From 42db5151e1a5134487ceb0ddefecbf44a53db6dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Aur=C3=A9lien=20Lamercerie?=
<aurelien.lamercerie@tetras-libre.fr>
Date: Fri, 3 Mar 2023 10:17:30 +0100
Subject: [PATCH] Main method parsing LN sentences to generate AMR graphs
---
.gitignore | 1 +
README.md | 41 ++-
amrbatch/amrld/.gitignore | 7 -
amrbatch/amrld/test/bio_ras_0001_1.json | 61 ----
amrbatch/amrld/test/bio_ras_0001_1.rdf | 39 ---
amrbatch/amrld/test/bio_ras_0001_1.txt | 15 -
amrbatch/amrld/test/pmid-11777939-32_amr.rdf | 70 -----
amrbatch/amrld/test/pmid-11777939-32_amr.txt | 20 --
amrbatch/amrld/test/test.amr.graph | 12 -
amrbatch/amrld/wk/__wk__.txt | 1 +
amrbatch/amrld/wk/test-01.stog.amr.nt | 22 ++
amrbatch/amrld/wk/test-01.stog.amr.penman | 4 +
amrbatch/amrld/wk/test-02.stog.amr.nt | 19 ++
amrbatch/amrld/wk/test-02.stog.amr.penman | 6 +
amrbatch/filepath_manager.py | 112 +++++++
amrbatch/logging.conf | 39 +++
amrbatch/main.py | 295 +++++++++++++++++-
tests/amrbatch.log | 48 +++
.../test-01/test-01.stog.amr.dot | 6 +
.../Test-20230302/test-01/test-01.stog.amr.nt | 21 ++
.../test-01/test-01.stog.amr.penman | 4 +
.../test-01/test-01.stog.amr.png | Bin 0 -> 11670 bytes
.../test-01/test-01.stog.amr.ttl | 36 +++
.../test-02/test-02.stog.amr.dot | 9 +
.../Test-20230302/test-02/test-02.stog.amr.nt | 18 ++
.../test-02/test-02.stog.amr.penman | 6 +
.../test-02/test-02.stog.amr.png | Bin 0 -> 18820 bytes
.../test-02/test-02.stog.amr.ttl | 29 ++
tests/output/Test-20230302/test.sentence.txt | 2 +
.../test-01/test-01.stog.amr.dot | 6 +
.../Test-20230303/test-01/test-01.stog.amr.nt | 22 ++
.../test-01/test-01.stog.amr.penman | 4 +
.../test-01/test-01.stog.amr.png | Bin 0 -> 11670 bytes
.../test-01/test-01.stog.amr.ttl | 36 +++
.../test-02/test-02.stog.amr.dot | 9 +
.../Test-20230303/test-02/test-02.stog.amr.nt | 19 ++
.../test-02/test-02.stog.amr.penman | 6 +
.../test-02/test-02.stog.amr.png | Bin 0 -> 18820 bytes
.../test-02/test-02.stog.amr.ttl | 29 ++
tests/output/Test-20230303/test.sentence.txt | 2 +
tests/test_amrbatch_main.py | 23 +-
41 files changed, 851 insertions(+), 248 deletions(-)
delete mode 100644 amrbatch/amrld/.gitignore
delete mode 100644 amrbatch/amrld/test/bio_ras_0001_1.json
delete mode 100644 amrbatch/amrld/test/bio_ras_0001_1.rdf
delete mode 100644 amrbatch/amrld/test/bio_ras_0001_1.txt
delete mode 100644 amrbatch/amrld/test/pmid-11777939-32_amr.rdf
delete mode 100755 amrbatch/amrld/test/pmid-11777939-32_amr.txt
delete mode 100644 amrbatch/amrld/test/test.amr.graph
create mode 100644 amrbatch/amrld/wk/__wk__.txt
create mode 100644 amrbatch/amrld/wk/test-01.stog.amr.nt
create mode 100644 amrbatch/amrld/wk/test-01.stog.amr.penman
create mode 100644 amrbatch/amrld/wk/test-02.stog.amr.nt
create mode 100644 amrbatch/amrld/wk/test-02.stog.amr.penman
create mode 100644 amrbatch/filepath_manager.py
create mode 100644 amrbatch/logging.conf
create mode 100644 tests/amrbatch.log
create mode 100644 tests/output/Test-20230302/test-01/test-01.stog.amr.dot
create mode 100644 tests/output/Test-20230302/test-01/test-01.stog.amr.nt
create mode 100644 tests/output/Test-20230302/test-01/test-01.stog.amr.penman
create mode 100644 tests/output/Test-20230302/test-01/test-01.stog.amr.png
create mode 100644 tests/output/Test-20230302/test-01/test-01.stog.amr.ttl
create mode 100644 tests/output/Test-20230302/test-02/test-02.stog.amr.dot
create mode 100644 tests/output/Test-20230302/test-02/test-02.stog.amr.nt
create mode 100644 tests/output/Test-20230302/test-02/test-02.stog.amr.penman
create mode 100644 tests/output/Test-20230302/test-02/test-02.stog.amr.png
create mode 100644 tests/output/Test-20230302/test-02/test-02.stog.amr.ttl
create mode 100644 tests/output/Test-20230302/test.sentence.txt
create mode 100644 tests/output/Test-20230303/test-01/test-01.stog.amr.dot
create mode 100644 tests/output/Test-20230303/test-01/test-01.stog.amr.nt
create mode 100644 tests/output/Test-20230303/test-01/test-01.stog.amr.penman
create mode 100644 tests/output/Test-20230303/test-01/test-01.stog.amr.png
create mode 100644 tests/output/Test-20230303/test-01/test-01.stog.amr.ttl
create mode 100644 tests/output/Test-20230303/test-02/test-02.stog.amr.dot
create mode 100644 tests/output/Test-20230303/test-02/test-02.stog.amr.nt
create mode 100644 tests/output/Test-20230303/test-02/test-02.stog.amr.penman
create mode 100644 tests/output/Test-20230303/test-02/test-02.stog.amr.png
create mode 100644 tests/output/Test-20230303/test-02/test-02.stog.amr.ttl
create mode 100644 tests/output/Test-20230303/test.sentence.txt
diff --git a/.gitignore b/.gitignore
index 954ce385..2e448788 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@ __pycache__
*.todo
*.ttl.tbc
*catalog-v001.xml
+venv/*
diff --git a/README.md b/README.md
index ad601ef4..5fc94690 100644
--- a/README.md
+++ b/README.md
@@ -5,11 +5,48 @@ AMR Batch is a python library to parse natural language sentences in order to bu
This library is currently under development, and therefore in unstable state.
-## Environment Setup
-The python code has been tested under Python 3.7 and Linux Manjaro, but should be run on most common systems (Linux, Windows, Mac).
+
+### Installation
+This project was developp under Python 3.7 and Manjaro Linux system, but should be run on most common systems (Linux, Windows, Mac).
All dependencies are listed in requirements.txt.
+First, it is recommended to use a [virtual environment](https://docs.python.org/fr/3/tutorial/venv.html).
+For example, 'venv' can be create and use with the following commands:
+
+ python3 -m venv venv
+
+ source venv/bin/activate
+
+The necessary libraries are defined in the file 'requirements.txt', and can be installed in the virtual environment using package installer as pip:
+
+ pip install -r requirements.txt
+
+See specific installation instructions about amrlib
+([amrlib-install](https://amrlib.readthedocs.io/en/latest/install/)).
+
+So, it is necessary to install the models used by amrlib library.
+Models can be downloaded from
+[amrlib-models](https://github.com/bjascob/amrlib-models).
+
+These files need to be extracted and reside in a directory. The path to this directory can then be passed as a parameter of the main method. The model STOG 'xfm_bart_large-v0_1_0' (from source dir 'amrbatch/models/') is used by default if no model is given.
+
+
## Usage
The script **test_amrbatch_main.py** (test directory) gives an example of using the library.
+# References
+-------------------------------------------------------------------------------
+
+[amrlib](https://github.com/bjascob/amrlib):
+A python library that makes AMR parsing, generation and visualization simple.
