#161 add reference ordering information to RefMetadata

app/firebase-py/functions/main.test.py

@@ -141,5 +141,13 @@
 json_obj = json.loads(serialized)
 print(f"semantics: {json_obj['semantics']}")
 
+# Sorting the refs metadata dictionary by the 'order' attribute
+sorted_refs = sorted(
+    json_obj["support"]["refs_meta"].items(),
+    key=lambda x: x[1]["order"],
+)
+
+print(f"ordered references: {[url for url, _ in sorted_refs]}")
+
 with open("last_output.json", "wb") as file:
     file.write(serialized.encode("utf-8"))

nlp/desci_sense/shared_functions/interface.py

@@ -201,6 +201,13 @@ class RefMetadata(BaseModel):
     mentioned in a post.
     """
 
+    ref_id: int = Field(
+        description="Unique ID of reference (1 indexed)",
+    )
+    order: int = Field(
+        default=0,
+        description="1 indexed ordering of reference, sorted by ascending appearance order in the post. 1 - first, 2 - 2nd,. 0 - unassigned",
+    )
     citoid_url: Union[str, None] = Field(
         description="URL used by citoid (might have different subdomain or final slashes).",
     )

nlp/desci_sense/shared_functions/web_extractors/metadata_extractors.py

@@ -37,12 +37,13 @@ def normalize_citoid_metadata(
 ):
     assert len(target_urls) == len(metadata_list)
     results = []
-    for url, metadata in zip(target_urls, metadata_list):
+    for i, (url, metadata) in enumerate(zip(target_urls, metadata_list)):
         metadata["original_url"] = url
         summary = metadata.get("abstractNote", "")
         results.append(
             RefMetadata(
                 **{
+                    "ref_id": i + 1,
                     "citoid_url": metadata.get("url", None),
                     "url": metadata.get("original_url", None),
                     "item_type": metadata.get("itemType", None),
@@ -198,12 +199,14 @@ def get_ref_post_metadata_list(
     post: RefPost,
     md_dict: Dict[str, RefMetadata],
     extra_urls: List[str] = None,
+    add_ordering: bool = True,
 ) -> List[RefMetadata]:
     """
     Returns list of the post's reference metadata.
     If extra urls are provided, they are also counted as part of the post ref
     urls (for example extra_urls could include unprocessed urls due to max length
     limits).
+    If `add_ordering`, add reference ordering info to each metadata item.
     """
     all_ref_urls = post.md_ref_urls()
 
@@ -212,9 +215,12 @@ def get_ref_post_metadata_list(
     all_ref_urls += remove_dups_ordered(extra_urls)
 
     md_list = []
-    for ref in all_ref_urls:
+    for i, ref in enumerate(all_ref_urls):
         if ref in md_dict:
             md = md_dict.get(ref)
             if md:
+                if add_ordering:
+                    # add ordering info (1-indexed)
+                    md.order = i + 1
                 md_list.append(md)
     return md_list

nlp/tests/test_multi_chain_app_interface.py

@@ -183,16 +183,27 @@ def test_app_config():
         "https://x.com/FDAadcomms/status/1798107142219796794",
     ]
     check_uris_in_graph(res.semantics, expected_uris)
+    # check ordering
+    for i, url in enumerate(expected_uris):
+        assert res.support.refs_meta[url].order == i + 1
+        assert res.support.refs_meta[url].url == url
 
 
 # "mistralai/mixtral-8x7b-instruct"
 # "mistralai/mistral-7b-instruct:free"
 # "google/gemma-7b-it"
 if __name__ == "__main__":
     multi_config = init_multi_chain_parser_config(
-        llm_type="mistralai/mistral-7b-instruct:free", post_process_type="firebase"
+        # ref_tagger_llm_type="mistralai/mistral-7b-instruct",
+        # kw_llm_type="mistralai/mistral-7b-instruct",
+        # topic_llm_type="mistralai/mistral-7b-instruct",
+        ref_tagger_llm_type="mistralai/mistral-7b-instruct:free",
+        kw_llm_type="mistralai/mistral-7b-instruct:free",
+        topic_llm_type="mistralai/mistral-7b-instruct:free",
+        post_process_type="firebase",
     )
     mcp = MultiChainParser(multi_config)
-    thread = get_short_thread()
+    thread = get_thread_1()
     pi = ParserInput(thread_post=thread, max_posts=30)
     res = mcp.process_parser_input(pi)
+    refs = list(res.support.refs_meta.values())

nlp/tests/test_multi_chain_post_processing.py

@@ -44,6 +44,13 @@
 https://arxiv.org/abs/2402.04607
 """
 
