of the shared base)
+  info "Installing pyodide-build …"
+  uv pip install pyodide-build 2>&1 | tail -3
+  success "pyodide-build $(pyodide --version 2>/dev/null || echo '(installed)')"
+
+  setup_emsdk
+}
+
+# ── Clone / update sources ──────────────────────────────────────────────────
+clone_repos() {
+  info "Cloning / updating repositories …"
+  for entry in "${REPOS[@]}"; do
+    IFS='|' read -r name url _subdir <<< "${entry}"
+    local dest="${SOURCES_DIR}/${name}"
+    if [[ -d "${dest}/.git" ]]; then
+      info "  ${name}: pulling latest …"
+      git -C "${dest}" pull --ff-only 2>&1 | tail -1
+    else
+      info "  ${name}: cloning …"
+      git clone "${url}" "${dest}" 2>&1 | tail -1
+    fi
+  done
+  success "All repositories ready"
+}
+
+# ── Build WASM wheels ───────────────────────────────────────────────────────
+build_wheels() {
+  # Make sure emsdk env is active in this shell
+  if [[ -f "${EMSDK_DIR}/emsdk_env.sh" ]]; then
+    # shellcheck disable=SC1091
+    source "${EMSDK_DIR}/emsdk_env.sh" 2>/dev/null
+  fi
+  # shellcheck disable=SC1091
+  source "${VENV_DIR}/bin/activate"
+
+  local total=${#REPOS[@]}
+  local built=0
+  local failed=0
+  local failed_names=()
+
+  # ── Source patches ─────────────────────────────────────────────────────
+
+  # gen3users: old poetry.masonry.api → poetry.core.masonry.api
+  local gen3users_pyproject="${SOURCES_DIR}/gen3users/pyproject.toml"
+  if [[ -f "${gen3users_pyproject}" ]]; then
+    sed -i '' 's|build-backend = "poetry.masonry.api"|build-backend = "poetry.core.masonry.api"|' "${gen3users_pyproject}"
+    info "Patched gen3users: build-backend updated to poetry.core.masonry.api"
+  fi
+
+  # gen3sdk-python: relax indexclient pin
+  local gen3sdk_pyproject="${SOURCES_DIR}/gen3sdk-python/pyproject.toml"
+  if [[ -f "${gen3sdk_pyproject}" ]]; then
+    sed -i '' 's/indexclient = "\^2\.3\.0"/indexclient = ">=2.3.0"/' "${gen3sdk_pyproject}"
+    info "Patched gen3sdk-python: indexclient constraint relaxed to >=2.3.0"
+  fi
+
+  # dictionaryutils: relax jsonschema pin
+  local dictionaryutils_pyproject="${SOURCES_DIR}/dictionaryutils/pyproject.toml"
+  if [[ -f "${dictionaryutils_pyproject}" ]]; then
+    sed -i '' 's/jsonschema = "<=4\.23\.0"/jsonschema = ">=4.0.0"/' "${dictionaryutils_pyproject}"
+    info "Patched dictionaryutils: jsonschema constraint relaxed to >=4.0.0"
+  fi
+
+  # psqlgraph: multiple fixes for WASM compatibility
+  local psqlgraph_pyproject="${SOURCES_DIR}/psqlgraph/pyproject.toml"
+  if [[ -f "${psqlgraph_pyproject}" ]]; then
+    sed -i '' 's/"sqlalchemy~=1\.4"/"sqlalchemy>=1.4"/' "${psqlgraph_pyproject}"
+    sed -i '' 's/, "versionista>=1\.1\.0"//' "${psqlgraph_pyproject}"
+    sed -i '' 's/local_scheme = "versionista-local-format"/local_scheme = "no-local-version"/' "${psqlgraph_pyproject}"
