Upload batch 23 (20 files, last=openalex-snapshot/data/fields/manifest)

.gitattributes

@@ -196,3 +196,5 @@ MAPLE/Chemistry/papers.json filter=lfs diff=lfs merge=lfs -text
 MAPLE/Philosophy/papers.json filter=lfs diff=lfs merge=lfs -text
 MAPLE/Biology/authors.txt filter=lfs diff=lfs merge=lfs -text
 MAPLE/Biology/papers.json filter=lfs diff=lfs merge=lfs -text
+logs/csrankings_citations_2336133.out filter=lfs diff=lfs merge=lfs -text
+logs/enrich_sscholar_2348858.out filter=lfs diff=lfs merge=lfs -text

MAPLE/Biology/venues.txt

@@ -0,0 +1,100 @@
+137773608	nature	Nature
+3880285	science	Science
+110447773	cell	Cell
+125754415	proceedings of the national academy of sciences of the united states of america	Proceedings of the National Academy of Sciences of the United States of America
+137905309	nature genetics	Nature Genetics
+134668137	nucleic acids research	Nucleic Acids Research
+140251998	journal of biological chemistry	Journal of Biological Chemistry
+22947807	journal of experimental medicine	Journal of Experimental Medicine
+96410829	journal of cell biology	Journal of Cell Biology
+114430552	journal of clinical investigation	Journal of Clinical Investigation
+168778273	genes development	Genes & Development
+168522863	cancer research	Cancer Research
+127916151	the embo journal	The EMBO Journal
+203256638	nature medicine	Nature Medicine
+38008053	journal of immunology	Journal of Immunology
+200071133	blood	Blood
+45757444	neuron	Neuron
+5555990	the journal of neuroscience	The Journal of Neuroscience
+106963461	nature biotechnology	Nature Biotechnology
+199671312	immunity	Immunity
+81455967	molecular and cellular biology	Molecular and Cellular Biology
+156208185	molecular cell	Molecular Cell
+196724125	nature reviews molecular cell biology	Nature Reviews Molecular Cell Biology
+86558740	development	Development
+48849333	the plant cell	The Plant Cell
+8553189	nature reviews genetics	Nature Reviews Genetics
+158228368	applied and environmental microbiology	Applied and Environmental Microbiology
+2785285	the journal of comparative neurology	The Journal of Comparative Neurology
+41063453	nature immunology	Nature Immunology
+96615428	journal of virology	Journal of Virology
+128439998	oncogene	Oncogene
+160464432	nature reviews cancer	Nature Reviews Cancer
+93373720	nature reviews immunology	Nature Reviews Immunology
+151741590	nature cell biology	Nature Cell Biology
+42294715	plant physiology	Plant Physiology
+41066938	biochimica et biophysica acta	Biochimica et Biophysica Acta
+35917800	ecology	Ecology
+128425624	current biology	Current Biology
+133274750	journal of bacteriology	Journal of Bacteriology
+65932378	genetics	Genetics
+109088427	annual review of immunology	Annual Review of Immunology
+203035050	physiological reviews	Physiological Reviews
+134425043	american journal of human genetics	American Journal of Human Genetics
+49861241	the lancet	The Lancet
+53860259	annual review of biochemistry	Annual Review of Biochemistry
+202381698	plos one	PLOS ONE
+10652568	circulation research	Circulation Research
+5677253	journal of cell science	Journal of Cell Science
+46058472	journal of molecular biology	Journal of Molecular Biology
+43092948	genome research	Genome Research
+79131028	trends in ecology and evolution	Trends in Ecology and Evolution
+25671836	cancer cell	Cancer Cell
+145577119	american journal of pathology	American Journal of Pathology
+122176235	the american naturalist	The American Naturalist
+53087977	journal of clinical microbiology	Journal of Clinical Microbiology
+56802129	nature reviews microbiology	Nature Reviews Microbiology
+129060628	diabetes	Diabetes
+67862205	plant journal	Plant Journal
+157527038	endocrinology	Endocrinology
+128227336	infection and immunity	Infection and Immunity
+44425019	biochemical journal	Biochemical Journal
+143352558	gastroenterology	Gastroenterology
+136233269	trends in biochemical sciences	Trends in Biochemical Sciences
+166515463	human molecular genetics	Human Molecular Genetics
+2298632	nature neuroscience	Nature Neuroscience
+151589183	biochemical and biophysical research communications	Biochemical and Biophysical Research Communications
+102549058	molecular microbiology	Molecular Microbiology
+103771297	current opinion in cell biology	Current Opinion in Cell Biology
+136634221	developmental biology	Developmental Biology
+47215897	antimicrobial agents and chemotherapy	Antimicrobial Agents and Chemotherapy
+87560609	evolution	Evolution
+183149254	clinical cancer research	Clinical Cancer Research
+154343897	plos biology	PLOS Biology
+96638545	brain research	Brain Research
+104830714	febs letters	FEBS Letters
+201780205	trends in plant science	Trends in Plant Science
+25293849	the faseb journal	The FASEB Journal
+112662651	clinical microbiology reviews	Clinical Microbiology Reviews
+13493133	endocrine reviews	Endocrine Reviews
+67154222	oecologia	Oecologia
+3006207977	proceedings of the royal society b biological sciences	Proceedings of The Royal Society B: Biological Sciences
+58631098	new phytologist	New Phytologist
+92576693	annual review of entomology	Annual Review of Entomology
+83804233	developmental cell	Developmental Cell
+127827428	nature methods	Nature Methods
+54542293	the journal of infectious diseases	The Journal of Infectious Diseases
+177533077	cell metabolism	Cell Metabolism
+139283865	trends in genetics	Trends in Genetics
+205775358	the journal of clinical endocrinology and metabolism	The Journal of Clinical Endocrinology and Metabolism
+62468778	the new england journal of medicine	The New England Journal of Medicine
+128124174	cell stem cell	Cell Stem Cell
+81160022	genome biology	Genome Biology
+6147291	virology	Virology
+75702506	gene	Gene
+119405978	annual review of ecology evolution and systematics	Annual Review of Ecology, Evolution, and Systematics
+114966740	trends in neurosciences	Trends in Neurosciences
+118628157	trends in cell biology	Trends in Cell Biology
+126191069	european journal of immunology	European Journal of Immunology
+188085164	molecular biology of the cell	Molecular Biology of the Cell
+32610980	journal of experimental botany	Journal of Experimental Botany

logs/csrankings_citations_2336133.out

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logs/enrich_sscholar_2348858.err

@@ -0,0 +1,17 @@
+-------------------------------------------------------------------------------
+There are messages associated with the following module(s):
+-------------------------------------------------------------------------------
+
+awscli/2.13.37:
+   !!! WARNING !!!! The AWS Command Line Interface stores credentials in
+   plaintext in your $HOME/.aws directory. Be sure to maintain proper
+   user-only permissions on your $HOME directory (i.e. chmod 700 $HOME).
+   That will prevent access by other users. Be aware, all HPRC staff have
+   the ability to view your AWS credentials. If that is a concern, please
+   take whatever measures you feel appropriate. We are currently
+   investigating encryption options for the files in $HOME/.aws and hope to
+   offer possible remedies soon.
+
+-------------------------------------------------------------------------------
+
+

logs/enrich_sscholar_2348858.out

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logs/llama32_all_fields_2832379.err

