Update pdfalto 0.6.1

CHANGELOG.md

@@ -10,10 +10,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - Training web API: list ongoing trainings (`GET /api/allTraining`) and interrupt a running training (`DELETE /api/killTraining`). Killing a training releases the per-model lock so the model can be retrained; interruption is best-effort for native (Wapiti/DeLFT) back-ends.
 
 ### Changed
+- Updated pdfalto to 0.6.1. Notable for GROBID: deterministic output (an uninitialised read and a use-after-free made line/block grouping depend on heap contents, so the same PDF could yield different `<TextLine>`/`<TextBlock>` structure across runs), bounded peak memory on very large or vector-heavy documents, and several text-extraction fixes. The command-line options GROBID passes are unchanged.
+- pdfalto is now given GROBID's configured temp directory (`grobid.temp`, by default `grobid-home/tmp`) through `TMPDIR`. Since 0.6.1 pdfalto streams large page DOMs to a scratch file to bound peak memory and picks its location from `TMPDIR`, falling back to `/tmp` — which is tmpfs in most containers, so spilling there leaves peak memory unchanged and risks ENOSPC.
 - Lexicon: introduced `Lexicon.builder()` to optionally pre-load chosen gazetteers *eagerly* (`.withDefaults()`, `.withJournals()`, `.withFunders()`, `.withOrganisations()`, etc.). Loading stays **lazy by default**: any gazetteer not named in the builder loads transparently on first lookup, so a `Lexicon` from any entry point is always fully functional and never throws for a missing gazetteer — `withX()` only controls *when* a gazetteer loads, not whether a lookup succeeds. `withDefaults()` eagerly loads the original constructor's set (wordforms, people, countries). `Lexicon.getInstance()` is now `@Deprecated` (prefer the builder) but its behavior is unchanged: eager wordforms/people/countries, everything else lazy.
 - Lexicon: added 4 missing ISO 3166-1 country codes (BQ, CW, SS, SX) and migrated AN (Netherlands Antilles) to its ISO 3166-3 transitional form ANHH.
 - Documentation: expanded the End-to-end evaluation guide (dedicated multi-dataset runner-script section for `run_evaluation.sh` with an options table and more invocation examples) and the Configuration reference; recorded the Hugging Face DOI (10.57967/hf/9553) for the `grobid-evaluation` dataset.
 
+### Fixed
+- Handle the exit codes pdfalto 0.6.1 introduced. Code 5 reports that the ALTO was written correctly but page streaming was disabled mid-run, so peak memory was no longer bounded; both execution paths rejected any non-zero exit and would have discarded these successful conversions. It is now a logged warning. Codes 4 (ALTO write failed) and 98 (allocation failure) are reported as `PDFALTO_CONVERSION_FAILURE` instead of falling through to `BAD_INPUT_DATA`, which blamed the PDF for a pdfalto-side failure.
+
 ### Security
 - Prevent command injection through crafted PDF file names in the non-server `pdfalto` path: the command is no longer interpolated into a `bash -c` string but passed as positional parameters and exec'd via `"$@"` (GHSA-mgxf-7mg7-qpmf).
 - Stop leaking a JVM thread per request on the `/api/modelTraining` endpoint by shutting down the per-request executor (GHSA-g2r5-4c8r-c84f).

doc/benchmarks/Benchmarking-plos.md

@@ -48,7 +48,7 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | keywords                    | 0         | 0         | 0         | 0       |
 | title                       | 95.18     | 94.7      | 94.94     | 1000    |
 |                             |           |           |           |         |
-| **all fields (micro avg.)** | **24.02** | **25.18** | **24.59** | 4861    |
+| **all fields (micro avg.)** | **24.02** | **25.18** | **24.58** | 4861    |
 | all fields (macro avg.)     | 61.27     | 61.26     | 61.26     | 4861    |
 
 #### Soft Matching (ignoring punctuation, case and space characters mismatches)
@@ -58,13 +58,13 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | label                       | precision | recall    | f1        | support |
 |-----------------------------|-----------|-----------|-----------|---------|
 | abstract                    | 49.34     | 50.94     | 50.13     | 960     |
-| affiliation_linked          | 73.43     | 78.47     | 75.87     | 963     |
+| affiliation_linked          | 73.43     | 78.49     | 75.87     | 963     |
 | authors                     | 98.97     | 98.97     | 98.97     | 969     |
 | first_author                | 99.17     | 99.17     | 99.17     | 969     |
 | keywords                    | 0         | 0         | 0         | 0       |
 | title                       | 98.79     | 98.3      | 98.55     | 1000    |
 |                             |           |           |           |         |
-| **all fields (micro avg.)** | **77.52** | **81.27** | **79.35** | 4861    |
+| **all fields (micro avg.)** | **77.52** | **81.28** | **79.36** | 4861    |
 | all fields (macro avg.)     | 83.94     | 85.17     | 84.54     | 4861    |
 
 #### Levenshtein Matching (Minimum Levenshtein distance at 0.8)
@@ -74,13 +74,13 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | label                       | precision | recall    | f1     | support |
 |-----------------------------|-----------|-----------|--------|---------|
 | abstract                    | 75.28     | 77.71     | 76.47  | 960     |
-| affiliation_linked          | 78.35     | 83.74     | 80.95  | 963     |
+| affiliation_linked          | 78.35     | 83.75     | 80.96  | 963     |
 | authors                     | 99.38     | 99.38     | 99.38  | 969     |
 | first_author                | 99.28     | 99.28     | 99.28  | 969     |
 | keywords                    | 0         | 0         | 0      | 0       |
 | title                       | 99.3      | 98.8      | 99.05  | 1000    |
 |                             |           |           |        |         |
-| **all fields (micro avg.)** | **83.04** | **87.06** | **85** | 4861    |
+| **all fields (micro avg.)** | **83.04** | **87.07** | **85** | 4861    |
 | all fields (macro avg.)     | 90.32     | 91.78     | 91.03  | 4861    |
 