+    sed -i '' 's/version_scheme = "versionista-format"/version_scheme = "guess-next-dev"/' "${psqlgraph_pyproject}"
+    sed -i '' '/"psycopg2"/d' "${psqlgraph_pyproject}"
+    sed -i '' '/"xlocal"/d' "${psqlgraph_pyproject}"
+    info "Patched psqlgraph: sqlalchemy >=1.4, removed versionista + psycopg2 + xlocal"
+
+    local psql_py="${SOURCES_DIR}/psqlgraph/src/psqlgraph/psql.py"
+    if [[ -f "${psql_py}" ]]; then
+      python3 - "${psql_py}" <<'PYEOF'
+import sys, re
+
+path = sys.argv[1]
+text = open(path).read()
+stub = '''\
+try:
+    import xlocal
+except ImportError:
+    class _XLocalInst:
+        class _Ctx:
+            def __init__(self, parent, **kw):
+                self._parent, self._kw = parent, kw
+            def __enter__(self):
+                for k, v in self._kw.items():
+                    setattr(self._parent, k, v)
+                return self._parent
+            def __exit__(self, *a):
+                for k in self._kw:
+                    self._parent.__dict__.pop(k, None)
+        def __call__(self, **kw):
+            return self._Ctx(self, **kw)
+    class _xlocal_module:
+        xlocal = _XLocalInst
+    xlocal = _xlocal_module()'''
+text = re.sub(r'^import xlocal$', stub, text, flags=re.MULTILINE)
+open(path, 'w').write(text)
+PYEOF
+      info "Patched psqlgraph/psql.py: xlocal import wrapped in try/except stub"
+    fi
+  fi
+
+  # ── Build loop ─────────────────────────────────────────────────────────
+  info "Building ${total} packages …"
+  echo ""
+
+  for entry in "${REPOS[@]}"; do
+    IFS='|' read -r name _url subdir <<< "${entry}"
+    local src="${SOURCES_DIR}/${name}"
+    local build_dir="${src}"
+    [[ -n "${subdir}" ]] && build_dir="${src}/${subdir}"
+    local logfile="${LOG_DIR}/${name}.log"
+    local start_ts
+    start_ts=$(date +%s)
+
+    local label="${name}"
+    [[ -n "${subdir}" ]] && label="${name}/${subdir}"
+    printf "  [%d/%d] %-25s " $((built + failed + 1)) "${total}" "${label}"
+
+    if (cd "${build_dir}" && pyodide build) > "${logfile}" 2>&1; then
+      local end_ts
+      end_ts=$(date +%s)
+      echo -e "${GREEN}OK${NC}  ($(elapsed $((end_ts - start_ts))))"
+      ((built++))
+    else
+      local end_ts
+      end_ts=$(date +%s)
+      echo -e "${RED}FAILED${NC}  ($(elapsed $((end_ts - start_ts)))) — see ${logfile}"
+      ((failed++))
+      failed_names+=("${name}")
+    fi
+  done
+
+  echo ""
+
+  # ── Collect wheels ─────────────────────────────────────────────────────
+  info "Collecting .whl files into ${OUTPUT_DIR} …"
+  local count=0
+  for entry in "${REPOS[@]}"; do
+    IFS='|' read -r name _url subdir <<< "${entry}"
+    local src="${SOURCES_DIR}/${name}"
+    local build_dir="${src}"
+    [[ -n "${subdir}" ]] && build_dir="${src}/${subdir}"