@@ -0,0 +1,181 @@
+/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py:110: FutureWarning: Using `TRANSFORMERS_CACHE` is deprecated and will be removed in v5 of Transformers. Use `HF_HOME` instead.
+  warnings.warn(
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0324050>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 9f34e89b-ab77-4f27-9f8b-314e9defcf37)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 1s [Retry 1/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0308910>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: ca5d895d-f145-4521-84ff-0dfa87355f95)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 2s [Retry 2/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0308e10>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: c6c95d9e-2a3e-419c-b4f2-837fe748b5cf)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 4s [Retry 3/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309090>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 1e11b07d-3c23-43c4-8622-1e7b8e11933a)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 8s [Retry 4/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309310>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 1c16c1a4-099b-4520-9b98-3e27329ed53e)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 8s [Retry 5/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 71b038e5-cf01-4083-bb05-ceca365b1292)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 198, in _new_conn
+    sock = connection.create_connection(
+        (self._dns_host, self.port),
+    ...<2 lines>...
+        socket_options=self.socket_options,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/connection.py", line 85, in create_connection
+    raise err
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/connection.py", line 73, in create_connection
+    sock.connect(sa)
+    ~~~~~~~~~~~~^^^^
+OSError: [Errno 101] Network is unreachable
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 773, in urlopen
+    self._prepare_proxy(conn)
+    ~~~~~~~~~~~~~~~~~~~^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 1042, in _prepare_proxy
+    conn.connect()
+    ~~~~~~~~~~~~^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 704, in connect
+    self.sock = sock = self._new_conn()
+                       ~~~~~~~~~~~~~~^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 213, in _new_conn
+    raise NewConnectionError(
+        self, f"Failed to establish a new connection: {e}"
+    ) from e
+urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x14e0b0309590>: Failed to establish a new connection: [Errno 101] Network is unreachable
+
+The above exception was the direct cause of the following exception:
+
+urllib3.exceptions.ProxyError: ('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309590>: Failed to establish a new connection: [Errno 101] Network is unreachable'))
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/adapters.py", line 667, in send
+    resp = conn.urlopen(
+        method=request.method,
+    ...<9 lines>...
+        chunked=chunked,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 841, in urlopen
+    retries = retries.increment(
+        method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2]
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/retry.py", line 519, in increment
+    raise MaxRetryError(_pool, url, reason) from reason  # type: ignore[arg-type]
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 372, in <module>
+    main()
+    ~~~~^^
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 262, in main
+    backend = ModelBackend()
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 231, in __init__
+    self.llm = LLM(**llm_kwargs)
+               ~~~^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/entrypoints/llm.py", line 297, in __init__
+    self.llm_engine = LLMEngine.from_engine_args(
+                      ~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        engine_args=engine_args, usage_context=UsageContext.LLM_CLASS)
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/v1/engine/llm_engine.py", line 169, in from_engine_args
+    vllm_config = engine_args.create_engine_config(usage_context)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/engine/arg_utils.py", line 1135, in create_engine_config
+    self.speculative_config) = maybe_override_with_speculators(
+                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        model=self.model,
+        ^^^^^^^^^^^^^^^^^
+    ...<3 lines>...
+        vllm_speculative_config=self.speculative_config,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/transformers_utils/config.py", line 501, in maybe_override_with_speculators
+    config_dict, _ = PretrainedConfig.get_config_dict(
+                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        model if gguf_model_repo is None else gguf_model_repo,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    ...<3 lines>...
+        **kwargs,
+        ^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/configuration_utils.py", line 662, in get_config_dict
+    config_dict, kwargs = cls._get_config_dict(pretrained_model_name_or_path, **kwargs)
+                          ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/configuration_utils.py", line 721, in _get_config_dict
+    resolved_config_file = cached_file(
+        pretrained_model_name_or_path,
+    ...<10 lines>...
+        _commit_hash=commit_hash,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 322, in cached_file
+    file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 567, in cached_files
+    raise e
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 479, in cached_files
+    hf_hub_download(
+    ~~~~~~~~~~~~~~~^
+        path_or_repo_id,
+        ^^^^^^^^^^^^^^^^
+    ...<10 lines>...
+        local_files_only=local_files_only,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
+    return fn(*args, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1007, in hf_hub_download
+    return _hf_hub_download_to_cache_dir(
+        # Destination
+    ...<14 lines>...
+        force_download=force_download,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1070, in _hf_hub_download_to_cache_dir
+    (url_to_download, etag, commit_hash, expected_size, xet_file_data, head_call_error) = _get_metadata_or_catch_error(
+                                                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        repo_id=repo_id,
+        ^^^^^^^^^^^^^^^^
+    ...<10 lines>...
+        relative_filename=relative_filename,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1543, in _get_metadata_or_catch_error
+    metadata = get_hf_file_metadata(
+        url=url, proxies=proxies, timeout=etag_timeout, headers=headers, token=token, endpoint=endpoint
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
+    return fn(*args, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1460, in get_hf_file_metadata
+    r = _request_wrapper(
+        method="HEAD",
+    ...<5 lines>...
+        timeout=timeout,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 283, in _request_wrapper
+    response = _request_wrapper(
+        method=method,
+    ...<2 lines>...
+        **params,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 306, in _request_wrapper
+    response = http_backoff(method=method, url=url, **params)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 325, in http_backoff
+    raise err
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 306, in http_backoff
+    response = session.request(method=method, url=url, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/sessions.py", line 589, in request
+    resp = self.send(prep, **send_kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/sessions.py", line 703, in send
+    r = adapter.send(request, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 95, in send
+    return super().send(request, *args, **kwargs)
+           ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/adapters.py", line 694, in send
+    raise ProxyError(e, request=request)
+requests.exceptions.ProxyError: (MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x14e0b0309590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 71b038e5-cf01-4083-bb05-ceca365b1292)')
+slurmstepd: error: *** JOB 2832379 ON fc040 CANCELLED AT 2025-11-13T17:25:15 ***

logs/llama32_all_fields_2832379.out

@@ -0,0 +1,2 @@
+INFO 11-13 17:08:58 [__init__.py:216] Automatically detected platform cuda.
+INFO 11-13 17:20:28 [utils.py:233] non-default args: {'dtype': 'bfloat16', 'disable_log_stats': True, 'model': 'meta-llama/Llama-3.2-3B-Instruct'}

logs/llama32_all_fields_2832403.err

@@ -0,0 +1,180 @@
+/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py:110: FutureWarning: Using `TRANSFORMERS_CACHE` is deprecated and will be removed in v5 of Transformers. Use `HF_HOME` instead.