 #### Ratcliff/Obershelp Matching (Minimum Ratcliff/Obershelp similarity at 0.95)
@@ -90,14 +90,14 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | label                       | precision | recall    | f1        | support |
 |-----------------------------|-----------|-----------|-----------|---------|
 | abstract                    | 64.78     | 66.88     | 65.81     | 960     |
-| affiliation_linked          | 76.05     | 81.27     | 78.57     | 963     |
+| affiliation_linked          | 76.07     | 81.31     | 78.61     | 963     |
 | authors                     | 99.28     | 99.28     | 99.28     | 969     |
 | first_author                | 99.17     | 99.17     | 99.17     | 969     |
 | keywords                    | 0         | 0         | 0         | 0       |
 | title                       | 98.99     | 98.5      | 98.75     | 1000    |
 |                             |           |           |           |         |
-| **all fields (micro avg.)** | **80.58** | **84.48** | **82.49** | 4861    |
-| all fields (macro avg.)     | 87.66     | 89.02     | 88.32     | 4861    |
+| **all fields (micro avg.)** | **80.6**  | **84.51** | **82.51** | 4861    |
+| all fields (macro avg.)     | 87.66     | 89.03     | 88.32     | 4861    |
 
 Note: the "affiliation_linked" field above is a linking-aware metric (each author is paired with its gold counterpart
 and their attached affiliations compared). Its support column reports the number of articles the metric is computed
@@ -244,10 +244,10 @@ Total expected references: 	 48449 - 48.45 references per article
 Total predicted references: 	 47775 - 47.77 references per article
 
 Total expected citation contexts: 	 69755 - 69.75 citation contexts per article
-Total predicted citation contexts: 	 73296 - 73.3 citation contexts per article
+Total predicted citation contexts: 	 73298 - 73.3 citation contexts per article
 
-Total correct predicted citation contexts: 	 57033 - 57.03 citation contexts per article
-Total wrong predicted citation contexts: 	 16263 (wrong callout matching, callout missing in NLM, or matching with a bib. ref. not aligned with a bib.ref. in NLM)
+Total correct predicted citation contexts: 	 57034 - 57.03 citation contexts per article
+Total wrong predicted citation contexts: 	 16264 (wrong callout matching, callout missing in NLM, or matching with a bib. ref. not aligned with a bib.ref. in NLM)
 
 Precision citation contexts: 	 77.81
 Recall citation contexts: 	 81.76
@@ -273,14 +273,14 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | conflict_stmt               | 92.57     | 91.89     | 92.23     | 962     |
 | figure_title                | 0.18      | 0.09      | 0.12      | 8943    |
 | funding_stmt                | 5.79      | 31.12     | 9.77      | 1507    |
-| reference_citation          | 87.98     | 94.53     | 91.13     | 69741   |
+| reference_citation          | 87.97     | 94.53     | 91.13     | 69741   |
 | reference_figure            | 74.11     | 85.79     | 79.52     | 11010   |
 | reference_table             | 70.21     | 94.32     | 80.5      | 5159    |
-| section_title               | 72.98     | 66.28     | 69.47     | 17540   |
+| section_title               | 72.97     | 66.29     | 69.47     | 17540   |
 | table_title                 | 0         | 0         | 0         | 6092    |
 |                             |           |           |           |         |
 | **all fields (micro avg.)** | **74.56** | **76.95** | **75.74** | 121733  |
-| all fields (macro avg.)     | 51.28     | 58        | 53.4      | 121733  |
+| all fields (macro avg.)     | 51.28     | 58.01     | 53.4      | 121733  |
 
 #### Soft Matching (ignoring punctuation, case and space characters mismatches)
 
@@ -292,13 +292,13 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | conflict_stmt               | 95.6      | 94.91     | 95.25    | 962     |
 | figure_title                | 93.18     | 45.82     | 61.43    | 8943    |
 | funding_stmt                | 7.33      | 39.35     | 12.35    | 1507    |
-| reference_citation          | 87.98     | 94.54     | 91.14    | 69741   |
+| reference_citation          | 87.97     | 94.54     | 91.14    | 69741   |
 | reference_figure            | 74.35     | 86.07     | 79.78    | 11010   |
 | reference_table             | 70.37     | 94.53     | 80.68    | 5159    |
-| section_title               | 78.78     | 71.56     | 75       | 17540   |
+| section_title               | 78.77     | 71.56     | 75       | 17540   |
 | table_title                 | 52.96     | 7.49      | 13.12    | 6092    |
 |                             |           |           |          |         |
-| **all fields (micro avg.)** | **79.25** | **81.79** | **80.5** | 121733  |
+| **all fields (micro avg.)** | **79.24** | **81.79** | **80.5** | 121733  |
 | all fields (macro avg.)     | 71.79     | 68.92     | 66.06    | 121733  |
 
 **Document-level ratio results**
@@ -311,5 +311,5 @@ Evaluation on 1000 random PDF files out of 998 PDF (ratio 1.0).
 | **all fields (micro avg.)** | **99.71** | **99.83** | **99.77** | 1741    |
 | all fields (macro avg.)     | 99.69     | 99.89     | 99.79     | 1741    |
 
-Evaluation metrics produced in 123.164 seconds
+Evaluation metrics produced in 102.355 seconds