+
+
+[amr-ld](https://github.com/BMKEG/amr-ld/):
+A Python library for mapping AMRs to linked data formats (such as RDF and JSON-LD).
+
+Burns, G.A., Hermjakob, U., Ambite, J.L. (2016).
+Abstract Meaning Representations as Linked Data.
+In: , et al. The Semantic Web – ISWC 2016. ISWC 2016.
+Lecture Notes in Computer Science(), vol 9982. Springer, Cham.
+https://doi.org/10.1007/978-3-319-46547-0_2
diff --git a/amrbatch/amrld/.gitignore b/amrbatch/amrld/.gitignore
deleted file mode 100644
index ee142b2e..00000000
--- a/amrbatch/amrld/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-.project
-.pydevproject
-.history
-.settings
-*.pyc
-out.rdf
-.DS_Store
diff --git a/amrbatch/amrld/test/bio_ras_0001_1.json b/amrbatch/amrld/test/bio_ras_0001_1.json
deleted file mode 100644
index c790bd5f..00000000
--- a/amrbatch/amrld/test/bio_ras_0001_1.json
+++ /dev/null
@@ -1,61 +0,0 @@
-[
- {
- "root": {
- "domain": {
- "op1": {
- "@id": "g",
- "@type": "gene",
- "name": {
- "@id": "n",
- "@type": "name",
- "op1": "KRAS"
- }
- },
- "@id": "a",
- "@type": "and",
- "op2": {
- "@id": "g2",
- "@type": "gene",
- "name": {
- "@id": "n2",
- "@type": "name",
- "op1": "PIK3CA"
- }
- },
- "op3": {
- "@id": "g3",
- "@type": "gene",
- "name": {
- "@id": "n3",
- "@type": "name",
- "op1": "BRAF"
- }
- }
- },
- "@id": "o",
- "@type": "oncogene",
- "location": {
- "@id": "c",
- "@type": "cancer"
- }
- },
- "has-date": "2014-08-13T14:22:25",
- "@context": {
- "and": "http://amr.isi.edu/rdf/core-amr#and",
- "oncogene": "http://amr.isi.edu/rdf/core-amr#oncogene",
- "kill-01": "https://verbs.colorado.edu/propbank#kill-01",
- "name": "http://amr.isi.edu/rdf/core-amr#name",
- "cancer": "http://amr.isi.edu/rdf/core-amr#cancer",
- "most": "http://amr.isi.edu/rdf/core-amr#most",
- "@base": "http://amr.isi.edu/amr_data/bio.ras_0001_1#",
- "human": "http://amr.isi.edu/rdf/core-amr#human",
- "gene": "http://amr.isi.edu/entity-types#gene",
- "root": "http://amr.isi.edu/rdf/core-amr#root",
- "frequent": "http://amr.isi.edu/rdf/core-amr#frequent",
- "mutate-01": "https://verbs.colorado.edu/propbank#mutate-01"
- },
- "@id": "bio.ras_0001_1",
- "@type": "http://amr.isi.edu/rdf/core-amr#AMR",
- "has-sentence": "The most frequently mutated oncogenes in the deadliest cancers responsible for human mortality are KRAS , PIK3CA and BRAF ."
- }
-]
\ No newline at end of file
diff --git a/amrbatch/amrld/test/bio_ras_0001_1.rdf b/amrbatch/amrld/test/bio_ras_0001_1.rdf
deleted file mode 100644
index 642dab56..00000000
--- a/amrbatch/amrld/test/bio_ras_0001_1.rdf
+++ /dev/null
@@ -1,39 +0,0 @@
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#k> <http://amr.isi.edu/rdf/core-amr#ARG1> <http://amr.isi.edu/amr_data/bio.ras_0001_1#h> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "The most frequently mutated oncogenes in the deadliest cancers responsible for human mortality are KRAS , PIK3CA and BRAF ." .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#f> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#frequent> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#name> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#gene> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#a> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#and> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#o> <http://amr.isi.edu/rdf/core-amr#location> <http://amr.isi.edu/amr_data/bio.ras_0001_1#c> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "bio.ras_0001_1" .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#m> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#most> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#f> <http://amr.isi.edu/rdf/core-amr#degree> <http://amr.isi.edu/amr_data/bio.ras_0001_1#m3> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#name> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#name> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#a> <http://amr.isi.edu/rdf/core-amr#op3> <http://amr.isi.edu/amr_data/bio.ras_0001_1#g3> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#k> <http://amr.isi.edu/rdf/core-amr#ARG0> <http://amr.isi.edu/amr_data/bio.ras_0001_1#c> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#a> <http://amr.isi.edu/rdf/core-amr#op1> <http://amr.isi.edu/amr_data/bio.ras_0001_1#g> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n2> <http://amr.isi.edu/rdf/core-amr#op1> "PIK3CA" .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g> <http://amr.isi.edu/rdf/core-amr#name> <http://amr.isi.edu/amr_data/bio.ras_0001_1#n> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#m3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#most> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#o> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#oncogene> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#m2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://verbs.colorado.edu/propbank#mutate-01> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#k> <http://amr.isi.edu/rdf/core-amr#degree> <http://amr.isi.edu/amr_data/bio.ras_0001_1#m> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#m2> <http://amr.isi.edu/rdf/core-amr#frequency> <http://amr.isi.edu/amr_data/bio.ras_0001_1#f> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#k> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://verbs.colorado.edu/propbank#kill-01> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#h> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#human> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g3> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#gene> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/bio.ras_0001_1#o> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#c> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#cancer> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n3> <http://amr.isi.edu/rdf/core-amr#op1> "BRAF" .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#o> <http://amr.isi.edu/rdf/core-amr#TOP> <http://amr.isi.edu/amr_data/bio.ras_0001_1#o> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#o> <http://amr.isi.edu/rdf/core-amr#domain> <http://amr.isi.edu/amr_data/bio.ras_0001_1#a> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g2> <http://amr.isi.edu/rdf/core-amr#name> <http://amr.isi.edu/amr_data/bio.ras_0001_1#n2> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#gene> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#n> <http://amr.isi.edu/rdf/core-amr#op1> "KRAS" .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#m2> <http://amr.isi.edu/rdf/core-amr#ARG1> <http://amr.isi.edu/amr_data/bio.ras_0001_1#o> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#g3> <http://amr.isi.edu/rdf/core-amr#name> <http://amr.isi.edu/amr_data/bio.ras_0001_1#n3> .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#root01> <http://amr.isi.edu/rdf/core-amr#has-date> "2014-08-13T14:22:25" .
-<http://amr.isi.edu/amr_data/bio.ras_0001_1#a> <http://amr.isi.edu/rdf/core-amr#op2> <http://amr.isi.edu/amr_data/bio.ras_0001_1#g2> .
-
diff --git a/amrbatch/amrld/test/bio_ras_0001_1.txt b/amrbatch/amrld/test/bio_ras_0001_1.txt
deleted file mode 100644
index c79b0e4d..00000000
--- a/amrbatch/amrld/test/bio_ras_0001_1.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-# ::id bio.ras_0001_1 ::date 2014-08-13T14:22:25
-# ::snt The most frequently mutated oncogenes in the deadliest cancers responsible for human mortality are KRAS , PIK3CA and BRAF .
-
-(o / oncogene
- :domain (a / and
- :op1 (g / gene :name (n / name :op1 "KRAS"))
- :op2 (g2 / gene :name (n2 / name :op1 "PIK3CA"))
- :op3 (g3 / gene :name (n3 / name :op1 "BRAF")))
- :location (c / cancer
- :ARG0-of (k / kill-01
- :ARG1 (h / human)
- :degree (m / most)))
- :ARG1-of (m2 / mutate-01
- :frequency (f / frequent
- :degree (m3 / most))))
diff --git a/amrbatch/amrld/test/pmid-11777939-32_amr.rdf b/amrbatch/amrld/test/pmid-11777939-32_amr.rdf
deleted file mode 100644
index 9c69ec8b..00000000
--- a/amrbatch/amrld/test/pmid-11777939-32_amr.rdf
+++ /dev/null
@@ -1,70 +0,0 @@
-@prefix ns1: <http://amr.isi.edu/rdf/core-amr#> .
