multiple updates

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ on:  # yamllint disable-line rule:truthy
   workflow_dispatch:
 
 env:
-  POETRY_VERSION: 1.8.3
+  POETRY_VERSION: 1.8.4
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
 

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 ---
 repos:
   - repo: https://github.com/python-poetry/poetry
-    rev: 1.8.3
+    rev: 1.8.4
     hooks:
       - id: poetry-check
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: check-json
@@ -16,13 +16,18 @@ repos:
       - id: name-tests-test
       - id: pretty-format-json
         args: [--autofix, --no-ensure-ascii]
+        exclude: \.ipynb$
       - id: trailing-whitespace
+  - repo: https://github.com/srstevenson/nb-clean
+    rev: 4.0.1
+    hooks:
+      - id: nb-clean
   - repo: https://github.com/facebook/usort
     rev: v1.0.8
     hooks:
       - id: usort
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
         args: [--preview]
@@ -33,7 +38,7 @@ repos:
         args: [--exit-zero]
         verbose: true
         additional_dependencies:
-          - flake8-bugbear == 24.4.26
+          - flake8-bugbear == 24.10.31
   - repo: https://github.com/adrienverge/yamllint
     rev: v1.35.1
     hooks:

examples/demo.ipynb

@@ -1,98 +1,134 @@
 {
-  "cells": [
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "import requests\n",
-        "from pyambit.datamodel import Substances, Study \n",
-        "import nexusformat.nexus.tree as nx\n",
-        "import os.path\n",
-        "import tempfile\n",
-        "# to_nexus is not added without this import\n",
-        "from pyambit import nexus_writer\n",
-        "import json"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "def query(url = \"https://apps.ideaconsult.net/gracious/substance/\" ,params = {\"max\" : 1}):\n",
-        "    substances = None\n",
-        "    headers = {'Accept': 'application/json'}\n",
-        "    result = requests.get(url,params=params,headers=headers)\n",
-        "    if result.status_code==200:\n",
-        "        response =  result.json()\n",
-        "        substances = Substances.model_construct(**response)\n",
-        "        for substance in substances.substance:\n",
-        "            url_study = \"{}/study\".format(substance.URI)\n",
-        "            study = requests.get(url_study,headers=headers)\n",
-        "            if study.status_code==200:\n",
-        "                response_study = study.json()\n",
-        "                substance.study = Study.model_construct(**response_study).study\n",
-        "\n",
-        "    return substances\n",
-        "\n",
-        "def write_studies_nexus(substances):\n",
-        "    for substance in substances.substance:\n",
-        "        for study in substance.study:\n",
-        "            file = os.path.join(tempfile.gettempdir(), \"study_{}.nxs\".format(study.uuid))\n",
-        "            nxroot = nx.NXroot()\n",
-        "            try:\n",
-        "                study.to_nexus(nxroot)\n",
-        "                nxroot.save(file, mode=\"w\")\n",
-        "            except Exception as err:\n",
-        "                #print(\"error\",file,str(err))\n",
-        "                print(file)"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "\n",
-        "try:\n",
-        "    substances = query(params = {\"max\" : 10})   \n",
-        "    _json = substances.model_dump(exclude_none=True)\n",
-        "    new_substances = Substances.model_construct(**_json)\n",
-        "    #test roundtrip\n",
-        "    assert substances == new_substances\n",
-        "\n",
-        "    file = os.path.join(tempfile.gettempdir(), \"remote.json\")\n",
-        "    print(file)\n",
-        "    with open(file, 'w', encoding='utf-8') as file:\n",
-        "        file.write(substances.model_dump_json(exclude_none=True))\n",
-        "    write_studies_nexus(substances)\n",
-        "except Exception as x:\n",
-        "    print(x)"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {},
-      "outputs": [],