+  warnings.warn(
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148954050>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 0437bef0-fccb-492f-98dd-e548ef962124)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 1s [Retry 1/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148940910>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: fb8ad498-a24e-4d75-8619-82cdf0619d17)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 2s [Retry 2/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148940e10>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 66bd2844-7273-4a66-ab79-0ea895dda339)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 4s [Retry 3/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941090>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 565522ad-928f-49ac-b274-2169a6b1d293)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 8s [Retry 4/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941310>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: 895edf8c-f7d9-4163-a13d-9799b50a8542)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Retrying in 8s [Retry 5/5].
+'(MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: e07de39e-29b8-4d5e-98ce-73de7489d4dc)')' thrown while requesting HEAD https://huggingface.co/meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 198, in _new_conn
+    sock = connection.create_connection(
+        (self._dns_host, self.port),
+    ...<2 lines>...
+        socket_options=self.socket_options,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/connection.py", line 85, in create_connection
+    raise err
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/connection.py", line 73, in create_connection
+    sock.connect(sa)
+    ~~~~~~~~~~~~^^^^
+OSError: [Errno 101] Network is unreachable
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 773, in urlopen
+    self._prepare_proxy(conn)
+    ~~~~~~~~~~~~~~~~~~~^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 1042, in _prepare_proxy
+    conn.connect()
+    ~~~~~~~~~~~~^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 704, in connect
+    self.sock = sock = self._new_conn()
+                       ~~~~~~~~~~~~~~^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connection.py", line 213, in _new_conn
+    raise NewConnectionError(
+        self, f"Failed to establish a new connection: {e}"
+    ) from e
+urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x147148941590>: Failed to establish a new connection: [Errno 101] Network is unreachable
+
+The above exception was the direct cause of the following exception:
+
+urllib3.exceptions.ProxyError: ('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941590>: Failed to establish a new connection: [Errno 101] Network is unreachable'))
+
+The above exception was the direct cause of the following exception:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/adapters.py", line 667, in send
+    resp = conn.urlopen(
+        method=request.method,
+    ...<9 lines>...
+        chunked=chunked,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/connectionpool.py", line 841, in urlopen
+    retries = retries.increment(
+        method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2]
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/urllib3/util/retry.py", line 519, in increment
+    raise MaxRetryError(_pool, url, reason) from reason  # type: ignore[arg-type]
+    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 412, in <module>
+    main()
+    ~~~~^^
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 302, in main
+    backend = ModelBackend()
+  File "/scratch/user/hangxiao/paper_impact/construct_citations_dataset/llama32_all_fields_eval.py", line 255, in __init__
+    self.llm = LLM(**llm_kwargs)
+               ~~~^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/entrypoints/llm.py", line 297, in __init__
+    self.llm_engine = LLMEngine.from_engine_args(
+                      ~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        engine_args=engine_args, usage_context=UsageContext.LLM_CLASS)
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/v1/engine/llm_engine.py", line 169, in from_engine_args
+    vllm_config = engine_args.create_engine_config(usage_context)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/engine/arg_utils.py", line 1135, in create_engine_config
+    self.speculative_config) = maybe_override_with_speculators(
+                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        model=self.model,
+        ^^^^^^^^^^^^^^^^^
+    ...<3 lines>...
+        vllm_speculative_config=self.speculative_config,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/transformers_utils/config.py", line 501, in maybe_override_with_speculators
+    config_dict, _ = PretrainedConfig.get_config_dict(
+                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        model if gguf_model_repo is None else gguf_model_repo,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    ...<3 lines>...
+        **kwargs,
+        ^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/configuration_utils.py", line 662, in get_config_dict
+    config_dict, kwargs = cls._get_config_dict(pretrained_model_name_or_path, **kwargs)
+                          ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/configuration_utils.py", line 721, in _get_config_dict
+    resolved_config_file = cached_file(
+        pretrained_model_name_or_path,
+    ...<10 lines>...
+        _commit_hash=commit_hash,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 322, in cached_file
+    file = cached_files(path_or_repo_id=path_or_repo_id, filenames=[filename], **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 567, in cached_files
+    raise e
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py", line 479, in cached_files
+    hf_hub_download(
+    ~~~~~~~~~~~~~~~^
+        path_or_repo_id,
+        ^^^^^^^^^^^^^^^^
+    ...<10 lines>...
+        local_files_only=local_files_only,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
+    return fn(*args, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1007, in hf_hub_download
+    return _hf_hub_download_to_cache_dir(
+        # Destination
+    ...<14 lines>...
+        force_download=force_download,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1070, in _hf_hub_download_to_cache_dir
+    (url_to_download, etag, commit_hash, expected_size, xet_file_data, head_call_error) = _get_metadata_or_catch_error(
+                                                                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
+        repo_id=repo_id,
+        ^^^^^^^^^^^^^^^^
+    ...<10 lines>...
+        relative_filename=relative_filename,
+        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+    )
+    ^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1543, in _get_metadata_or_catch_error
+    metadata = get_hf_file_metadata(
+        url=url, proxies=proxies, timeout=etag_timeout, headers=headers, token=token, endpoint=endpoint
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_validators.py", line 114, in _inner_fn
+    return fn(*args, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 1460, in get_hf_file_metadata
+    r = _request_wrapper(
+        method="HEAD",
+    ...<5 lines>...
+        timeout=timeout,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 283, in _request_wrapper
+    response = _request_wrapper(
+        method=method,
+    ...<2 lines>...
+        **params,
+    )
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/file_download.py", line 306, in _request_wrapper
+    response = http_backoff(method=method, url=url, **params)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 325, in http_backoff
+    raise err
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 306, in http_backoff
+    response = session.request(method=method, url=url, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/sessions.py", line 589, in request
+    resp = self.send(prep, **send_kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/sessions.py", line 703, in send
+    r = adapter.send(request, **kwargs)
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/huggingface_hub/utils/_http.py", line 95, in send
+    return super().send(request, *args, **kwargs)
+           ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/requests/adapters.py", line 694, in send
+    raise ProxyError(e, request=request)
+requests.exceptions.ProxyError: (MaxRetryError("HTTPSConnectionPool(host='huggingface.co', port=443): Max retries exceeded with url: /meta-llama/Llama-3.2-3B-Instruct/resolve/main/config.json (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x147148941590>: Failed to establish a new connection: [Errno 101] Network is unreachable')))"), '(Request ID: e07de39e-29b8-4d5e-98ce-73de7489d4dc)')