-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix xml: <http://www.w3.org/XML/1998/namespace> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#root01> a ns1:AMR ;
- ns1:has-date "2015-02-27T00:14:25" ;
- ns1:has-id "pmid_1177_7939.32" ;
- ns1:has-sentence "In previous studies, we showed that Sos-1, E3b1, and Eps8 could form a trimeric complex in vivo upon concomitant overexpression of the three proteins." ;
- ns1:root <http://amr.isi.edu/amr_data/pmid_1177_7939.32#s> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#c> a ns1:concomitant .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#e2> a <http://amr.isi.edu/entity-types#enzyme> ;
- ns1:name <http://amr.isi.edu/amr_data/pmid_1177_7939.32#n3> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#f> a <https://verbs.colorado.edu/propbank#form-01> ;
- ns1:ARG0 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#a> ;
- ns1:ARG1 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#m> ;
- ns1:condition <http://amr.isi.edu/amr_data/pmid_1177_7939.32#o> ;
- ns1:manner <http://amr.isi.edu/amr_data/pmid_1177_7939.32#i> ;
- ns1:mod <http://amr.isi.edu/amr_data/pmid_1177_7939.32#p> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#i> a ns1:in-vivo .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#m> a <http://amr.isi.edu/entity-types#macro-molecular-complex> ;
- ns1:mod <http://amr.isi.edu/amr_data/pmid_1177_7939.32#t> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#n> a ns1:name ;
- ns1:op1 "Sos-1" .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#n2> a ns1:name ;
- ns1:op1 "E3b1" .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#n3> a ns1:name ;
- ns1:op1 "Eps8" .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#o> a <https://verbs.colorado.edu/propbank#overexpress-00> ;
- ns1:ARG2 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#a> ;
- ns1:manner <http://amr.isi.edu/amr_data/pmid_1177_7939.32#c> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#p> a ns1:possible .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#p2> a <http://amr.isi.edu/entity-types#protein> ;
- ns1:name <http://amr.isi.edu/amr_data/pmid_1177_7939.32#n> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#p3> a <http://amr.isi.edu/entity-types#protein> ;
- ns1:name <http://amr.isi.edu/amr_data/pmid_1177_7939.32#n2> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#p5> a ns1:previous .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#s2> a ns1:study ;
- ns1:time <http://amr.isi.edu/amr_data/pmid_1177_7939.32#p5> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#t> a ns1:trimeric .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#w> a ns1:we .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#a> a ns1:and ;
- ns1:op1 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#p2> ;
- ns1:op2 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#p3> ;
- ns1:op3 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#e2> .
-
-<http://amr.isi.edu/amr_data/pmid_1177_7939.32#s> a <https://verbs.colorado.edu/propbank#show-01> ;
- ns1:ARG0 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#w> ;
- ns1:ARG1 <http://amr.isi.edu/amr_data/pmid_1177_7939.32#f> ;
- ns1:TOP <http://amr.isi.edu/amr_data/pmid_1177_7939.32#s> ;
- ns1:medium <http://amr.isi.edu/amr_data/pmid_1177_7939.32#s2> .
-
diff --git a/amrbatch/amrld/test/pmid-11777939-32_amr.txt b/amrbatch/amrld/test/pmid-11777939-32_amr.txt
deleted file mode 100755
index d53255b7..00000000
--- a/amrbatch/amrld/test/pmid-11777939-32_amr.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# ::id pmid_1177_7939.32 ::date 2015-02-27T00:14:25 ::authors mrizea
-# ::snt In previous studies, we showed that Sos-1, E3b1, and Eps8 could form a trimeric complex in vivo upon concomitant overexpression of the three proteins.
-# ::note Sentence+ loaded by script SntLoaderUlf1.7.pl
-# ::save-date Wed Apr 1, 2015 ::user bbadarau ::file pmid_1177_7939_32.txt
-(s / show-01
- :ARG0 (w / we)
- :ARG1 (f / form-01
- :ARG0 (a / and
- :op1 (p2 / protein :name (n / name :op1 "Sos-1"))
- :op2 (p3 / protein :name (n2 / name :op1 "E3b1"))
- :op3 (e2 / enzyme :name (n3 / name :op1 "Eps8")))
- :ARG1 (m / macro-molecular-complex
- :mod (t / trimeric))
- :mod (p / possible)
- :manner (i / in-vivo)
- :condition (o / overexpress-00
- :ARG2 a
- :manner (c / concomitant)))
- :medium (s2 / study
- :time (p5 / previous)))
\ No newline at end of file
diff --git a/amrbatch/amrld/test/test.amr.graph b/amrbatch/amrld/test/test.amr.graph
deleted file mode 100644
index d374bd90..00000000
--- a/amrbatch/amrld/test/test.amr.graph
+++ /dev/null
@@ -1,12 +0,0 @@
-# ::id test-1
-# ::snt The sun is a star.
-(s / star
- :domain (s2 / sun))
-
-# ::id test-2
-# ::snt Earth is a planet.
-(p / planet
- :domain p
- :name (n / name
- :op1 "Earth"))
-
diff --git a/amrbatch/amrld/wk/__wk__.txt b/amrbatch/amrld/wk/__wk__.txt
new file mode 100644
index 00000000..8d1c8b69
--- /dev/null
+++ b/amrbatch/amrld/wk/__wk__.txt
@@ -0,0 +1 @@
+
diff --git a/amrbatch/amrld/wk/test-01.stog.amr.nt b/amrbatch/amrld/wk/test-01.stog.amr.nt
new file mode 100644
index 00000000..49251ca4
--- /dev/null
+++ b/amrbatch/amrld/wk/test-01.stog.amr.nt
@@ -0,0 +1,22 @@
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "The sun is a star." .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/amr_data/test-01#s> <http://amr.isi.edu/rdf/amr-terms#domain> <http://amr.isi.edu/amr_data/test-01#s2> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/entity-types#star> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-01" .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
+<http://amr.isi.edu/rdf/amr-terms#domain> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-01#s> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#star> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-01#s> .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-01#s2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/amr-terms#sun> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/rdf/amr-terms#sun> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+
diff --git a/amrbatch/amrld/wk/test-01.stog.amr.penman b/amrbatch/amrld/wk/test-01.stog.amr.penman
new file mode 100644
index 00000000..4f70746d
--- /dev/null
+++ b/amrbatch/amrld/wk/test-01.stog.amr.penman
@@ -0,0 +1,4 @@
+# ::id test-01
+# ::snt The sun is a star.
+(s / star
+ :domain (s2 / sun))
\ No newline at end of file
diff --git a/amrbatch/amrld/wk/test-02.stog.amr.nt b/amrbatch/amrld/wk/test-02.stog.amr.nt
new file mode 100644
index 00000000..92e70c98
--- /dev/null
+++ b/amrbatch/amrld/wk/test-02.stog.amr.nt
@@ -0,0 +1,19 @@
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/2000/01/rdf-schema#label> "Earth" .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-02#p> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/entity-types#planet> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#planet> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-02" .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "Earth is a planet." .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
+
diff --git a/amrbatch/amrld/wk/test-02.stog.amr.penman b/amrbatch/amrld/wk/test-02.stog.amr.penman
new file mode 100644
index 00000000..c43f2d1e
--- /dev/null
+++ b/amrbatch/amrld/wk/test-02.stog.amr.penman
@@ -0,0 +1,6 @@
+# ::id test-02
+# ::snt Earth is a planet.
+(p / planet
+ :domain p
+ :name (n / name
+ :op1 "Earth"))
\ No newline at end of file
diff --git a/amrbatch/filepath_manager.py b/amrbatch/filepath_manager.py
new file mode 100644
index 00000000..4075cff5
--- /dev/null
+++ b/amrbatch/filepath_manager.py
@@ -0,0 +1,112 @@
+#!/usr/bin/python3.10
+# -*-coding:Utf-8 -*
+
+#==============================================================================
+# AMR Batch: Filepath Manager
+#------------------------------------------------------------------------------
+# Handler to manage file paths.
