fixed e2e meds transform bug with eicu where the extraction config st…

…ill had the infusionDrug table. Added ACES and meds-dev label extraction

.gitignore

@@ -361,3 +361,5 @@ $RECYCLE.BIN/
 meds_env/*
 src/MEDS_DEV/demo/download/*
 src/MEDS_DEV/demo/content/*
+
+demo/work_dir

demo/configs/extract_MIMIC.yaml

@@ -27,10 +27,10 @@ stage_configs:
     infer_schema_length: 999999999
   split_and_shard_subjects:
     n_subjects_per_shard: 1000
-  split_fracs:
-    train: 0.5
-    tuning: 0.25
-    held_out: 0.25
+    split_fracs:
+      train: 0.5
+      tuning: 0.25
+      held_out: 0.25
 
 stages:
   - shard_events

demo/extract_meds_data.ipynb

@@ -3619,7 +3619,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -3635,7 +3635,6 @@
     "import tempfile\n",
     "import os\n",
     "from pathlib import Path\n",
-    "temp_dir = tempfile.TemporaryDirectory()\n",
     "notebook_dir = os.getcwd()\n",
     "\n",
     "ROOT_DIR=f\"{notebook_dir}/work_dir/eicu_demo/\"\n",

demo/meds_tab.ipynb

@@ -9,83 +9,6 @@
     "# Using an example MEDS tool, ACES for labeling"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "colab": {
-     "base_uri": "https://localhost:8080/"
-    },
-    "collapsed": true,
-    "id": "z3_pG9YAWpKy",
-    "outputId": "efa4c286-413d-4a91-a53d-fb41769cd4f2"
-   },
-   "outputs": [],
-   "source": [
-    "#@title Install ACES\n",
-    "\n",
-    "\n",
-    "!pip install es-aces"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "id": "H6fqe217XDhi"
-   },
-   "outputs": [],
-   "source": [
-    "# From the ACES documentation\n",
-    "\n",
-    "task_config = \"\"\"\n",
-    "description: >-\n",
-    "  This file specifies the base configuration for the prediction of a hospital los being greater than 3days,\n",
-    "  leveraging only the first 48 hours of data after admission, with a 24 hour gap between the input window\n",
-    "  and the target window. Patients who die or are discharged in the gap window are excluded. Note that this\n",
-    "  task is in-**hospital** los, not in-**ICU** los which is a different task.\n",
-    "\n",
-    "predicates:\n",
-    "  hospital_admission:\n",
-    "    code: {regex: \"HOSPITAL_ADMISSION//.*\"}\n",
-    "  hospital_discharge:\n",
-    "    code: {regex: \"HOSPITAL_DISCHARGE//.*\"}\n",
-    "  death:\n",
-    "    code: MEDS_DEATH\n",
-    "  discharge_or_death:\n",
-    "    expr: or(hospital_discharge, death)\n",
-    "\n",
-    "trigger: hospital_admission\n",
-    "\n",
-    "windows:\n",
-    "  input:\n",
-    "    start: NULL\n",
-    "    end: trigger + 48h\n",
-    "    start_inclusive: True\n",
-    "    end_inclusive: True\n",
-    "    index_timestamp: end\n",
-    "  gap:\n",
-    "    start: input.end\n",
-    "    end: start + 24h\n",
-    "    start_inclusive: False\n",
-    "    end_inclusive: True\n",
-    "    has:\n",
-    "      hospital_admission: (None, 0)\n",
-    "      discharge_or_death: (None, 0)\n",
-    "  target:\n",
-    "    start: trigger\n",
-    "    end: start + 3d\n",
-    "    start_inclusive: False\n",
-    "    end_inclusive: True\n",
-    "    label: discharge_or_death\n",
-    "\"\"\"\n",
-    "!mkdir /content/tasks/ -p\n",
-    "TASK_NAME = \"in_hospital_3d_los_after_48h\"\n",
-    "TASK_CONFIG_FP = f\"/content/tasks/{TASK_NAME}.yaml\"\n",
-    "with open(TASK_CONFIG_FP, 'w') as f:\n",
-    "    f.write(task_config)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

pyproject.toml

@@ -28,7 +28,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-dependencies = ["meds==0.3.3", "es-aces==0.5.0"]
+dependencies = ["meds>=0.3.3", "es-aces>=0.5.0"]
 
 [tool.setuptools_scm]