logs/llama32_all_fields_2832403.out

@@ -0,0 +1,2 @@
+INFO 11-13 17:51:45 [__init__.py:216] Automatically detected platform cuda.
+INFO 11-13 18:07:02 [utils.py:233] non-default args: {'dtype': 'bfloat16', 'disable_log_stats': True, 'model': 'meta-llama/Llama-3.2-3B-Instruct'}

logs/llama32_best_paper_17085241.err

@@ -0,0 +1,541 @@
+/scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/transformers/utils/hub.py:110: FutureWarning: Using `TRANSFORMERS_CACHE` is deprecated and will be removed in v5 of Transformers. Use `HF_HOME` instead.
+  warnings.warn(
+`torch_dtype` is deprecated! Use `dtype` instead!
+(EngineCore_DP0 pid=3289378) /scratch/user/hangxiao/.conda/envs/paper_impact/lib/python3.13/site-packages/vllm/executor/uniproc_executor.py:60: UserWarning: Failed to get the IP address, using 0.0.0.0 by default.The value can be set by the environment variable VLLM_HOST_IP or HOST_IP.
+(EngineCore_DP0 pid=3289378)   get_ip(), get_open_port())
+(EngineCore_DP0 pid=3289378) 
+(EngineCore_DP0 pid=3289378) 
+(EngineCore_DP0 pid=3289378) 
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logs/llama32_best_paper_17085241.out

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+Initializing model backend...
+INFO 11-14 08:53:53 [__init__.py:216] Automatically detected platform cuda.
+INFO 11-14 09:00:11 [utils.py:233] non-default args: {'dtype': 'bfloat16', 'disable_log_stats': True, 'model': 'meta-llama/Llama-3.2-3B-Instruct'}
+INFO 11-14 09:00:12 [model.py:547] Resolved architecture: LlamaForCausalLM
+INFO 11-14 09:00:12 [model.py:1510] Using max model len 131072
+INFO 11-14 09:00:39 [scheduler.py:205] Chunked prefill is enabled with max_num_batched_tokens=8192.
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:00:41 [core.py:644] Waiting for init message from front-end.
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:00:41 [core.py:77] Initializing a V1 LLM engine (v0.11.0) with config: model='meta-llama/Llama-3.2-3B-Instruct', speculative_config=None, tokenizer='meta-llama/Llama-3.2-3B-Instruct', skip_tokenizer_init=False, tokenizer_mode=auto, revision=None, tokenizer_revision=None, trust_remote_code=False, dtype=torch.bfloat16, max_seq_len=131072, download_dir=None, load_format=auto, tensor_parallel_size=1, pipeline_parallel_size=1, data_parallel_size=1, disable_custom_all_reduce=False, quantization=None, enforce_eager=False, kv_cache_dtype=auto, device_config=cuda, structured_outputs_config=StructuredOutputsConfig(backend='auto', disable_fallback=False, disable_any_whitespace=False, disable_additional_properties=False, reasoning_parser=''), observability_config=ObservabilityConfig(show_hidden_metrics_for_version=None, otlp_traces_endpoint=None, collect_detailed_traces=None), seed=0, served_model_name=meta-llama/Llama-3.2-3B-Instruct, enable_prefix_caching=True, chunked_prefill_enabled=True, pooler_config=None, compilation_config={"level":3,"debug_dump_path":"","cache_dir":"","backend":"","custom_ops":[],"splitting_ops":["vllm.unified_attention","vllm.unified_attention_with_output","vllm.mamba_mixer2","vllm.mamba_mixer","vllm.short_conv","vllm.linear_attention","vllm.plamo2_mamba_mixer","vllm.gdn_attention","vllm.sparse_attn_indexer"],"use_inductor":true,"compile_sizes":[],"inductor_compile_config":{"enable_auto_functionalized_v2":false},"inductor_passes":{},"cudagraph_mode":[2,1],"use_cudagraph":true,"cudagraph_num_of_warmups":1,"cudagraph_capture_sizes":[512,504,496,488,480,472,464,456,448,440,432,424,416,408,400,392,384,376,368,360,352,344,336,328,320,312,304,296,288,280,272,264,256,248,240,232,224,216,208,200,192,184,176,168,160,152,144,136,128,120,112,104,96,88,80,72,64,56,48,40,32,24,16,8,4,2,1],"cudagraph_copy_inputs":false,"full_cuda_graph":false,"use_inductor_graph_partition":false,"pass_config":{},"max_capture_size":512,"local_cache_dir":null}
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+[Gloo] Rank 0 is connected to 0 peer ranks. Expected number of connected peer ranks is : 0
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:01:49 [parallel_state.py:1208] rank 0 in world size 1 is assigned as DP rank 0, PP rank 0, TP rank 0, EP rank 0
+(EngineCore_DP0 pid=3289378) WARNING 11-14 09:01:50 [topk_topp_sampler.py:66] FlashInfer is not available. Falling back to the PyTorch-native implementation of top-p & top-k sampling. For the best performance, please install FlashInfer.
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:01:51 [gpu_model_runner.py:2602] Starting to load model meta-llama/Llama-3.2-3B-Instruct...
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:01:51 [gpu_model_runner.py:2634] Loading model from scratch...
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:01:58 [cuda.py:366] Using Flash Attention backend on V1 engine.
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:01:59 [weight_utils.py:392] Using model weights format ['*.safetensors']
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:02:09 [default_loader.py:267] Loading weights took 9.46 seconds
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:02:09 [gpu_model_runner.py:2653] Model loading took 6.0160 GiB and 17.367721 seconds
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:30 [backends.py:548] Using cache directory: /home/hangxiao/.cache/vllm/torch_compile_cache/60631d1593/rank_0_0/backbone for vLLM's torch.compile
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:30 [backends.py:559] Dynamo bytecode transform time: 140.60 s
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:35 [backends.py:164] Directly load the compiled graph(s) for dynamic shape from the cache, took 4.680 s
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:44 [monitor.py:34] torch.compile takes 140.60 s in total
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:52 [gpu_worker.py:298] Available KV cache memory: 28.18 GiB
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:53 [kv_cache_utils.py:1087] GPU KV cache size: 263,824 tokens
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:04:53 [kv_cache_utils.py:1091] Maximum concurrency for 131,072 tokens per request: 2.01x
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:05:03 [gpu_model_runner.py:3480] Graph capturing finished in 11 secs, took 2.57 GiB
+(EngineCore_DP0 pid=3289378) INFO 11-14 09:05:03 [core.py:210] init engine (profile, create kv cache, warmup model) took 174.03 seconds
+INFO 11-14 09:05:04 [llm.py:306] Supported_tasks: ['generate']
+Backend initialized: local vLLM mode
+
+=== Evaluating split: test ===
+{
+  "split": "test",
+  "pairs_count": 2385,
+  "evaluated_count": 2068,
+  "skipped_count": 317,
+  "correct_predictions": 1015,
+  "accuracy": 0.49081237911025144
+}
+
+=== Summary ===
+{
+  "split": "test",
+  "accuracy": 0.49081237911025144,
+  "pairs_count": 2385,
+  "evaluated_pairs": 2068,
+  "skipped_pairs": 317,
+  "correct_predictions": 1015,
+  "elapsed_seconds": 1312.522710800171,
+  "model_name": "meta-llama/Llama-3.2-3B-Instruct",
+  "api_base": "http://127.0.0.1:8000/v1",
+  "backend_mode": "local_vllm"
+}
+
+Results saved to:
+  Summary: /scratch/user/hangxiao/paper_impact/best_paper/llama32_best_paper_results.json
+  Details: /scratch/user/hangxiao/paper_impact/best_paper/llama32_best_paper_predictions.jsonl