+#==============================================================================
+
+import sys, os, glob
+import shutil
+
+# Reference Suffix
+TEXT_SUFFIX = ".txt"
+SENTENCE_SUFFIX = ".sentence.txt"
+PENMAN_AMR_GRAPH_SUFFIX = ".stog.amr.penman"
+DOT_AMR_GRAPH_SUFFIX = ".stog.amr.dot"
+PNG_AMR_GRAPH_SUFFIX = ".stog.amr.png"
+AMR_RDF_SUFFIX = ".stog.amr.nt"
+AMR_TTL_SUFFIX = ".stog.amr.ttl"
+
+# AMRLD Parameters
+LIB_PATH = os.path.dirname(os.path.abspath(__file__)) + '/'
+AMRLD_DIR = f'{LIB_PATH}amrld/'
+WK_DIR = 'wk/'
+AMRLD_WORKDIR = AMRLD_DIR + WK_DIR
+
+
+#==============================================================================
+# Class
+#==============================================================================
+
+class FilepathManager:
+ """ Class to handle filepaths.
+ """
+
+ #--------------------------------------------------------------------------
+ # Constructor
+ #--------------------------------------------------------------------------
+
+ def __init__(self, input_filepath, output_dirpath=None):
+
+ self.base_reference = os.path.splitext(os.path.basename(input_filepath))[0]
+
+ self.input_filepath = input_filepath
+ self.input_dirpath = os.path.dirname(input_filepath)
+
+ if output_dirpath is None:
+ self.output_dirpath = self._input_dirpath
+ else:
+ self.output_dirpath = output_dirpath
+
+
+ #--------------------------------------------------------------------------
+ # Filepath Accessors
+ #--------------------------------------------------------------------------
+
+ def get_workdata_output_dirpath(self, data_ref):
+ return f'{self.output_dirpath}{data_ref}/'
+
+ def get_sentence_output_filepath(self):
+ return f'{self.output_dirpath}{self.base_reference}{SENTENCE_SUFFIX}'
+
+ def get_data_output_filepath(self, data):
+ return f'{self.output_dirpath}{data["output_data_dir"]}'
+
+ def get_penman_amr_graph_output_filepath(self, data):
+ dirpath = self.get_data_output_filepath(data)
+ filename = f'{data["data_ref"]}{PENMAN_AMR_GRAPH_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_dot_amr_graph_output_filepath(self, data):
+ dirpath = self.get_data_output_filepath(data)
+ filename = f'{data["data_ref"]}{DOT_AMR_GRAPH_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_png_amr_graph_output_filepath(self, data):
+ dirpath = self.get_data_output_filepath(data)
+ filename = f'{data["data_ref"]}{PNG_AMR_GRAPH_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_rdf_triple_output_filepath(self, data):
+ dirpath = self.get_data_output_filepath(data)
+ filename = f'{data["data_ref"]}{AMR_RDF_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_rdf_turtle_output_filepath(self, data):
+ dirpath = self.get_data_output_filepath(data)
+ filename = f'{data["data_ref"]}{AMR_TTL_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_graph_amrld_filepath(self, data):
+ dirpath = f'{AMRLD_WORKDIR}'
+ filename = f'{data["data_ref"]}{PENMAN_AMR_GRAPH_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_rdf_amrld_filepath(self, data):
+ dirpath = f'{AMRLD_WORKDIR}'
+ filename = f'{data["data_ref"]}{AMR_RDF_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_graph_wk_filepath(self, data):
+ dirpath = f'{WK_DIR}'
+ filename = f'{data["data_ref"]}{PENMAN_AMR_GRAPH_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+ def get_amr_rdf_wk_filepath(self, data):
+ dirpath = f'{WK_DIR}'
+ filename = f'{data["data_ref"]}{AMR_RDF_SUFFIX}'
+ return f'{dirpath}{filename}'
+
+
diff --git a/amrbatch/logging.conf b/amrbatch/logging.conf
new file mode 100644
index 00000000..6006ebdb
--- /dev/null
+++ b/amrbatch/logging.conf
@@ -0,0 +1,39 @@
+[loggers]
+keys=root
+
+[handlers]
+keys=consoleSimpleHandler,consoleWarningHandler,fileHandler
+
+[formatters]
+keys=simpleFormat,warningFormat,fileFormat
+
+[logger_root]
+level=DEBUG
+handlers=consoleWarningHandler,consoleSimpleHandler,fileHandler
+
+[handler_consoleSimpleHandler]
+class=StreamHandler
+level=INFO
+formatter=simpleFormat
+args=(sys.stdout,)
+
+[handler_consoleWarningHandler]
+class=StreamHandler
+level=WARNING
+formatter=warningFormat
+args=(sys.stdout,)
+
+[handler_fileHandler]
+class=FileHandler
+level=DEBUG
+formatter=fileFormat
+args=('amrbatch.log', 'w+', 'utf8')
+
+[formatter_simpleFormat]
+format=%(message)s
+
+[formatter_warningFormat]
+format=%(asctime)s - %(levelname)s (%(name)s, %(lineno)d)
+
+[formatter_fileFormat]
+format= - %(levelname)s - %(message)s
diff --git a/amrbatch/main.py b/amrbatch/main.py
index a60a622b..336a0df2 100644
--- a/amrbatch/main.py
+++ b/amrbatch/main.py
@@ -8,39 +8,278 @@
#==============================================================================
import sys, os, glob
-import shutil
+import shutil, re
+import subprocess
+import amrlib
from rdflib import Graph
+import traceback
+import logging.config
+from amrlib.graph_processing.amr_plot import AMRPlot
+from filepath_manager import FilepathManager
+# -- Config File Path
+LIB_PATH = os.path.dirname(os.path.abspath(__file__)) + '/'
+LOGGING_CONF_FILE_PATH = f'{LIB_PATH}logging.conf'
+CONFIG_FILE_PATH = f'{LIB_PATH}config.xml'
+
+# AMRLD Parameters
+AMRLD_DIR = f'{LIB_PATH}amrld/'
+AMRLD_WORKDIR = f'{AMRLD_DIR}wk/'
+
+# -- Logging
+logging.config.fileConfig(LOGGING_CONF_FILE_PATH, disable_existing_loggers=True)
+logger = logging.getLogger('root')
+
+
+
+#==============================================================================
+# Functions to manage in-process data
+#==============================================================================
+
+def is_valid_sentence(sentence):
+ """ True if the sentence is correct.
+ """
+ is_empty = ((sentence == "") | (sentence == "\n"))
+ lang_mark_re = re.compile("\([a-z]+\)(.)*")
+ is_language_mark = lang_mark_re.match(sentence) is not None
+ return not (is_empty | is_language_mark)
+
+
+def clean_sentence(sentence):
+ """ Sentence cleanup as needed """
+ sentence = re.sub("(\.)*\\n", "", sentence)
+ return sentence
+
+
+def define_new_data(base_ref, number, sentence):
+
+ number_str = str(number).rjust(2,"0")
+ data_ref = base_ref + "-" + number_str
+ output_data_dir = data_ref + "/"
+ id_line_str = "# ::id " + data_ref + "\n"
+ sentence = clean_sentence(sentence)
+ sentence += "."