+    if compgen -G "${build_dir}/dist/*.whl" > /dev/null 2>&1; then
+      cp "${build_dir}"/dist/*.whl "${OUTPUT_DIR}/"
+      ((count += $(ls -1 "${build_dir}"/dist/*.whl 2>/dev/null | wc -l)))
+    fi
+  done
+
+  # ── Normalise platform tags ────────────────────────────────────────────
+  for whl in "${OUTPUT_DIR}"/*p313-cp313-pyemscripten_2025_0_wasm32.whl; do
+    [[ -f "${whl}" ]] || continue
+    new_whl="${whl/p313-cp313-pyemscripten_2025_0_wasm32/py3-none-any}"
+    mv "${whl}" "${new_whl}"
+    info "Renamed $(basename "${whl}") → $(basename "${new_whl}")"
+  done
+
+  # ── Summary ────────────────────────────────────────────────────────────
+  echo ""
+  echo "========================================="
+  echo "  Build Summary"
+  echo "========================================="
+  echo "  Succeeded : ${built}"
+  echo "  Failed    : ${failed}"
+  echo "  Wheels    : ${count} file(s) in ${OUTPUT_DIR}/"
+  if (( failed > 0 )); then
+    echo ""
+    echo "  Failed packages:"
+    for n in "${failed_names[@]}"; do
+      echo "    - ${n}  (log: ${LOG_DIR}/${n}.log)"
+    done
+  fi
+  echo "========================================="
+  echo ""
+
+  if (( failed > 0 )); then
+    warn "Some packages failed. Check the logs above."
+    return 1
+  fi
+
+  success "All wheels built and collected in ${OUTPUT_DIR}/"
+  echo ""
+  ls -lh "${OUTPUT_DIR}"/*.whl
+}
+
+# ── Clean ────────────────────────────────────────────────────────────────────
+clean() {
+  # Need the path variables but don't need the full env setup
+  ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+  SRC_DIR="$ROOT_DIR/free-private"
+  BUILD_DIR="${2:-$SRC_DIR/build}"
+  WORK_DIR="$BUILD_DIR/work"
+  OUTPUT_DIR="$BUILD_DIR/pypi"
+  LOG_DIR="$BUILD_DIR/logs"
+
+  echo -e '\033[0;36m[INFO]\033[0m  Cleaning build artifacts …'
+  rm -rf "${WORK_DIR}" "${OUTPUT_DIR}" "${LOG_DIR}"
+  echo -e '\033[0;32m[OK]\033[0m    Clean complete'
+}
+
+# ── Main ─────────────────────────────────────────────────────────────────────
+main() {
+  local mode="${1:-all}"
+
+  case "${mode}" in
+    --setup)
+      setup_environment
+      ;;
+    --build)
+      source_shared_env
+      clone_repos
+      build_wheels
+      ;;
+    --clean)
+      clean
+      ;;
+    --help|-h)
+      echo "Usage: $0 [--setup | --build | --clean | --help]"
+      echo ""
+      echo "  (no flag)   Full run: setup environment, clone repos, build wheels"
+      echo "  --setup     Set up Python, venv, pyodide-build, and emsdk"
+      echo "  --build     Clone/update repos and build WASM wheels (requires prior --setup)"
+      echo "  --clean     Remove work/, dist/, and logs/"
+      echo "  --help      Show this message"
+      ;;
+    *)
+      setup_environment
+      clone_repos
+      build_wheels
+      ;;
+  esac
+}
+
+main "$@"

