refactor and extend review.py endpoints

nb.ipynb

@@ -0,0 +1,325 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "24ac830c",
+   "metadata": {},
+   "source": [
+    "## Initialize"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "841c00cd",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "from rayyan import StatelessRayyan as client\n",
+    "from rayyan.review import Review\n",
+    "from rayyan.mylib import MyLib\n",
+    "\n",
+    "access_token = \"\"\n",
+    "_client = client(access_token, url=\"https://rayyan.ai\")\n",
+    "mylib_client = client(access_token, url=\"https://mylib.rayyan.ai\")\n",
+    "\n",
+    "_review = Review(_client)\n",
+    "my_lib = MyLib(mylib_client)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d8675105",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# List articles in my library\n",
+    "print(\"Listing a directory in my library\")\n",
+    "resp = my_lib.list_directory(\"/\")\n",
+    "print(resp)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8f18454f",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Variables reused across tests\n",
+    "review_id = 1646756\n",
+    "stage_id = 177729 # Data Extraction\n",
+    "sample_id = \"27989\"\n",
+    "question_id = 20170\n",
+    "criterion_id = 490407"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e3e31a28",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Import aricle from mylib\n",
+    "file = {\n",
+    "    \"key\": \"pubmed-covid-set-22.txt\",\n",
+    "    \"size\": 40667022,\n",
+    "    \"metadata\": {\n",
+    "      \"metadata_signature\": \"dada04d571e3c2f3c3237c01a2e2de90c2b1068d83d4f95ec9eaf2e70707a81f\",\n",
+    "      \"total_articles\": \"10000\",\n",
+    "      \"type\": \"ref\"\n",
+    "    }\n",
+    "  }\n",
+    "\n",
+    "file = resp['items'][8]\n",
+    "file_parsed = {\n",
+    "  \"key\": file[\"key\"],\n",
+    "  \"size\": file[\"file_size\"],\n",
+    "  \"metadata\": {\n",
+    "    \"metadata_signature\": file[\"metadata\"][\"metadata_signature\"],\n",
+    "    \"total_articles\": file[\"metadata\"][\"total_articles\"],\n",
+    "    \"type\": file[\"metadata\"][\"type\"]\n",
+    "  }\n",
+    "}\n",
+    "resp = _review.import_from_mylibrary_to_review(review_id=review_id, file=file_parsed)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cb0c1556",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# Full text\n",
+    "print(\"Listing articles with full text\")\n",
+    "resp = _review.list_articles_with_fulltext(review_id=review_id)\n",
+    "print(resp)\n",
+    "\n",
+    "full_text_id = resp['data'][0]['fulltexts'][0]['id']\n",
+    "resp = _review.get_fulltext_link(full_text_id)\n",
+    "print(resp['url'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c01a34b4",
+   "metadata": {},
+   "source": [
+    "## Testing Questions, Criteria, MyLibrary Import and AI Screener endpoints"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "70fe0b60",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# --- Samples ---\n",
+    "print(\"Creating sample...\")\n",
+    "resp = _review.create_sample(\n",
+    "    review_id=review_id,\n",
+    "    samples=[{\"name\": \"created_by_python_sdk\", \"total\": 10}]\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Listing samples...\")\n",
+    "resp = _review.list_samples(review_id=review_id)\n",
+    "print(resp)\n",
+    "\n",
+    "resp = _review.list_stages(review_id=review_id)\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Updating sample...\")\n",
+    "resp = _review.update_sample(\n",
+    "    review_id=review_id,\n",
+    "    sample_id=sample_id,\n",
+    "    sample={\"name\": \"Name Changed by python sdk\"}\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Deleting sample...\")\n",
+    "resp = _review.delete_sample(\n",
+    "    review_id=review_id,\n",
+    "    sample_id=sample_id\n",
+    ")\n",
+    "print(resp)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b039c4ad",
+   "metadata": {},
+   "source": [
+    "# --- Questions ---\n",
+    "print(\"Creating question...\")\n",
+    "resp = _review.create_question(\n",
+    "    review_id=review_id,\n",
+    "    stage_id=stage_id,\n",
+    "    question={\n",