+
+ new_data = {
+ "base_ref" : data_ref,
+ "number" : number,
+ "output_data_dir" : output_data_dir,
+ "data_ref" : data_ref,
+ "id_line_str" : id_line_str,
+ "sentence" : sentence,
+ "graph" : ""
+ }
+ return new_data
+
+
+def get_amr_graph_list(workdata_list):
+ amr_graph_list = []
+ for workdata in workdata_list:
+ amr_graph_list.append(workdata['graph'])
+ return amr_graph_list
+
#==============================================================================
-# Steps
+# Preparation Steps
#==============================================================================
-# TODO
+def __prepare_workdata(filepath_manager):
+ logger.info('-- Reading input files to recover a list of sentences')
+ input_filepath = filepath_manager.input_filepath
+ base_reference = filepath_manager.base_reference
+
+ workdata_list = list()
+
+ sentence_number = 0
+ with open(input_filepath, "r") as reading_file: # r = read
+ for line in reading_file.readlines():
+ sentences = line.split(". ")
+ for sentence in sentences:
+ if is_valid_sentence(sentence):
+ sentence_number += 1
+ new_data = define_new_data(base_reference, sentence_number, sentence)
+ workdata_list.append(new_data)
+ logger.debug(f' *** sentence {sentence_number} *** \n{new_data}')
+
+ logger.info(f'----- number of sentences: {len(workdata_list)}')
+ return workdata_list
+
+
+def __build_output_dir_tree(filepath_manager, workdata_list):
+ base_output_dirpath = filepath_manager.output_dirpath
+ logger.debug(f'-- Making output directory tree ({base_output_dirpath})')
+ os.makedirs(base_output_dirpath, exist_ok=True)
+ for data in workdata_list:
+ output_dir = filepath_manager.get_workdata_output_dirpath(data["output_data_dir"])
+ os.makedirs(output_dir, exist_ok=True)
+
+
+def __generate_sentence_file(filepath_manager, workdata_list):
+ sentence_filepath = filepath_manager.get_sentence_output_filepath()
+ logger.debug(f"-- Generating sentence file ")
+ with open(sentence_filepath, "w") as writing_file: # w = write
+ first = True
+ for workdata in workdata_list:
+ if not first: writing_file.write("\n")
+ writing_file.write(workdata["sentence"])
+ first = False
+
+
#==============================================================================
-# AMR Main Methods
+# Conversion Steps
#==============================================================================
-def parse_sentences_from_file(input_file_path,
- output_penman_file_path=None,
- technical_dir_path=None):
+def __generate_penman_amr_graph(filepath_manager, data):
+ """ AMR graph generation in penman format """
+
+ graph = data["graph"]
+ output_filepath = filepath_manager.get_penman_amr_graph_output_filepath(data)
+ logger.debug(f"----- AMR Graph file (penman): {os.path.basename(output_filepath)}")
+ with open(output_filepath, "w") as writing_file: # w = write
+ writing_file.write(data["id_line_str"])
+ writing_file.write(graph)
+
+
+
+def __generate_dot_amr_graph(filepath_manager, data):
+ """ AMR graph generation in dot and png format """
+
+ graph = data["graph"]
+
+ try:
+ # -- generating dot/png files using AMRLib and GraphViz
+ dot_filename = filepath_manager.get_dot_amr_graph_output_filepath(data)
+ format = 'png'
+ logger.debug(f'----- AMR Graph file (dot): {os.path.basename(dot_filename)}')
+ plot = AMRPlot(dot_filename, format)
+ plot.build_from_graph(graph)
+ plot.graph.render()
+
+ render_fn = dot_filename + '.' + format # -- renaming PNG file
+ good_png_fn = filepath_manager.get_png_amr_graph_output_filepath(data)
+ logger.debug(f'----- AMR Graph file (png): {{os.path.basename(good_png_fn)}}')
+ os.rename(render_fn, good_png_fn)
+
+ except:
+ logger.warning('Exception when trying to plot')
+ traceback.print_exc()
+
+
+
+
+def __convert_sentences_to_graphs(amr_model, workdata_list):
+ """ Converting text sentences to AMR graphs """
+
+ logger.info("-- Loading AMR model")
+ stog = amrlib.load_stog_model(model_dir=amr_model)
+
+ logger.info("-- Converting sentences to AMR graphs")
+ wd_number = 0
+ for data in workdata_list:
+ wd_number += 1
+ stog_result = stog.parse_sents([data["sentence"]])
+ logger.info(f'----- Sentence {wd_number} successfully processed')
+ logger.debug(stog_result)
+ data["graph"] = stog_result[0]
+
+ logger.info(f'----- Total processed graph number: {wd_number}')
+ return workdata_list
+
+
+
+def __generate_amr_graph_files(filepath_manager, workdata_list):
+ logger.info("-- Generating AMR graph files")
+ for data in workdata_list:
+ __generate_penman_amr_graph(filepath_manager, data)
+ __generate_dot_amr_graph(filepath_manager, data)
+
+
+
+#==============================================================================
+# Serialization Steps
+#==============================================================================
+
+def __serialize_amr_graph_to_rdf_triple(filepath_manager, data):
+ """ Serialize AMR graph to AMR-RDF triple """
+
+ # -- Filepath
+ input_file = filepath_manager.get_penman_amr_graph_output_filepath(data)
+ input_amrld_file = filepath_manager.get_amr_graph_amrld_filepath(data)
+ output_amrld_file = filepath_manager.get_amr_rdf_amrld_filepath(data)
+ input_wk_file = filepath_manager.get_amr_graph_wk_filepath(data)
+ output_wk_file = filepath_manager.get_amr_rdf_wk_filepath(data)
+ amr_triple_file = filepath_manager.get_amr_rdf_triple_output_filepath(data)
+
+ # -- AMR-LD processing
+ amrld_process = ["python3", "amr_to_rdf.py",
+ "-i", input_wk_file,
+ "-o", output_wk_file]
+ if (os.path.isfile(input_file)):
+ logger.info("-- Serialize AMR graphs to RDF using amr-ld library")
+ logger.debug(f'----- penman filepath: {input_file}')
+ logger.debug(f'----- AMRLD filepath: {input_amrld_file}')
+ shutil.copyfile(input_file, input_amrld_file)
+ current_dirpath = os.getcwd()
+ os.chdir(AMRLD_DIR)
+ subprocess.run(amrld_process)
+ os.chdir(current_dirpath)
+
+ # -- Copy result
+ if (os.path.isfile(output_amrld_file)):
+ logger.info(f'-- Generating AMR RDF file (triple): {os.path.basename(amr_triple_file)}')
+ shutil.copyfile(output_amrld_file, amr_triple_file)
+
+
+def __convert_rdf_triple_to_rdf_turtle(filepath_manager, data):
+ """ Converting AMR-RDF triple to AMR-RDF turtle """
+
+ # -- Filepath
+ amr_triple_file = filepath_manager.get_amr_rdf_triple_output_filepath(data)
+ amr_turtle_file = filepath_manager.get_amr_rdf_turtle_output_filepath(data)
+
+ # -- Conversion
+ if (os.path.isfile(amr_triple_file)):
+ logger.info(f'-- Generating AMR RDF file (turtle): {os.path.basename(amr_turtle_file)}')
+ g = Graph()
+ g.parse(amr_triple_file)
+ g.serialize(destination=amr_turtle_file, format='turtle')
+
+
+
+def __convert_amr_graphs_to_rdf(filepath_manager, data_list):
+ """ Converting AMR graphs to AMR-RDF """
+
+ for data in data_list:
+ __serialize_amr_graph_to_rdf_triple(filepath_manager, data)
+ __convert_rdf_triple_to_rdf_turtle(filepath_manager, data)
+
+
+
+#==============================================================================
+# Main Method(s)
+#==============================================================================
+
+def parse_sentences_from_file(input_filepath,
+ amr_model_path,
+ output_dirpath=None,
+ amrld_serialization=False):
"""
Method to parse an input file containing natural language sentences and
construct the corresponding AMR graphs (and their RDF serializations if required).
The method returns an AMR graph string in PENMAN format. AMR graphs are also
- serialized in RDF turtle format using the AMR-LD library if requested
- (by defining output_turtle_file_path as a parameter).
+ serialized in RDF turtle format using the AMR-LD library if required
+ (by defining turtle_output_file_path as parameter).
Parameters
----------
- input_file_path: a path to a text file.
- output_penman_file_path: a file path where the output graphs is written in PENMAN format if defined (the function still outputs the string).
- output_turtle_file_path: a file path where the output AMRLD representation is written in TURTLE format if defined.
+ input_filepath: a path to a text file.
+ output_dirpath: a directory path where the output data are written if defined (the function still outputs the string).
+ turtle_output_file_path: a file path where the output AMRLD representation is written in TURTLE format if defined.
technical_dir_path: a dir path where some technical and log files are written if defined.