openalex-snapshot/LICENSE.txt

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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+    this CC0 or use of the Work.

openalex-snapshot/README.txt

@@ -0,0 +1,4 @@
+OPENALEX STANDARD-FORMAT README
+
+This data is updated approximately once per month.
+Documentation is at https://docs.openalex.org

openalex-snapshot/RELEASE_NOTES.txt

@@ -0,0 +1,245 @@
+OPENALEX STANDARD-FORMAT SNAPSHOT RELEASE NOTES
+
+RELEASE 2025-03-31
+- added new works
+
+RELEASE 2025-02-27
+- added new works
+
+RELEASE 2025-01-29
+- removed 350k abstracts with invalid or junk content
+- after this release, the snapshot will be updated quarterly
+
+RELEASE 2024-12-31
+- used new ROR matching algorithm to assign affiliations to institutions with zero works; 7.6k additional institutions now have work affiliations
+- added affiliations to 4.5M authorships
+
+RELEASE 2024-11-25
+- added 3.5 million new author IDs after fixing bug introduced by ORCID integration
+- added 103 new sources (journals) that started publishing in latter part of 2024
+- ingested 145 author change requests with new curation form
+- added/removed institution affiliations for 3.5k works based on works-magnet curation requests
+- processed 50 source curation requests
+- curated 5 institutions that were lacking affiliations
+
+RELEASE 2024-10-31
+- detect additional paratext
+- fixed author alternate names bug
+
+RELEASE 2024-09-27
+- added ~14M affiliations to works
+- adjusted year retrieved from Crossref, using the earliest from issued, published, approved, created, deposited. This affects ~20M works.
+
+RELEASE 2024-08-29
+- add new object citation_normalized_percentile to works, which is a percentile rank of citations normalized by the number of works in the same year and subfield
+- add more references to works using previous MAG snapshot
+- restored some missing affiliations
+
+RELEASE 2024-07-30
+- new work type: retraction
+- used data from Pubmed to reclassify 4M works from type "article" to one of: editorial, erratum, letter, preprint, review, retraction
+- improved type classification for works using string matching
+- change titles (display_name) for ~30k journals based on data from Crossref
+- delete 187,452 works: deleted Zenodo records. (merge into deleted id: W4285719527)
+- clean up author names: remove non-name strings prepended to certain author names; remove non-printing characters and whitespace, delete authors with bad names (only whitespace, only numbers)
+
+RELEASE 2024-06-30
+- add new affiliations field to Work.authorships, allowing more detailed mapping of raw affiliation strings to institutions
+- new is_core boolean added to sources and associated works based on dataset from CWTS: https://zenodo.org/records/10949671
+- fixed bug causing some works' OA status to be out of sync with Unpaywall
+- APC estimates (apc_paid) are no longer given for works with OA status of closed, bronze, or green
+
+RELEASE 2024-05-30
+- added 151M new references to works (7.61% increase) by matching references without DOIs using title/author/publication year
+- updated authorship information for 17.9M works by syncing Crossref changes
+- added 4 new work types, reclassifying existing works: “preprint” (5.7M), “libguides” (1.8M), “review” (820k), and “supplementary-materials” (50k)
+- "super system" institutions such as University of California System are removed from institution lineage
+- added datasets from DataCite: 1.07M from Cambridge Structural Database and 709k from Harvard Dataverse
+
+RELEASE 2024-04-25
+- added affiliations to ~2.5M works using open access PDFs parsed by grobid
+- ingested 3.4M works from DataCite, primarily from Zenodo, Arxiv, and Figshare
+- fixed language detection bug that occurred when title and abstract all uppercase
+- override language assignment for some major English-language journals
+- remove Author.last_known_institution in favor of Author.last_known_institution (in progress)
+- remove Work.authorships.raw_affiliation_string in favor of Work.authorships.raw_affiliation_strings (in progress)
+
+RELEASE 2024-03-27
+- set up automatic updates for Retraction Watch (see https://doi.org/10.13003/c23rw1d9 for info about Retraction Watch)
+- marked ~2k additional works as retracted, and corrected 1-2k works that were incorrectly labeled is_retracted
+- add siblings to domains, field, subfields
+
+RELEASE 2024-02-27
+- added topics to works
+- modified ID format for topic domain, field, and subfield within works, from integer to openalex string. About 60% of
+    works have the new format. The remaining 40% will be updated by the next release.
+- added new topics, domains, fields, and subfields entities to the snapshot
+- fixed host_organization bug within sources
+
+RELEASE 2024-01-24
+- added Author.last_known_institutions, a list of institutions for the affiliations of the author's most recent work (last_known_affiliation will be deprecated in the future)
+- added indexed_in to works
+- merged around 300 institutions based on ROR data
+- removed the license type "publisher-specific, author manuscript" from ~140k work locations, changing them to either "publisher-specific-oa" or closed
+
+RELEASE 2023-12-20
+- added Author.affiliations, an author's 10 most recent associated institutions and years of publications
+- merged 566k duplicated works associated with HAL repository
+- removed old author IDs (ID less than 5000000000) from merged_ids/authors
+- changed cited_by_percentile_year in works to an integer
+
+RELEASE 2023-11-21
+- improved affiliation matching for over 2 million works
+- added keywords to works
+- added cited_by_percentile_year to works
+- removed 3.9 million authors with 0 works (merged into deleted profile)
+- improved oa status classification, converting 2.1 million closed works to open access statuses
+ (ongoing - credit: https://subugoe.github.io/scholcomm_analytics/posts/oalex_oa_status/)
+
+RELEASE 2023-10-18
+- added new works
+- added more sources
+
+RELEASE 2023-09-20
+- added raw author name to authorships objects in works
+- institution lineage (parent institution IDs) available in works, authors, institutions
+- sustainable development goals assigned to 209 million works
+- improved institution matching for 1.1 million works
+- countries distinct count available in works
+- added ~700 new sources
+- matched primary source for 248,647 old works
+- abstract inverted index is correct object in snapshot (InvertedIndex key removed)
+- updated_dates are in full ISO format
+- documentation scripts updated for current snapshot
+
+RELEASE 2023-08-18
+- released new authors disambiguation feature
+- fixed missing source assignment for 5.7M works
+- improved affiliation matching resulting in additional ~1.1M works matched to institutions
+- works with more than 100 authors no longer have authors truncated
+- modified Work.type, added Work.type_crossref
+- added APC data for 3,508 journals
+- added authorships.countries attribute
+- resolved minor snapshot bugs affecting abstract_inverted_index and manifest, removed "@" fields
+
+RELEASE 2023-07-11
+- add references_count to works
+- add records across all entities
+- updated and improved records across all entities
+
+RELEASE 2023-06-02
+- add new works
+- add apc_payment to works
+- add locations_count to works
+- improved coverage of alternate titles, homepage, country code for funders, publishers, and sources
+
+RELEASE 2023-05-03
+- add funders entity
+- add grants to works
+- add APC payments to sources
+
+RELEASE 2023-03-28
+- truncate work display_names to 500 characters
+- truncate author display_names to 100 characters
+- added summary stats for every entity type except works
+- added new publishers and works
+
+RELEASE 2023-02-21
+- merged ~170 million authors into deleted author record as part of disambigation project
+- renamed venues to sources
+- add publishers entity
+- added new works
+
+RELEASE 2022-12-21
+- the values in host_venue have been added to alternate_host_venues in works, which paves way for the new locations
+list that will contain all possible venues for a work
+- added new works
+
+RELEASE 2022-11-14
+- new fields in venues: type, apc_usd, alternate_titles, abbreviated_title, fatcat_id, and wikidata_id
+- added new works
+
+RELEASE 2022-10-10
+- implemented automated concept tagger v3, which provides complete paths to concept level 0
+- restored 170M "lost" citations that were in MAG and we deleted
+- added new works
+
+RELEASE 2022-09-16
+- added 1.3 million new Works
+- removed 700 thousand duplicate Authors
+
+RELEASE 2022-08-09
+- removed duplicate institutions for each author in Work.authorships
+- made DOIs unique across Works. removed incorrect DOIs from 500K works and merged 1M sets of works with the same DOI.
+- added 900K new Works
+
+RELEASE 2022-07-09
+- added new papers and corresponding data
+- added missing related works
+- updated many concepts using improved algorithm
+- updated many affiliation mappings using improved algorithm
+- removed duplicate Authors and Works
+
+RELEASE 2022-06-09
+- added new papers and corresponding data
+- added about 28 million papers with Crossref DOIs
+- added 23 thousand new journal webpage links, thanks in large part to DOAJ data
+- fixed a bug with cited_by_year in venues
+- new works now use an improved algorithm for mapping affiliation data to ROR IDs
+- merged some duplicate institutions and venues (all references have been consolidated to one of the IDs)
+
+RELEASE 2022-05-12
+- added new papers and corresponding data
+
+RELEASE 2022-04-30
+- implemented automated concept tagger v2, which uses more fields to assign concepts to works
+- added new papers and corresponding data
+- updated 8715 venues that had issn_l listed but no issns in "issns" key
+
+RELEASE 2022-04-07
+- added new papers and corresponding data
+- add DOIs to 1,242,303 existing works
+- new related works to many works missing them
+
+RELEASE 2022-03-11
+- added new papers and corresponding data
+- added 1181 new journals to Venues
+- updated publisher, title, ISSNs on a few hundred journals
+
+RELEASE 2022-03-01
+- added new papers and corresponding data
+- added 45 new journals to Venues
+- added ancestors to 1500 Concepts without ancestors
+- fixed a bug with some tabs in the publisher field in Venues and Works
+
+RELEASE 2022-02-22
+- added new papers and corresponding data
+- added "created_date" to all entities
+
+Partial release on 2022-02-04 (updated Institutions and Venues)
+- ensured each institution has a distinct ROR (identified some institutions that will be merged in a future release, details TBD)
+- updated institution names and data to match what is in ROR
+- added all ROR institutions to Institutions (about 81,000 new institutions)
+- matched papers to new institutions (some errors, but will improve over time)
+- updated last known institution for millions of authors
+- don't show citation counts for future years in "counts_by_year"
+- ensured each journal has a distinct ISSN-L (identified some journals that will be merged in a future release, details TBD)
+- add many new journals to venues table, link to works when possible (about 73,000 new journals)
+- add more links from works to venues using Crossref data
+
+RELEASE 2022-01-31
+- added new papers and corresponding data
+- remove blank lines
+- citation counts for concepts use improved algorithm
+
+RELEASE 2022-01-24
+- added work.abstract_inverted_index
+- added work.affiliations.raw_affiliation_string
+- changed the type of work.cited_by_api_url: was a list by mistake, now a string
+- removed ids that have a NULL value from the "ids" dict for all five entity types
+- corrected the spelling of institution.associated_institutions
+- does not include new entities since last release: a new snapshot will be released soon with recently-published works
+
+RELEASE 2022-01-02
+Released on Jan 2, 2022 at s3://openalex/data/
+- First release