+TEST_POST_TEXT_W_2_REF = """
+I really liked these two papers!
+https://arxiv.org/abs/2402.04607
+
+https://arxiv.org/abs/2401.14000
+"""
+
 
 def test_combined_pp():
     multi_config = create_multi_config_for_tests()
@@ -54,7 +61,22 @@ def test_combined_pp():
     assert len(res.keywords) > 0
     assert len(res.metadata_list) == 1
     assert res.filter_classification == SciFilterClassfication.CITOID_DETECTED_RESEARCH
+    assert res.metadata_list[0].order == 1
+
 
+def test_combined_2_pp():
+    multi_config = create_multi_config_for_tests()
+    multi_config.post_process_type = PostProcessType.COMBINED
+    mcp = MultiChainParser(multi_config)
+    res = mcp.process_text(TEST_POST_TEXT_W_2_REF)
+    assert res.item_types == ["preprint", "conferencePaper"]
+    assert len(res.keywords) > 0
+    assert len(res.metadata_list) == 2
+    assert res.filter_classification == SciFilterClassfication.CITOID_DETECTED_RESEARCH
+    assert res.metadata_list[0].order == 1
+    assert res.metadata_list[0].url == "https://arxiv.org/abs/2402.04607"
+    assert res.metadata_list[1].order == 2
+    assert res.metadata_list[1].url == "https://arxiv.org/abs/2401.14000"
 
 def test_firebase_pp():
     multi_config = create_multi_config_for_tests()
@@ -109,22 +131,28 @@ def test_multi_chain_batch_pp_combined():
         == "https://royalsocietypublishing.org/doi/10.1098/rstb.2022.0267"
     )
     assert len(out_0.metadata_list) == 1
+    assert out_0.metadata_list[0].order == 1
 
     out_1 = res[1]
     assert len(out_1.metadata_list) == 1
     assert (
         out_1.metadata_list[0].url
         == "https://write.as/ulrikehahn/some-thoughts-on-social-media-for-science"
     )
+    assert out_1.metadata_list[0].order == 1
 
     out_2 = res[2]
     assert len(out_2.metadata_list) == 2
+
+    # ordering not preserved yet for masto so don't test that yet
     assert set(out_2.reference_urls) == set(
         [
             "https://paragraph.xyz/@sense-nets/sense-nets-intro",
             "https://paragraph.xyz/@sense-nets/2-project-plan",
         ]
     )
+
+
 
 
 def test_convert_item_types_to_rdf_triplets_single_entry():
@@ -195,12 +223,47 @@ def test_short_post_no_ref_i146():
 
 
 if __name__ == "__main__":
-    multi_config = create_multi_config_for_tests()
-    multi_config.post_process_type = PostProcessType.FIREBASE
-    mcp = MultiChainParser(multi_config)
-    res = mcp.process_text("yup")
-    print(res.semantics.serialize())
-
-    # len(res.support.refs_meta) == 1
-    # assert "test" in mcp.pparsers
-    # assert "Google Scholar is manipulatable" in prompt
+    # get a few posts for input
+    urls = [
+        "https://mastodon.social/@[email protected]/111405098400404613",
+        "https://mastodon.social/@[email protected]/111732713776994953",
+        "https://mastodon.social/@ronent/111687038322549430",
+    ]
+    post = scrape_post(urls[2])
+#     posts = [scrape_post(url) for url in urls]
+#     multi_config = create_multi_config_for_tests(llm_type="google/gemma-7b-it:free")
+#     multi_chain_parser = MultiChainParser(multi_config)
+#     multi_chain_parser.config.post_process_type = PostProcessType.COMBINED
+#     res = multi_chain_parser.batch_process_ref_posts(posts)
+
+#     out_0 = res[0]
+#     assert (
+#         out_0.metadata_list[0].url
+#         == "https://royalsocietypublishing.org/doi/10.1098/rstb.2022.0267"
+#     )
+#     assert len(out_0.metadata_list) == 1
+#     assert out_0.metadata_list[0].order == 1
+
+#     out_1 = res[1]
+#     assert len(out_1.metadata_list) == 1
+#     assert (
+#         out_1.metadata_list[0].url
+#         == "https://write.as/ulrikehahn/some-thoughts-on-social-media-for-science"
+#     )
+#     assert out_1.metadata_list[0].order == 1
+
+#     out_2 = res[2]
+#     assert len(out_2.metadata_list) == 2
+#     assert set(out_2.reference_urls) == set(
+#         [
+#             "https://paragraph.xyz/@sense-nets/sense-nets-intro",
+#             "https://paragraph.xyz/@sense-nets/2-project-plan",
+#         ]
+#     )
+
+#     sorted_refs = sorted(
+#     out_2.metadata_list,
+#     key=lambda x: x.order,
+# )
+#     assert sorted_refs[0].url == "https://paragraph.xyz/@sense-nets/sense-nets-intro"
+#     assert sorted_refs[1].url == "https://paragraph.xyz/@sense-nets/2-project-plan"