Returns
@@ -49,7 +288,35 @@ def parse_sentences_from_file(input_file_path,
"""
- pass
+ logger.info('[AMR Batch] NL Document Parsing')
+
+ # -- Prepare the sentences to be converted
+ logger.info('\n === Preparation === ')
+ filepath_manager = FilepathManager(input_filepath, output_dirpath)
+ logger.info(f'-- base reference: {filepath_manager.base_reference}')
+ logger.info(f'-- input filepath: {filepath_manager.input_filepath}')
+ logger.info(f'-- output dirpath: {filepath_manager.output_dirpath}')
+ assert os.path.exists(input_filepath), f'input file does not exists ({input_filepath})'
+ workdata_list = __prepare_workdata(filepath_manager)
+ __build_output_dir_tree(filepath_manager, workdata_list)
+ __generate_sentence_file(filepath_manager, workdata_list)
+
+ # -- Convert sentences to graphs
+ logger.info('\n === Text Convert to AMR Graphs === ')
+ logger.info(f'-- library: amrlib')
+ logger.debug(f' ({AMRLD_DIR})')
+ logger.info(f'-- model: {os.path.basename(amr_model_path)}')
+ logger.debug(f' ({amr_model_path})')
+ logger.debug(f'-- working directory: {AMRLD_WORKDIR}')
+ workdata_list = __convert_sentences_to_graphs(amr_model_path, workdata_list)
+ __generate_amr_graph_files(filepath_manager, workdata_list)
+
+ if amrld_serialization==True:
+ # -- Convert graphs to RDF
+ logger.info('\n === AMR Graphs Serialization to AMR-RDF Representation === ')
+ logger.info("-- library: amrlk")
+ __convert_amr_graphs_to_rdf(filepath_manager, workdata_list)
+
- return ''
+ return get_amr_graph_list(workdata_list)
diff --git a/tests/amrbatch.log b/tests/amrbatch.log
new file mode 100644
index 00000000..1c35a300
--- /dev/null
+++ b/tests/amrbatch.log
@@ -0,0 +1,48 @@
+- INFO - [AMR Batch] NL Document Parsing
+- INFO -
+ === Preparation ===
+- INFO - -- base reference: test
+- INFO - -- input filepath: /home/lamenji/Workspace/Tetras/amrbatch/tests/input/test.txt
+- INFO - -- output dirpath: /home/lamenji/Workspace/Tetras/amrbatch/tests/output/Test-20230303/
+- INFO - -- Reading input files to recover a list of sentences
+- DEBUG - *** sentence 1 ***
+{'base_ref': 'test-01', 'number': 1, 'output_data_dir': 'test-01/', 'data_ref': 'test-01', 'id_line_str': '# ::id test-01\n', 'sentence': 'The sun is a star.', 'graph': ''}
+- DEBUG - *** sentence 2 ***
+{'base_ref': 'test-02', 'number': 2, 'output_data_dir': 'test-02/', 'data_ref': 'test-02', 'id_line_str': '# ::id test-02\n', 'sentence': 'Earth is a planet.', 'graph': ''}
+- INFO - ----- number of sentences: 2
+- DEBUG - -- Making output directory tree (/home/lamenji/Workspace/Tetras/amrbatch/tests/output/Test-20230303/)
+- DEBUG - -- Generating sentence file
+- INFO -
+ === Text Convert to AMR Graphs ===
+- INFO - -- library: amrlib
+- DEBUG - (/home/lamenji/Workspace/Tetras/amrbatch/amrbatch/amrld/)
+- INFO - -- model: model_parse_xfm_bart_large-v0_1_0
+- DEBUG - (/home/lamenji/Workspace/Tetras/amrbatch/tests/../amr_models/model_parse_xfm_bart_large-v0_1_0)
+- DEBUG - -- working directory: /home/lamenji/Workspace/Tetras/amrbatch/amrbatch/amrld/wk/
+- INFO - -- Loading AMR model
+- INFO - -- Converting sentences to AMR graphs
+- INFO - ----- Sentence 1 successfully processed
+- DEBUG - ['# ::snt The sun is a star.\n(s / star\n :domain (s2 / sun))']
+- INFO - ----- Sentence 2 successfully processed
+- DEBUG - ['# ::snt Earth is a planet.\n(p / planet\n :domain p\n :name (n / name\n :op1 "Earth"))']
+- INFO - ----- Total processed graph number: 2
+- INFO - -- Generating AMR graph files
+- DEBUG - ----- AMR Graph file (penman): test-01.stog.amr.penman
+- DEBUG - ----- AMR Graph file (dot): test-01.stog.amr.dot
+- DEBUG - ----- AMR Graph file (png): {os.path.basename(good_png_fn)}
+- DEBUG - ----- AMR Graph file (penman): test-02.stog.amr.penman
+- DEBUG - ----- AMR Graph file (dot): test-02.stog.amr.dot
+- DEBUG - ----- AMR Graph file (png): {os.path.basename(good_png_fn)}
+- INFO -
+ === AMR Graphs Serialization to AMR-RDF Representation ===
+- INFO - -- library: amrlk
+- INFO - -- Serialize AMR graphs to RDF using amr-ld library
+- DEBUG - ----- penman filepath: /home/lamenji/Workspace/Tetras/amrbatch/tests/output/Test-20230303/test-01/test-01.stog.amr.penman
+- DEBUG - ----- AMRLD filepath: /home/lamenji/Workspace/Tetras/amrbatch/amrbatch/amrld/wk/test-01.stog.amr.penman
+- INFO - -- Generating AMR RDF file (triple): test-01.stog.amr.nt
+- INFO - -- Generating AMR RDF file (turtle): test-01.stog.amr.ttl
+- INFO - -- Serialize AMR graphs to RDF using amr-ld library
+- DEBUG - ----- penman filepath: /home/lamenji/Workspace/Tetras/amrbatch/tests/output/Test-20230303/test-02/test-02.stog.amr.penman
+- DEBUG - ----- AMRLD filepath: /home/lamenji/Workspace/Tetras/amrbatch/amrbatch/amrld/wk/test-02.stog.amr.penman
+- INFO - -- Generating AMR RDF file (triple): test-02.stog.amr.nt
+- INFO - -- Generating AMR RDF file (turtle): test-02.stog.amr.ttl
diff --git a/tests/output/Test-20230302/test-01/test-01.stog.amr.dot b/tests/output/Test-20230302/test-01/test-01.stog.amr.dot
new file mode 100644
index 00000000..57af6466
--- /dev/null
+++ b/tests/output/Test-20230302/test-01/test-01.stog.amr.dot
@@ -0,0 +1,6 @@
+digraph amr_graph {
+ rankdir=LR size="12,8"
+ s [label="s/star" shape=circle]
+ s2 [label="s2/sun" shape=circle]
+ s -> s2 [label=":domain"]
+}
diff --git a/tests/output/Test-20230302/test-01/test-01.stog.amr.nt b/tests/output/Test-20230302/test-01/test-01.stog.amr.nt
new file mode 100644
index 00000000..6ebc9919
--- /dev/null
+++ b/tests/output/Test-20230302/test-01/test-01.stog.amr.nt
@@ -0,0 +1,21 @@
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/entity-types#star> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/amr-terms#sun> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "The sun is a star." .
+<http://amr.isi.edu/amr_data/test-01#s2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/amr-terms#sun> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/amr_data/test-01#s> <http://amr.isi.edu/rdf/amr-terms#domain> <http://amr.isi.edu/amr_data/test-01#s2> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/amr-terms#domain> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/amr_data/test-01#s> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#star> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-01" .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-01#s> .
diff --git a/tests/output/Test-20230302/test-01/test-01.stog.amr.penman b/tests/output/Test-20230302/test-01/test-01.stog.amr.penman
new file mode 100644
index 00000000..4f70746d
--- /dev/null
+++ b/tests/output/Test-20230302/test-01/test-01.stog.amr.penman
@@ -0,0 +1,4 @@
+# ::id test-01
+# ::snt The sun is a star.
+(s / star
+ :domain (s2 / sun))
\ No newline at end of file
diff --git a/tests/output/Test-20230302/test-01/test-01.stog.amr.png b/tests/output/Test-20230302/test-01/test-01.stog.amr.png
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diff --git a/tests/output/Test-20230302/test-01/test-01.stog.amr.ttl b/tests/output/Test-20230302/test-01/test-01.stog.amr.ttl
new file mode 100644
index 00000000..4ad04c79
--- /dev/null
+++ b/tests/output/Test-20230302/test-01/test-01.stog.amr.ttl
@@ -0,0 +1,36 @@
+@prefix ns1: <http://amr.isi.edu/rdf/core-amr#> .