openalex-snapshot/browse.html

@@ -0,0 +1,749 @@
+<!DOCTYPE html>
+
+<!--
+Copyright 2014-2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
+
+Licensed under the Apache License, Version 2.0 (the "License").
+
+You may not use this file except in compliance with the License. A copy
+of the License is located at
+
+https://aws.amazon.com/apache2.0/
+
+or in the "license" file accompanying this file. This file is distributed
+on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+either express or implied. See the License for the specific language governing
+permissions and limitations under the License.
+-->
+
+<html lang="en">
+
+<head>
+    <title>AWS S3 Explorer</title>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <link rel="shortcut icon" href="https://aws.amazon.com/favicon.ico">
+    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.0/css/bootstrap.min.css" integrity="sha384-PmY9l28YgO4JwMKbTvgaS7XNZJ30MK9FAZjjzXtlqyZCqBY6X6bXIkM++IkyinN+" crossorigin="anonymous">
+    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.0/css/bootstrap-theme.min.css" integrity="sha384-jzngWsPS6op3fgRCDTESqrEJwRKck+CILhJVO5VvaAZCq8JYf8HsR/HPpBOOPZfR" crossorigin="anonymous">
+    <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/all.css">
+    <link rel="stylesheet" href="https://cdn.datatables.net/1.10.19/css/dataTables.bootstrap.min.css">
+    <style type="text/css">
+        #wrapper {
+            padding-left: 0;
+        }
+
+        #page-wrapper {
+            width: 100%;
+            padding: 5px 15px;
+        }
+
+        #tb-s3objects {
+            width: 100% !Important;
+        }
+
+        a {
+            color: #00B7FF;
+        }
+
+        body {
+            font: 14px "Lucida Grande", Helvetica, Arial, sans-serif;
+        }
+
+        td {
+            font: 12px "Lucida Grande", Helvetica, Arial, sans-serif;
+        }
+
+        .title {
+            padding: 6px 12px;
+        }
+
+        .breadcrumb {
+            margin-bottom: 0;
+        }
+
+        #navbuttons .btn {
+            padding: 3px 6px;
+        }
+    </style>
+</head>
+
+<!-- DEBUG: Enable this for red outline on all elements -->
+<!-- <style media="screen" type="text/css"> * { outline: 1px red solid; } </style> -->
+
+<body>
+    <div id="page-wrapper">
+        <div class="row">
+            <div class="col-lg-12">
+                <div class="panel panel-primary">
+
+                    <!-- Panel including title, breadcrumbs, and controls -->
+                    <div class="panel-heading clearfix">
+                        <!-- Title and breadcrumbs -->
+                        <div class="btn-group pull-left">
+                            <!-- App title -->
+                            <div class="title pull-left">
+                                AWS S3 Explorer&nbsp;
+                            </div>
+                            <!-- Bucket breadcrumbs -->
+                            <div class="pull-right">
+                                <ul id="breadcrumb" class="breadcrumb pull-right">
+                                    <li class="active">
+                                        <a href="#">&lt;bucket&gt;</a>
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+                        <!-- Controls -->
+                        <div id="navbuttons" class="pull-right">
+                            <div>
+                                <!-- Hide folders checkbox -->
+                                <div class="btn-group">
+                                    <label class="btn">
+                                        <input type="checkbox" id="hidefolders">&nbsp;Hide folders?
+                                    </label>
+                                </div>
+                                <!-- Folder/Bucket radio group -->
+                                <div class="btn-group" data-toggle="buttons">
+                                    <label class="btn btn-primary active" title="View all objects in folder">
+                                        <i class="fa fa-angle-double-up"></i>
+                                        <input type="radio" name="optionsdepth" value="folder" id="optionfolder" checked>&nbsp;Folder
+                                    </label>
+                                    <label class="btn btn-primary" title="View all objects in bucket">
+                                        <i class="fa fa-angle-double-down"></i>
+                                        <input type="radio" name="optionsdepth" value="bucket" id="optionbucket">&nbsp;Bucket
+                                    </label>
+                                </div>
+                                <!-- Bucket selection -->
+                                <div class="btn-group" id="bucket">
+                                    <i id="bucket-chooser" style="cursor: pointer;" class="btn fa fa-cog fa-2x" title="Switch to a different S3 Bucket"></i>
+                                </div>
+                                <!-- Dual purpose: progress spinner and refresh button, plus object count -->
+                                <div class="btn-group" id="refresh">
+                                    <span id="bucket-loader" style="cursor: pointer;" class="btn fa fa-refresh fa-2x pull-left" title="Refresh"></span>
+                                    <span id="badgecount" class="badge pull-right" title="Object count">42</span>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+
+                    <!-- Panel including S3 object table -->
+                    <div class="panel-body">
+                        <table class="table table-bordered table-hover table-striped" id="tb-s3objects">
+                            <thead>
+                                <tr>
+                                    <th>Object</th>
+                                    <th>Folder</th>
+                                    <th>Last Modified</th>
+                                    <th>Timestamp</th>
+                                    <th>Size</th>
+                                </tr>
+                            </thead>
+                            <tbody id="tbody-s3objects"></tbody>
+                        </table>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+</body>
+
+</html>
+
+<script src="https://code.jquery.com/jquery-3.4.1.min.js"></script>
+<script src="https://stackpath.bootstrapcdn.com/bootstrap/3.4.0/js/bootstrap.min.js" integrity="sha384-vhJnz1OVIdLktyixHY4Uk3OHEwdQqPppqYR8+5mjsauETgLOcEynD9oPHhhz18Nw" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/bootbox.js/4.4.0/bootbox.min.js"></script>
+<script src="https://sdk.amazonaws.com/js/aws-sdk-2.207.0.min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/moment.js/2.22.0/moment.min.js"></script>
+<script src="https://cdn.datatables.net/1.10.19/js/jquery.dataTables.min.js"></script>
+<script src="https://cdn.datatables.net/1.10.19/js/dataTables.bootstrap.min.js"></script>
+
+<script type="text/javascript">
+    var HIDE_INDEX = true;
+    var s3exp_config = {
+        Region: '',
+        Bucket: '',
+        Prefix: '',
+        Delimiter: '/'
+    };
+    var s3exp_lister = null;
+    var s3exp_columns = {
+        key: 1,
+        folder: 2,
+        date: 3,
+        size: 4
+    };
+
+    AWS.config.region = 'us-east-1';
+    console.log('Region: ' + AWS.config.region);
+
+    // Initialize S3 SDK and the moment library (for time formatting utilities)
+    var s3 = new AWS.S3();
+    moment().format();
+
+    function bytesToSize(bytes) {
+        var sizes = ['Bytes', 'KB', 'MB', 'GB', 'TB'];
+        if (bytes === 0) return '0 Bytes';
+        var ii = parseInt(Math.floor(Math.log(bytes) / Math.log(1024)));
+        return Math.round(bytes / Math.pow(1024, ii), 2) + ' ' + sizes[ii];
+    }
+
+    // Custom startsWith function for String prototype
+    if (typeof String.prototype.startsWith != 'function') {
+        String.prototype.startsWith = function(str) {
+            return this.indexOf(str) == 0;
+        };
+    }
+
+    // Custom endsWith function for String prototype
+    if (typeof String.prototype.endsWith != 'function') {
+        String.prototype.endsWith = function(str) {
+            return this.slice(-str.length) == str;
+        };
+    }
+
+    function object2hrefvirt(bucket, key) {
+        var enckey = key.split('/').map(function(x) { return encodeURIComponent(x); }).join('/');
+
+        if (AWS.config.region === "us-east-1") {
+            return document.location.protocol + '//' + bucket + '.s3.amazonaws.com/' + enckey;
+        } else {
+            return document.location.protocol + '//' + bucket + '.s3-' + AWS.config.region + '.amazonaws.com/' + enckey;
+        }
+    }
+
+    function object2hrefpath(bucket, key) {
+        var enckey = key.split('/').map(function(x) { return encodeURIComponent(x); }).join('/');
+
+        if (AWS.config.region === "us-east-1") {
+            return document.location.protocol + "//s3.amazonaws.com/" + bucket + "/" + enckey;
+        } else {
+            return document.location.protocol + "//s3-' + AWS.config.region + '.amazonaws.com/" + bucket + "/" + enckey;
+        }
+    }
+
+    function htmlEscape(str) {
+        return str
+            .replace(/&/g, '&amp;')
+            .replace(/</g, '&lt;')
+            .replace(/>/g, '&gt;')
+            .replace(/"/g, '&quot;')
+            .replace(/'/g, '&#39;')
+            .replace(/\//g, '&#x2F;')
+            .replace(/`/g, '&#x60;')
+            .replace(/=/g, '&#x3D;');
+    }
+
+    function isthisdocument(bucket, key) {
+        return key === "index.html";
+    }
+
+    function isfolder(path) {
+        return path.endsWith('/');
+    }
+
+    // Convert cars/vw/golf.png to golf.png
+    function fullpath2filename(path) {
+        return htmlEscape(path.replace(/^.*[\\\/]/, ''));
+    }
+
+    // Convert cars/vw/golf.png to cars/vw
+    function fullpath2pathname(path) {
+        return htmlEscape(path.substring(0, path.lastIndexOf('/')));
+    }
+
+    // Convert cars/vw/ to vw/
+    function prefix2folder(prefix) {
+        var parts = prefix.split('/');
+        return htmlEscape(parts[parts.length - 2] + '/');
+    }
+
+    // Remove hash from document URL
+    function removeHash() {
+        history.pushState("", document.title, window.location.pathname + window.location.search);
+    }
+
+    // We are going to generate bucket/folder breadcrumbs. The resulting HTML will
+    // look something like this:
+    //
+    // <li>Home</li>
+    // <li>Library</li>
+    // <li class="active">Samples</li>
+    //
+    // Note: this code is a little complex right now so it would be good to find
+    // a simpler way to create the breadcrumbs.
+    function folder2breadcrumbs(data) {