package/dist/jupyterlite-builds/scripts/build-jupyterlite.sh

@@ -50,8 +50,17 @@ if [[ ! -x "$VENV_JUPYTER_LITE" ]]; then
   exit 1
 fi
 
+
+echo "$VENV_JUPYTER_LITE" build \
+       --config "$CONFIG_FILE" \
+       --lite-dir "$SRC_DIR" \
+       --output-dir "$BUILD_DIR/$TIER"
+
 "$VENV_JUPYTER_LITE" build \
   --config "$CONFIG_FILE" \
+  --lite-dir "$SRC_DIR" \
   --output-dir "$BUILD_DIR/$TIER"
 
+
+
 echo "$TIER-tier JupyterLite build complete: $BUILD_DIR/$TIER (venv: $VENV_DIR)"

package/dist/jupyterlite-builds/scripts/build-jupyterlite_v2.sh

@@ -0,0 +1,111 @@
+#!/usr/bin/env bash
+# =============================================================================
+# build-jupyterlite.sh — Build a JupyterLite site (free or remote tier)
+#
+# Sources setup-env.sh so the venv, Python version, and tooling are identical
+# to those used by build-gen3sdk-lite.sh.
+#
+# Usage:
+#   ./build-jupyterlite.sh <tier> [build_dir]
+#     tier: 'free' or 'remote'
+# =============================================================================
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+usage() {
+  echo "Usage: $0 <tier> [build_dir]"
+  echo "  tier: 'free' or 'remote'"
+  exit 1
+}
+
+TIER="${1:-}"
+if [[ "$TIER" != "free" && "$TIER" != "remote" ]]; then
+  usage
+fi
+
+# ── Derive SRC_DIR before sourcing shared env ────────────────────────────────
+# setup-env.sh respects pre-set ROOT_DIR / SRC_DIR / BUILD_DIR.
+export ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+
+if [[ "$TIER" == "free" ]]; then
+  export SRC_DIR="$ROOT_DIR/free-private"
+else
+  export SRC_DIR="$ROOT_DIR/remote-private"
+fi
+
+# Allow caller to override BUILD_DIR via the second positional arg.
+if [[ -n "${2:-}" ]]; then
+  export BUILD_DIR="$2"
+fi
+
+# ── Source shared environment (creates/reuses the venv) ──────────────────────
+# After this: VENV_DIR, OUTPUT_DIR, BUILD_DIR, etc. are set and the venv is
+# active with the same Python version + core tooling as build-gen3sdk-lite.
+# shellcheck disable=SC1091
+source "${SCRIPT_DIR}/setup-env.sh"
+
+# ── JupyterLite-specific tooling ────────────────────────────────────────────
+CONFIG_FILE="$SRC_DIR/jupyter_lite_config.json"
+REQUIREMENTS_FILE="$SRC_DIR/requirements.txt"
+VENV_JUPYTER_LITE="$VENV_DIR/bin/jupyter-lite"
+PYPI="$OUTPUT_DIR"   # wheels built by build-gen3sdk-lite land here
+
+if [[ ! -f "$REQUIREMENTS_FILE" ]]; then
+  echo "Missing requirements file: $REQUIREMENTS_FILE"
+  exit 1
+fi
+
+# Install JupyterLite requirements into the shared venv (uv for speed).
+info "Installing JupyterLite requirements …"
+uv pip install -r "$REQUIREMENTS_FILE" 2>&1 | tail -5
+success "JupyterLite requirements installed"
+
+if [[ ! -x "$VENV_JUPYTER_LITE" ]]; then
+  echo "jupyter-lite executable not found in $VENV_DIR after dependency install."
+  exit 1
+fi
+
+# ── Build ────────────────────────────────────────────────────────────────────
+if [[ "$TIER" == "free" ]]; then
+
+  # Patch config to use the absolute pypi path so jupyter-lite can find the
+  # custom wheels built by build-gen3sdk-lite.
+  PATCHED_CONFIG="$BUILD_DIR/jupyter_lite_config.json"
+  python - <<PYEOF
+import json
+
+with open('$CONFIG_FILE') as fh:
+    cfg = json.load(fh)
+
+addon = cfg.get('PyodideLockAddon', {})
+if 'wheels' in addon:
+    addon['wheels'] = ['$PYPI/']
+    cfg['PyodideLockAddon'] = addon
+
+with open('$PATCHED_CONFIG', 'w') as fh:
+    json.dump(cfg, fh, indent=2)
+PYEOF
+
+  info "Looking for wheels in $PYPI"
+  WHEEL_ARGS=()
+  if [[ -d "$PYPI" ]]; then
+    while IFS= read -r -d '' whl; do
+      WHEEL_ARGS+=(--piplite-wheels "$whl")
+    done < <(find "$PYPI" -maxdepth 1 -name "*.whl" -print0 | sort -z)
+  fi
+
+  info "Running: jupyter-lite build (free tier, ${#WHEEL_ARGS[@]} custom wheels)"
+  "$VENV_JUPYTER_LITE" build \
+    --config "$PATCHED_CONFIG" \
+    --lite-dir "$SRC_DIR" ${WHEEL_ARGS[@]+"${WHEEL_ARGS[@]}"} \
+    --output-dir "$BUILD_DIR/$TIER"
+else
+  info "Running: jupyter-lite build (remote tier)"
+  "$VENV_JUPYTER_LITE" build \
+    --config "$CONFIG_FILE" \
+    --lite-dir "$SRC_DIR" \
+    --output-dir "$BUILD_DIR/$TIER"
+fi
+
+success "$TIER-tier JupyterLite build complete: $BUILD_DIR/$TIER"

package/dist/server/cjs/server.js

@@ -1100,7 +1100,7 @@ function configFilePath() {
     }
     const extensions = source.additionalDisabledExtensions;
     // oxlint-disable-next-line no-console
-    console.log('addtional disabled extensions', source.additionalDisabledExtensions);
+    console.log('additional disabled extensions', source.additionalDisabledExtensions);
     if (extensions !== undefined) {
         if (Array.isArray(extensions) && extensions.every((entry)=>typeof entry === 'string')) {
             parsed.additionalDisabledExtensions = extensions;