+@prefix ns2: <http://amr.isi.edu/rdf/amr-terms#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+ns1:Concept a rdfs:Class ;
+ rdfs:label "AMR-Concept" .
+
+ns1:Role a rdfs:Class ;
+ rdfs:label "AMR-Role" .
+
+<http://amr.isi.edu/amr_data/test-01#root01> a ns1:AMR ;
+ ns1:has-id "test-01" ;
+ ns1:has-sentence "The sun is a star." ;
+ ns1:root <http://amr.isi.edu/amr_data/test-01#s> .
+
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> a ns1:Role ;
+ rdfs:label "AMR-PropBank-Role" .
+
+ns2:domain a ns1:Role .
+
+ns1:Frame a ns1:Concept ;
+ rdfs:label "AMR-PropBank-Frame" .
+
+<http://amr.isi.edu/amr_data/test-01#s> a <http://amr.isi.edu/entity-types#star> ;
+ ns2:domain <http://amr.isi.edu/amr_data/test-01#s2> .
+
+<http://amr.isi.edu/amr_data/test-01#s2> a ns2:sun .
+
+<http://amr.isi.edu/entity-types#star> a ns1:NamedEntity .
+
+ns2:sun a ns1:Concept .
+
+ns1:NamedEntity a ns1:Concept ;
+ rdfs:label "AMR-EntityType",
+ "AMR-Term" .
+
diff --git a/tests/output/Test-20230302/test-02/test-02.stog.amr.dot b/tests/output/Test-20230302/test-02/test-02.stog.amr.dot
new file mode 100644
index 00000000..1b8f97f7
--- /dev/null
+++ b/tests/output/Test-20230302/test-02/test-02.stog.amr.dot
@@ -0,0 +1,9 @@
+digraph amr_graph {
+ rankdir=LR size="12,8"
+ p [label="p/planet" shape=circle]
+ n [label="n/name" shape=circle]
+ p -> p [label=":domain"]
+ p -> n [label=":name"]
+ node_0 [label="\"Earth\"" shape=rectangle]
+ n -> node_0 [label=":op1"]
+}
diff --git a/tests/output/Test-20230302/test-02/test-02.stog.amr.nt b/tests/output/Test-20230302/test-02/test-02.stog.amr.nt
new file mode 100644
index 00000000..2cdb95fe
--- /dev/null
+++ b/tests/output/Test-20230302/test-02/test-02.stog.amr.nt
@@ -0,0 +1,18 @@
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-02" .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-02#p> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#planet> .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/2000/01/rdf-schema#label> "Earth" .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+<http://amr.isi.edu/entity-types#planet> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "Earth is a planet." .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
diff --git a/tests/output/Test-20230302/test-02/test-02.stog.amr.penman b/tests/output/Test-20230302/test-02/test-02.stog.amr.penman
new file mode 100644
index 00000000..c43f2d1e
--- /dev/null
+++ b/tests/output/Test-20230302/test-02/test-02.stog.amr.penman
@@ -0,0 +1,6 @@
+# ::id test-02
+# ::snt Earth is a planet.
+(p / planet
+ :domain p
+ :name (n / name
+ :op1 "Earth"))
\ No newline at end of file
diff --git a/tests/output/Test-20230302/test-02/test-02.stog.amr.png b/tests/output/Test-20230302/test-02/test-02.stog.amr.png
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diff --git a/tests/output/Test-20230302/test-02/test-02.stog.amr.ttl b/tests/output/Test-20230302/test-02/test-02.stog.amr.ttl
new file mode 100644
index 00000000..5f7d3d7f
--- /dev/null
+++ b/tests/output/Test-20230302/test-02/test-02.stog.amr.ttl
@@ -0,0 +1,29 @@
+@prefix ns1: <http://amr.isi.edu/rdf/core-amr#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+ns1:Concept a rdfs:Class ;
+ rdfs:label "AMR-Concept" .
+
+ns1:Role a rdfs:Class ;
+ rdfs:label "AMR-Role" .
+
+<http://amr.isi.edu/amr_data/test-02#root01> a ns1:AMR ;
+ ns1:has-id "test-02" ;
+ ns1:has-sentence "Earth is a planet." ;
+ ns1:root <http://amr.isi.edu/amr_data/test-02#p> .
+
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> a ns1:Role ;
+ rdfs:label "AMR-PropBank-Role" .
+
+ns1:Frame a ns1:Concept ;
+ rdfs:label "AMR-PropBank-Frame" .
+
+<http://amr.isi.edu/amr_data/test-02#p> a <http://amr.isi.edu/entity-types#planet> ;
+ rdfs:label "Earth" .
+
+<http://amr.isi.edu/entity-types#planet> a ns1:NamedEntity .
+
+ns1:NamedEntity a ns1:Concept ;
+ rdfs:label "AMR-EntityType",
+ "AMR-Term" .
+
diff --git a/tests/output/Test-20230302/test.sentence.txt b/tests/output/Test-20230302/test.sentence.txt
new file mode 100644
index 00000000..2bc85c3e
--- /dev/null
+++ b/tests/output/Test-20230302/test.sentence.txt
@@ -0,0 +1,2 @@
+The sun is a star.
+Earth is a planet.
\ No newline at end of file
diff --git a/tests/output/Test-20230303/test-01/test-01.stog.amr.dot b/tests/output/Test-20230303/test-01/test-01.stog.amr.dot
new file mode 100644
index 00000000..57af6466
--- /dev/null
+++ b/tests/output/Test-20230303/test-01/test-01.stog.amr.dot
@@ -0,0 +1,6 @@
+digraph amr_graph {
+ rankdir=LR size="12,8"
+ s [label="s/star" shape=circle]
+ s2 [label="s2/sun" shape=circle]
+ s -> s2 [label=":domain"]
+}
diff --git a/tests/output/Test-20230303/test-01/test-01.stog.amr.nt b/tests/output/Test-20230303/test-01/test-01.stog.amr.nt
new file mode 100644
index 00000000..49251ca4
--- /dev/null
+++ b/tests/output/Test-20230303/test-01/test-01.stog.amr.nt
@@ -0,0 +1,22 @@
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "The sun is a star." .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/amr_data/test-01#s> <http://amr.isi.edu/rdf/amr-terms#domain> <http://amr.isi.edu/amr_data/test-01#s2> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/entity-types#star> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-01" .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
+<http://amr.isi.edu/rdf/amr-terms#domain> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-01#s> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#star> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-01#s> .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-01#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-01#s2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/amr-terms#sun> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/rdf/amr-terms#sun> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+
diff --git a/tests/output/Test-20230303/test-01/test-01.stog.amr.penman b/tests/output/Test-20230303/test-01/test-01.stog.amr.penman
new file mode 100644
index 00000000..4f70746d
--- /dev/null
+++ b/tests/output/Test-20230303/test-01/test-01.stog.amr.penman
@@ -0,0 +1,4 @@
+# ::id test-01
+# ::snt The sun is a star.
+(s / star
+ :domain (s2 / sun))
\ No newline at end of file
diff --git a/tests/output/Test-20230303/test-01/test-01.stog.amr.png b/tests/output/Test-20230303/test-01/test-01.stog.amr.png
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diff --git a/tests/output/Test-20230303/test-01/test-01.stog.amr.ttl b/tests/output/Test-20230303/test-01/test-01.stog.amr.ttl
new file mode 100644
index 00000000..4ad04c79
--- /dev/null
+++ b/tests/output/Test-20230303/test-01/test-01.stog.amr.ttl
@@ -0,0 +1,36 @@
+@prefix ns1: <http://amr.isi.edu/rdf/core-amr#> .
+@prefix ns2: <http://amr.isi.edu/rdf/amr-terms#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+ns1:Concept a rdfs:Class ;
+ rdfs:label "AMR-Concept" .
+
+ns1:Role a rdfs:Class ;
+ rdfs:label "AMR-Role" .
+
+<http://amr.isi.edu/amr_data/test-01#root01> a ns1:AMR ;
+ ns1:has-id "test-01" ;
+ ns1:has-sentence "The sun is a star." ;
+ ns1:root <http://amr.isi.edu/amr_data/test-01#s> .