+        console.log('Bucket: ' + data.params.Bucket);
+        console.log('Prefix: ' + data.params.Prefix);
+
+        if (data.params.Prefix && data.params.Prefix.length > 0) {
+            console.log('Set hash: ' + data.params.Prefix);
+            window.location.hash = data.params.Prefix;
+        } else {
+            console.log('Remove hash');
+            removeHash();
+        }
+
+        // The parts array will contain the bucket name followed by all the
+        // segments of the prefix, exploded out as separate strings.
+        var parts = [data.params.Bucket];
+
+        if (data.params.Prefix) {
+            parts.push.apply(parts,
+                data.params.Prefix.endsWith('/') ?
+                data.params.Prefix.slice(0, -1).split('/') :
+                data.params.Prefix.split('/'));
+        }
+
+        console.log('Parts: ' + parts + ' (length=' + parts.length + ')');
+
+        // Empty the current breadcrumb list
+        $('#breadcrumb li').remove();
+
+        // Now build the new breadcrumb list
+        var buildprefix = '';
+        $.each(parts, function(ii, part) {
+            var ipart;
+
+            // Add the bucket (the bucket is always first)
+            if (ii === 0) {
+                var a1 = $('<a>').attr('href', '#').text(part);
+                ipart = $('<li>').append(a1);
+                a1.click(function(e) {
+                    e.preventDefault();
+                    console.log('Breadcrumb click bucket: ' + data.params.Bucket);
+                    s3exp_config = {
+                        Bucket: data.params.Bucket,
+                        Prefix: '',
+                        Delimiter: data.params.Delimiter
+                    };
+                    (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+                });
+                // Else add the folders within the bucket
+            } else {
+                buildprefix += part + '/';
+
+                if (ii == parts.length - 1) {
+                    ipart = $('<li>').addClass('active').text(part);
+                } else {
+                    var a2 = $('<a>').attr('href', '#').append(part);
+                    ipart = $('<li>').append(a2);
+
+                    // Closure needed to enclose the saved S3 prefix
+                    (function() {
+                        var saveprefix = buildprefix;
+                        // console.log('Part: ' + part + ' has buildprefix: ' + saveprefix);
+                        a2.click(function(e) {
+                            e.preventDefault();
+                            console.log('Breadcrumb click object prefix: ' + saveprefix);
+                            s3exp_config = {
+                                Bucket: data.params.Bucket,
+                                Prefix: saveprefix,
+                                Delimiter: data.params.Delimiter
+                            };
+                            (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+                        });
+                    })();
+                }
+            }
+            $('#breadcrumb').append(ipart);
+        });
+    }
+
+    function s3draw(data, complete) {
+        $('li.li-bucket').remove();
+        folder2breadcrumbs(data);
+
+        // Add each part of current path (S3 bucket plus folder hierarchy) into the breadcrumbs
+        $.each(data.CommonPrefixes, function(i, prefix) {
+            $('#tb-s3objects').DataTable().rows.add([{
+                Key: prefix.Prefix
+            }]);
+        });
+
+        // Add S3 objects to DataTable
+        $('#tb-s3objects').DataTable().rows.add(data.Contents).draw();
+    }
+
+    function s3list(config, completecb) {
+        console.log('s3list config: ' + JSON.stringify(config));
+        var params = {
+            Bucket: config.Bucket,
+            Prefix: config.Prefix,
+            Delimiter: config.Delimiter
+        };
+        var scope = {
+            Contents: [],
+            CommonPrefixes: [],
+            params: params,
+            stop: false,
+            completecb: completecb
+        };
+
+        return {
+            // This is the callback that the S3 API makes when an S3 listObjectsV2
+            // request completes (successfully or in error). Note that a single call
+            // to listObjectsV2 may not be enough to get all objects so we need to
+            // check if the returned data is truncated and, if so, make additional
+            // requests with a 'next marker' until we have all the objects.
+            cb: function(err, data) {
+                if (err) {
+                    console.log('Error: ' + JSON.stringify(err));
+                    console.log('Error: ' + err.stack);
+                    scope.stop = true;
+                    $('#bucket-loader').removeClass('fa-spin');
+                    bootbox.alert("Error accessing S3 bucket " + scope.params.Bucket + ". Error: " + err);
+                } else {
+                    // console.log('Data: ' + JSON.stringify(data));
+                    console.log("Options: " + $("input[name='optionsdepth']:checked").val());
+
+                    // Store marker before filtering data
+                    if (data.IsTruncated) {
+                        if (data.NextContinuationToken) {
+                            scope.params.ContinuationToken = data.NextContinuationToken;
+                        }
+                    }
+
+                    // Filter the folders out of the listed S3 objects
+                    // (could probably be done more efficiently)
+                    console.log("Filter: remove folders");
+                    data.Contents = data.Contents.filter(function(el) {
+                        return el.Key !== scope.params.Prefix;
+                    });
+
+                    // Optionally, filter the root index.html out of the listed S3 objects
+                    if (HIDE_INDEX) {
+                        console.log("Filter: remove index.html");
+                        data.Contents = data.Contents.filter(function(el) {
+                            return el.Key !== "index.html";
+                        });
+                    }
+
+                    // Accumulate the S3 objects and common prefixes
+                    scope.Contents.push.apply(scope.Contents, data.Contents);
+                    scope.CommonPrefixes.push.apply(scope.CommonPrefixes, data.CommonPrefixes);
+
+                    // Update badge count to show number of objects read
+                    $('#badgecount').text(scope.Contents.length + scope.CommonPrefixes.length);
+
+                    if (scope.stop) {
+                        console.log('Bucket ' + scope.params.Bucket + ' stopped');
+                    } else if (data.IsTruncated) {
+                        console.log('Bucket ' + scope.params.Bucket + ' truncated');
+                        s3.makeUnauthenticatedRequest('listObjectsV2', scope.params, scope.cb);
+                    } else {
+                        console.log('Bucket ' + scope.params.Bucket + ' has ' + scope.Contents.length + ' objects, including ' + scope.CommonPrefixes.length + ' prefixes');
+                        delete scope.params.ContinuationToken;
+                        if (scope.completecb) {
+                            scope.completecb(scope, true);
+                        }
+                        $('#bucket-loader').removeClass('fa-spin');
+                    }
+                }
+            },
+
+            // Start the spinner, clear the table, make an S3 listObjectsV2 request
+            go: function() {
+                scope.cb = this.cb;
+                $('#bucket-loader').addClass('fa-spin');
+                $('#tb-s3objects').DataTable().clear();
+                s3.makeUnauthenticatedRequest('listObjectsV2', scope.params, this.cb);
+            },
+
+            stop: function() {
+                scope.stop = true;
+                delete scope.params.ContinuationToken;
+                if (scope.completecb) {
+                    scope.completecb(scope, false);
+                }
+                $('#bucket-loader').removeClass('fa-spin');
+            }
+        };
+    }
+
+    function promptForBucketInput() {
+        bootbox.prompt("Please enter the S3 bucket name", function(result) {
+            if (result !== null) {
+                resetDepth();
+                s3exp_config = {
+                    Bucket: result,
+                    Delimiter: '/'
+                };
+                (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+            }
+        });
+    }
+
+    function resetDepth() {
+        $('#tb-s3objects').DataTable().column(1).visible(false);
+        $('input[name="optionsdepth"]').val(['folder']);
+        $('input[name="optionsdepth"][value="bucket"]').parent().removeClass('active');
+        $('input[name="optionsdepth"][value="folder"]').parent().addClass('active');
+    }
+
+    $(document).ready(function() {
+        console.log('ready');
+
+        // Click handler for refresh button (to invoke manual refresh)
+        $('#bucket-loader').click(function(e) {
+            if ($('#bucket-loader').hasClass('fa-spin')) {
+                // To do: We need to stop the S3 list that's going on
+                // bootbox.alert("Stop is not yet supported.");
+                s3exp_lister.stop();
+            } else {
+                delete s3exp_config.ContinuationToken;
+                (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+            }
+        });
+
+        // Click handler for bucket button (to allow user to change bucket)
+        $('#bucket-chooser').click(function(e) {
+            promptForBucketInput();
+        });
+
+        $('#hidefolders').click(function(e) {
+            $('#tb-s3objects').DataTable().draw();
+        });
+
+        // Folder/Bucket radio button handler
+        $("input:radio[name='optionsdepth']").change(function() {
+            console.log("Folder/Bucket option change to " + $(this).val());
+            console.log("Change options: " + $("input[name='optionsdepth']:checked").val());
+
+            // If user selected deep then we do need to do a full list
+            if ($(this).val() == 'bucket') {
+                console.log("Switch to bucket");
+                var choice = $(this).val();
+                $('#tb-s3objects').DataTable().column(1).visible(choice === 'bucket');
+                delete s3exp_config.ContinuationToken;
+                delete s3exp_config.Prefix;
+                s3exp_config.Delimiter = '';
+                (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+                // Else user selected folder then can do a delimiter list
+            } else {
+                console.log("Switch to folder");