+    "        \"type\": \"string\",\n",
+    "        \"title\": \"Added via Python SDK\",\n",
+    "        \"section_name\": \"Methods\",\n",
+    "        \"required\": True,\n",
+    "        \"body\": \"Describe your inclusion criteria\"\n",
+    "    }\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Listing questions...\")\n",
+    "resp = _review.list_questions(review_id=review_id, stage_id=stage_id)\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Getting a specific question...\")\n",
+    "resp = _review.get_question(review_id=review_id, stage_id=stage_id, question_id=question_id)\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Updating question...\")\n",
+    "resp = _review.update_question(\n",
+    "    review_id=review_id,\n",
+    "    stage_id=stage_id,\n",
+    "    question_id=question_id,\n",
+    "    question={\n",
+    "        \"type\": \"string\",\n",
+    "        \"title\": \"Updated Title by SDK\",\n",
+    "        \"section_name\": \"Results\",\n",
+    "        \"required\": False,\n",
+    "        \"body\": \"Updated body content\"\n",
+    "    }\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Deleting question...\")\n",
+    "resp = _review.delete_question(review_id=review_id, stage_id=stage_id, question_id=question_id)\n",
+    "print(resp)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3e6407b4",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "\n",
+    "# --- Criteria ---\n",
+    "print(\"Creating criterion...\")\n",
+    "resp = _review.create_criterion(\n",
+    "    review_id=review_id,\n",
+    "    criterion={\"kind\": \"inclusion\", \"text\": \"Must include RCTs\"}\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Listing criteria...\")\n",
+    "resp = _review.list_criteria(review_id=review_id)\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Updating criterion...\")\n",
+    "resp = _review.update_criterion(\n",
+    "    review_id=review_id,\n",
+    "    criterion_id=criterion_id,\n",
+    "    criterion={\"kind\": \"exclusion\", \"text\": \"Exclude case reports\"}\n",
+    ")\n",
+    "print(resp)\n",
+    "\n",
+    "print(\"Deleting criterion...\")\n",
+    "resp = _review.delete_criterion(review_id=review_id, criterion_id=criterion_id)\n",
+    "print(resp)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8ef8a2c5",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# --- MyLibrary Import ---\n",
+    "print(\"Importing file to library...\")\n",
+    "resp = _review.import_to_library(\n",
+    "    review_id=review_id,\n",
+    "    file={\n",
+    "        \"key\": \"/mnt/c/Users/amamd/Downloads/pubmed-covid-set-19.txt\",\n",
+    "        \"size\": 717,\n",
+    "        \"metadata\": {\n",
+    "            \"metadata_signature\": \"bea0cb4574d0a131bd0***\",\n",
+    "            \"total_articles\": \"3\",\n",
+    "            \"type\": \"ref\"\n",
+    "        }\n",
+    "    }\n",
+    ")\n",
+    "print(resp)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3d21fa3b",
+   "metadata": {
+    "vscode": {
+     "languageId": "plaintext"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# --- AI Screener ---\n",
+    "print(\"Creating AI screener...\")\n",
+    "resp = _review.create_ai_screener(\n",
+    "    review_id=review_id,\n",
+    "    extra={\n",
+    "    }\n",
+    ")\n",
+    "print(resp)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

rayyan/mylib.py

@@ -0,0 +1,18 @@
+
+from rayyan.types import RayyanProtocol as Rayyan
+
+
+class MyLib:
+    def __init__(self, rayyan: Rayyan):
+        self.__rayyan__ = rayyan
+
+    def list_directory(self, path) -> dict:
+        """List all files in the user's My Library.
+
+        Returns:
+            dict: A dictionary containing the list of files in My Library.
+        """
+        return self.__rayyan__.request.request_handler(
+            method="GET",
+            path=f"/ls/{path}"
+        )

rayyan/paths.py

@@ -9,5 +9,9 @@
 THIRD_PARTY_AUTH = "/api/v1/third_party_auth"
 # ________review________
 REVIEWS_ROUTE = "/api/v1/reviews"
+# ________fulltext________
+FULLTEXT_ROUTE = "/api/v1/fulltexts"
+# ________my library________
+MYLIBRARY_ROUTE = "/api/v1/my_library/import"
 # ________admin________
 ADMIN_ROUTE = "/admin"