-      "source": []
-    }
-  ],
-  "metadata": {
-    "kernelspec": {
-      "display_name": ".venv",
-      "language": "python",
-      "name": "python3"
-    },
-    "language_info": {
-      "name": "python",
-      "version": "3.12.5"
-    }
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import requests\n",
+    "from pyambit.datamodel import Substances, Study \n",
+    "import nexusformat.nexus.tree as nx\n",
+    "import os.path\n",
+    "import tempfile\n",
+    "# to_nexus is not added without this import\n",
+    "from pyambit import nexus_writer\n",
+    "import json\n",
+    "from IPython.display import display, HTML"
+   ]
   },
-  "nbformat": 4,
-  "nbformat_minor": 2
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def query(url = \"https://apps.ideaconsult.net/gracious/substance/\" ,params = {\"max\" : 1}):\n",
+    "    substances = None\n",
+    "    headers = {'Accept': 'application/json'}\n",
+    "    result = requests.get(url,params=params,headers=headers)\n",
+    "    if result.status_code==200:\n",
+    "        response =  result.json()\n",
+    "        substances = Substances.model_construct(**response)\n",
+    "        for substance in substances.substance:\n",
+    "            url_study = \"{}/study?max=10000\".format(substance.URI)\n",
+    "            study = requests.get(url_study,headers=headers)\n",
+    "            if study.status_code==200:\n",
+    "                response_study = study.json()\n",
+    "                substance.study = Study.model_construct(**response_study).study\n",
+    "            #break\n",
+    "\n",
+    "    return substances\n",
+    "\n",
+    "def write_studies_nexus(substances, single_file=True):\n",
+    "    if single_file:\n",
+    "        nxroot = nx.NXroot()\n",
+    "        substances.to_nexus(nxroot)\n",
+    "        file = os.path.join(tempfile.gettempdir(), \"remote.nxs\")\n",
+    "        print(file)\n",
+    "        nxroot.save(file, mode=\"w\")\n",
+    "    else:        \n",
+    "        for substance in substances.substance:\n",
+    "            for study in substance.study:\n",
+    "                file = os.path.join(tempfile.gettempdir(), \"study_{}.nxs\".format(study.uuid))\n",
+    "                print(file)\n",
+    "                nxroot = nx.NXroot()\n",
+    "                try:\n",
+    "                    study.to_nexus(nxroot)\n",
+    "                    nxroot.save(file, mode=\"w\")\n",
+    "                except Exception as err:\n",
+    "                    #print(\"error\",file,str(err))\n",
+    "                    print(file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import traceback"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "url = \"https://apps.ideaconsult.net/gracious/substance/\"\n",
+    "#url = \"http://localhost:9090/ambit2/substance/\"\n",
+    "#url = \"http://localhost:9090/ambit2/substance/POLY-e02442cc-8f7c-3a71-82cf-7df5888a4bfa\"\n",
+    "#url = \"http://localhost:9090/ambit2/substance/POLY-25d13fa6-c18b-35c8-b0f6-7325f5f3e505\"\n",
+    "try:\n",
+    "    substances = query(url=url,params = {\"max\" : 1})   \n",
+    "    _json = substances.model_dump(exclude_none=True)\n",
+    "    new_substances = Substances.model_construct(**_json)\n",
+    "    #test roundtrip\n",
+    "    assert substances == new_substances\n",
+    "\n",
+    "    file = os.path.join(tempfile.gettempdir(), \"remote.json\")\n",
+    "    print(file)\n",
+    "    with open(file, 'w', encoding='utf-8') as file:\n",
+    "        file.write(substances.model_dump_json(exclude_none=True))\n",
+    "    \n",
+    "    for s in substances.substance:\n",
+    "        for pa in s.study:\n",
+    "            effectarrays_only, df = pa.convert_effectrecords2array()\n",
+    "            display(df.dropna(axis=1,how=\"all\"))\n",
+    "            print(effectarrays_only)\n",
+    "            #break\n",
+    "    #write_studies_nexus(substances, single_file=False)\n",
+    "except Exception as x:\n",
+    "    traceback.print_exc()\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
 }