+
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> a ns1:Role ;
+ rdfs:label "AMR-PropBank-Role" .
+
+ns2:domain a ns1:Role .
+
+ns1:Frame a ns1:Concept ;
+ rdfs:label "AMR-PropBank-Frame" .
+
+<http://amr.isi.edu/amr_data/test-01#s> a <http://amr.isi.edu/entity-types#star> ;
+ ns2:domain <http://amr.isi.edu/amr_data/test-01#s2> .
+
+<http://amr.isi.edu/amr_data/test-01#s2> a ns2:sun .
+
+<http://amr.isi.edu/entity-types#star> a ns1:NamedEntity .
+
+ns2:sun a ns1:Concept .
+
+ns1:NamedEntity a ns1:Concept ;
+ rdfs:label "AMR-EntityType",
+ "AMR-Term" .
+
diff --git a/tests/output/Test-20230303/test-02/test-02.stog.amr.dot b/tests/output/Test-20230303/test-02/test-02.stog.amr.dot
new file mode 100644
index 00000000..1b8f97f7
--- /dev/null
+++ b/tests/output/Test-20230303/test-02/test-02.stog.amr.dot
@@ -0,0 +1,9 @@
+digraph amr_graph {
+ rankdir=LR size="12,8"
+ p [label="p/planet" shape=circle]
+ n [label="n/name" shape=circle]
+ p -> p [label=":domain"]
+ p -> n [label=":name"]
+ node_0 [label="\"Earth\"" shape=rectangle]
+ n -> node_0 [label=":op1"]
+}
diff --git a/tests/output/Test-20230303/test-02/test-02.stog.amr.nt b/tests/output/Test-20230303/test-02/test-02.stog.amr.nt
new file mode 100644
index 00000000..92e70c98
--- /dev/null
+++ b/tests/output/Test-20230303/test-02/test-02.stog.amr.nt
@@ -0,0 +1,19 @@
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Term" .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#AMR> .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/2000/01/rdf-schema#label> "Earth" .
+<http://amr.isi.edu/rdf/core-amr#Concept> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Concept" .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#root> <http://amr.isi.edu/amr_data/test-02#p> .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Role> .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-Role" .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#Concept> .
+<http://amr.isi.edu/entity-types#planet> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/rdf/core-amr#NamedEntity> .
+<http://amr.isi.edu/amr_data/test-02#p> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://amr.isi.edu/entity-types#planet> .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-id> "test-02" .
+<http://amr.isi.edu/amr_data/test-02#root01> <http://amr.isi.edu/rdf/core-amr#has-sentence> "Earth is a planet." .
+<http://amr.isi.edu/rdf/core-amr#Frame> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Frame" .
+<http://amr.isi.edu/rdf/core-amr#Role> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2000/01/rdf-schema#Class> .
+<http://amr.isi.edu/rdf/core-amr#NamedEntity> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-EntityType" .
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> <http://www.w3.org/2000/01/rdf-schema#label> "AMR-PropBank-Role" .
+
diff --git a/tests/output/Test-20230303/test-02/test-02.stog.amr.penman b/tests/output/Test-20230303/test-02/test-02.stog.amr.penman
new file mode 100644
index 00000000..c43f2d1e
--- /dev/null
+++ b/tests/output/Test-20230303/test-02/test-02.stog.amr.penman
@@ -0,0 +1,6 @@
+# ::id test-02
+# ::snt Earth is a planet.
+(p / planet
+ :domain p
+ :name (n / name
+ :op1 "Earth"))
\ No newline at end of file
diff --git a/tests/output/Test-20230303/test-02/test-02.stog.amr.png b/tests/output/Test-20230303/test-02/test-02.stog.amr.png
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diff --git a/tests/output/Test-20230303/test-02/test-02.stog.amr.ttl b/tests/output/Test-20230303/test-02/test-02.stog.amr.ttl
new file mode 100644
index 00000000..5f7d3d7f
--- /dev/null
+++ b/tests/output/Test-20230303/test-02/test-02.stog.amr.ttl
@@ -0,0 +1,29 @@
+@prefix ns1: <http://amr.isi.edu/rdf/core-amr#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+ns1:Concept a rdfs:Class ;
+ rdfs:label "AMR-Concept" .
+
+ns1:Role a rdfs:Class ;
+ rdfs:label "AMR-Role" .
+
+<http://amr.isi.edu/amr_data/test-02#root01> a ns1:AMR ;
+ ns1:has-id "test-02" ;
+ ns1:has-sentence "Earth is a planet." ;
+ ns1:root <http://amr.isi.edu/amr_data/test-02#p> .
+
+<http://amr.isi.edu/frames/ld/v1.2.2/FrameRole> a ns1:Role ;
+ rdfs:label "AMR-PropBank-Role" .
+
+ns1:Frame a ns1:Concept ;
+ rdfs:label "AMR-PropBank-Frame" .
+
+<http://amr.isi.edu/amr_data/test-02#p> a <http://amr.isi.edu/entity-types#planet> ;
+ rdfs:label "Earth" .
+
+<http://amr.isi.edu/entity-types#planet> a ns1:NamedEntity .
+
+ns1:NamedEntity a ns1:Concept ;
+ rdfs:label "AMR-EntityType",
+ "AMR-Term" .
+
diff --git a/tests/output/Test-20230303/test.sentence.txt b/tests/output/Test-20230303/test.sentence.txt
new file mode 100644
index 00000000..2bc85c3e
--- /dev/null
+++ b/tests/output/Test-20230303/test.sentence.txt
@@ -0,0 +1,2 @@
+The sun is a star.
+Earth is a planet.
\ No newline at end of file
diff --git a/tests/test_amrbatch_main.py b/tests/test_amrbatch_main.py
index f5d67831..5da50414 100644
--- a/tests/test_amrbatch_main.py
+++ b/tests/test_amrbatch_main.py
@@ -10,9 +10,10 @@
import subprocess, os
from datetime import datetime
-FILE_PATH = f'{os.path.dirname(os.path.abspath(__file__))}'
-INPUT_DIR_PATH = f'{FILE_PATH}/input/'
-OUTPUT_DIR_PATH = f'{FILE_PATH}/output/'
+TESTS_PATH = f'{os.path.dirname(os.path.abspath(__file__))}'
+INPUT_DIR_PATH = f'{TESTS_PATH}/input/'
+OUTPUT_DIR_PATH = f'{TESTS_PATH}/output/'
+AMR_MODEL_PATH = f'{TESTS_PATH}/../amr_models/model_parse_xfm_bart_large-v0_1_0'
from context import amrbatch
@@ -23,14 +24,15 @@ from context import amrbatch
#==============================================================================
# -- Input Data
-amrld_file_path = f'{INPUT_DIR_PATH}test.txt'
+input_filename = f'test.txt'
+input_filepath = f'{INPUT_DIR_PATH}{input_filename}'
# -- Output references
base_output_name = f'Test'
time_ref = f'{datetime.now().strftime("%Y%m%d")}'
-out_dir_path = f'{OUTPUT_DIR_PATH}{base_output_name}-{time_ref}/'
-os.makedirs(out_dir_path, exist_ok=True)
+output_dirpath = f'{OUTPUT_DIR_PATH}{base_output_name}-{time_ref}/'
+os.makedirs(output_dirpath, exist_ok=True)
penman_output_file = f'{base_output_name}.pnm'
turtle_output_file = f'{base_output_name}.ttl'
@@ -41,5 +43,10 @@ turtle_output_file = f'{base_output_name}.ttl'
#==============================================================================
# -- Parsing from a file
-amrbatch.parsing_sentences_from_file(
- input_file_path, penman_output_file=None, turtle_output_file=None)
+amr_graph_list = amrbatch.parse_sentences_from_file(
+ input_filepath, amr_model_path=AMR_MODEL_PATH,
+ output_dirpath=output_dirpath, amrld_serialization=True)
+
+print(f'\n *** TEST RESULT ***')
+for amr_graph in amr_graph_list:
+ print(f'\n{amr_graph}')
\ No newline at end of file
--
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