+                $('#tb-s3objects').DataTable().column(1).visible(false);
+                delete s3exp_config.ContinuationToken;
+                delete s3exp_config.Prefix;
+                s3exp_config.Delimiter = '/';
+                (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+            }
+        });
+
+        function renderObject(data, type, full) {
+            if (isthisdocument(s3exp_config.Bucket, data)) {
+                console.log("is this document: " + data);
+                return fullpath2filename(data);
+            } else if (isfolder(data)) {
+                console.log("is folder: " + data);
+                return '<a data-s3="folder" data-prefix="' + htmlEscape(data) + '" href="' + object2hrefvirt(s3exp_config.Bucket, data) + '">' + prefix2folder(data) + '</a>';
+            } else {
+                console.log("not folder/this document: " + data);
+                return '<a data-s3="object" href="' + object2hrefvirt(s3exp_config.Bucket, data) + '"download="' + fullpath2filename(data) + '">' + fullpath2filename(data) + '</a>';
+            }
+        }
+
+        function renderFolder(data, type, full) {
+            return isfolder(data) ? "" : fullpath2pathname(data);
+        }
+
+        // Initial DataTable settings
+        $('#tb-s3objects').DataTable({
+            iDisplayLength: 50,
+            order: [
+                [1, 'asc'],
+                [0, 'asc']
+            ],
+            aoColumnDefs: [{
+                "aTargets": [0],
+                "mData": "Key",
+                "mRender": function(data, type, full) {
+                    return (type == 'display') ? renderObject(data, type, full) : data;
+                },
+                "sType": "key"
+            }, {
+                "aTargets": [1],
+                "mData": "Key",
+                "mRender": function(data, type, full) {
+                    return renderFolder(data, type, full);
+                }
+            }, {
+                "aTargets": [2],
+                "mData": "LastModified",
+                "mRender": function(data, type, full) {
+                    return data ? moment(data).fromNow() : "";
+                }
+            }, {
+                "aTargets": [3],
+                "mData": "LastModified",
+                "mRender": function(data, type, full) {
+                    return data ? moment(data).local().format('YYYY-MM-DD HH:mm:ss') : "";
+                }
+            }, {
+                "aTargets": [4],
+                "mData": function(source, type, val) {
+                    return source.Size ? ((type == 'display') ? bytesToSize(source.Size) : source.Size) : "";
+                }
+            }, ]
+        });
+
+        $('#tb-s3objects').DataTable().column(s3exp_columns.key).visible(false);
+        console.log("jQuery version=" + $.fn.jquery);
+
+        // Custom sort for the Key column so that folders appear before objects
+        $.fn.dataTableExt.oSort['key-asc'] = function(a, b) {
+            var x = (isfolder(a) ? "0-" + a : "1-" + a).toLowerCase();
+            var y = (isfolder(b) ? "0-" + b : "1-" + b).toLowerCase();
+            return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+        };
+
+        $.fn.dataTableExt.oSort['key-desc'] = function(a, b) {
+            var x = (isfolder(a) ? "1-" + a : "0-" + a).toLowerCase();
+            var y = (isfolder(b) ? "1-" + b : "0-" + b).toLowerCase();
+            return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+        };
+
+        // Allow user to hide folders
+        $.fn.dataTableExt.afnFiltering.push(function(oSettings, aData, iDataIndex) {
+            console.log("hide folders");
+            return $('#hidefolders').is(':checked') ? !isfolder(aData[0]) : true;
+        });
+
+        // Delegated event handler for S3 object/folder clicks. This is delegated
+        // because the object/folder rows are added dynamically and we do not want
+        // to have to assign click handlers to each and every row.
+        $('#tb-s3objects').on('click', 'a', function(event) {
+            event.preventDefault();
+            var target = event.target;
+            console.log("target href=" + target.href);
+            console.log("target dataset=" + JSON.stringify(target.dataset));
+
+            // If the user has clicked on a folder then navigate into that folder
+            if (target.dataset.s3 === "folder") {
+                resetDepth();
+                delete s3exp_config.ContinuationToken;
+                s3exp_config.Prefix = target.dataset.prefix;
+                s3exp_config.Delimiter = $("input[name='optionsdepth']:checked").val() == "folder" ? "/" : "";
+                (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+                // Else user has clicked on an object so download it in new window/tab
+            } else {
+                window.open(target.href, '_blank');
+            }
+            return false;
+        });
+
+        // Document URL typically looks like this for path-style URLs:
+        // - https://s3.amazonaws.com/mybucket1/index.html
+        // - https://s3-us-west-2.amazonaws.com/mybucket2/index.html
+        //
+        // Document URL typically looks like this for virtual-hosted-style URLs:
+        // - https://mybucket1.s3.amazonaws.com/index.html
+        // - https://mybucket2.s3-us-west-2.amazonaws.com/index.html
+        //
+        // Document URL typically looks like this for S3 website hosting:
+        // - http://mybucket3.s3-website-us-east-1.amazonaws.com/
+        // - http://mybucket4.s3-website.eu-central-1.amazonaws.com/
+
+        // TODO: need to support S3 website hosting option
+        //
+        // If we're launched from a bucket then let's try to determine the bucket
+        // name so we can query it immediately, without requiring the user to
+        // supply the bucket name.
+        //
+        // If the region was anything other than US Standard then we will also need
+        // to infer the region so that we can initialize the S3 SDK properly.
+        console.log("Document URL: " + document.URL);
+        var urls = document.URL.split('/');
+        console.log("URL split: " + urls);
+
+        // Using technique from https://gist.github.com/jlong/2428561
+        // to parse the document URL.
+        var parser = document.createElement('a');
+        parser.href = document.URL;
+
+        // URL format is scheme://[user:password@]domain:port/path?query_string#fragment_id
+        // For example: http://example.com:3000/path/?name=abc#topic
+        console.log("protocol: " + parser.protocol); // => "http:"
+        console.log("hostname: " + parser.hostname); // => "example.com"
+        console.log("port    : " + parser.port); // => "3000"
+        console.log("pathname: " + parser.pathname); // => "/path/"
+        console.log("search  : " + parser.search); // => "?name=abc"
+        console.log("hash    : " + parser.hash); // => "#topic"
+        console.log("host    : " + parser.host); // => "example.com:3000"
+
+        // If initial bucket has been hard-coded above then use it, else try to
+        // derive the initial bucket from the document URL (useful if index.html was
+        // launched directly from within a bucket), else prompt the user.
+        if (s3exp_config.Bucket) {
+            (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+        } else if (parser.hostname.endsWith('amazonaws.com')) {
+            // Hostname is likely to be in one of the following forms:
+            // - s3.amazonaws.com
+            // - bucket1.s3.amazonaws.com
+            // - s3-us-west-2.amazonaws.com
+            // - bucket2.s3-us-west-2.amazonaws.com
+
+            // If using static website hosting, the hostname will be of the form:
+            // - bucket.s3-website.eu-central-1.amazonaws.com/
+
+            // The following is also a legal form, but we do not support it, so
+            // you should use s3-eu-central-1 rather than s3.eu-central-1:
+            // - bucket3.s3.eu-central-1.amazonaws.com
+
+            var bucket;
+            var region;
+            var hostnames = parser.hostname.split('.');
+            var pathnames = parser.pathname.split('/');
+
+            console.log("count of words in hostname=" + hostnames.length);
+            console.log("count of words in pathname=" + pathnames.length);
+
+            console.log("hostnames=" + hostnames);
+            console.log("pathnames=" + pathnames);
+
+            // If bucket prefix not included in hostname
+            if (hostnames[0].match(/^s3-/) || hostnames[0].match(/^s3$/)) {
+                bucket = pathnames[1];
+                region = hostnames[0];
+                console.log("path bucket=" + bucket);
+                console.log("path region=" + region);
+            } else {
+                bucket = hostnames[0];
+                region = hostnames[hostnames.length - 3];
+                console.log("host bucket=" + bucket);
+                console.log("host region=" + region);
+            }
+
+            // If we found statically-hosted website prefix or explicit region, for
+            // example s3-us-west-2, then get region else use the default of US Standard
+            if (region !== 's3') {
+                if (region.startsWith('s3-website-')) {
+                    AWS.config.region = region.substring(11);
+                } else if (region.startsWith('s3-') || region.startsWith('s3.')) {
+                    AWS.config.region = region.substring(3);
+                } else {
+                    AWS.config.region = region;
+                }
+            }
+
+            console.log("AWS region=" + AWS.config.region);
+            console.log("S3 bucket=" + bucket);
+
+            // Create and initialize S3 object
+            s3 = new AWS.S3();
+            s3exp_config = {
+                Bucket: bucket,
+                Delimiter: '/'
+            };
+
+            if (window.location.hash) {
+                console.log("Location hash=" + window.location.hash);
+                s3exp_config.Prefix = window.location.hash.substring(1);
+            }
+
+            // Do initial bucket list
+            (s3exp_lister = s3list(s3exp_config, s3draw)).go();
+        } else {
+            promptForBucketInput();
+        }
+    });
+</script>

openalex-snapshot/data/fields/manifest

@@ -0,0 +1,10 @@
+{
+  "entries": [
+    {"url": "s3://openalex/data/fields/updated_date=2024-04-01/part_000.gz", "meta": { "content_length": 5415, "record_count": 18 } },
+    {"url": "s3://openalex/data/fields/updated_date=2025-03-31/part_000.gz", "meta": { "content_length": 2338, "record_count": 8 } }
+  ],
+  "meta": {
+    "content_length": 7753,
+    "record_count": 26
+  }
+}