Add support for SBOL3 via SBOL-Converter

.gitignore

@@ -7,4 +7,5 @@ src/work/*
 sbol-validator/*
 *.bat
 src/DEPLOY_SECRET
-.DS_Store
+.DS_Store
+.venv

README.md

@@ -1,10 +1,13 @@
 # SBOL Validator
 [![Build Status](https://travis-ci.org/SynBioDex/SBOL-Validator.svg?branch=master)](https://travis-ci.org/SynBioDex/SBOL-Validator)  
-A web-based validator for SBOL files backed by libSBOLj's validation runtimes. This validator offers support for SBOL2, SBOL1.1, and GenBank.
+A web-based validator for SBOL files backed by the [SBOL-Converter](https://github.com/SynBioDex/SBOL-Converter), which bundles libSBOLj (SBOL2) and libSBOLj3 (SBOL3). This validator offers support for SBOL3, SBOL2, SBOL1.1, GenBank, FASTA, and GFF3, including conversion between them.
 Furthermore, it is accessible through a web GUI or a RESTful API. 
 
 The validator can be found [here](https://validator.sbolstandard.org) with an API endpoint found at `https://validator.sbolstandard.org/validate`.
 
+### Validation engine
+The backend shells out to `src/sbol-converter.jar`, the `jar-with-dependencies` build of the [SBOL-Converter](https://github.com/SynBioDex/SBOL-Converter) (which bundles libSBOLj and libSBOLj3). To update it, download the latest `sbol-converter-*-jar-with-dependencies.jar` asset from the [SBOL-Converter releases](https://github.com/SynBioDex/SBOL-Converter/releases) and replace `src/sbol-converter.jar`. A Java 21+ runtime is required.
+
 ### Installation
 First, bit about the way the application is structured.
 There are two main parts:

docker/converter.Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.9-alpine
 
-RUN apk add nginx openjdk17-jre python3-dev build-base linux-headers pcre-dev bash
+RUN apk add nginx openjdk21-jre python3-dev build-base linux-headers pcre-dev bash
 
 WORKDIR /opt/SBOL-Validator
 

docker/validator.Dockerfile

@@ -1,6 +1,6 @@
 FROM python:3.9-alpine
 
-RUN apk add nginx openjdk17-jre python3-dev build-base linux-headers pcre-dev bash
+RUN apk add nginx openjdk21-jre python3-dev build-base linux-headers pcre-dev bash
 
 WORKDIR /opt/SBOL-Validator
 

src/conversion-form/html/form.html

@@ -71,16 +71,13 @@ <h3 class="panel-title">
 									</h3>
 							</div>
 							<div class="panel-body">
-								<div
-                                                                  class="form-group" id="fileOptions">
-                                                                        <!--
+								<div class="form-group" id="fileOptions">
 									<div class="radio">
 										<label>
 											<input type="radio" name="output" value="SBOL3" id="sbol32" /> Output SBOL 3
 											<br />
 										</label>
-                                                                        </div>
-                                                                        -->
+									</div>
 									<div class="radio">
 										<label>
 											<input type="radio" name="output" value="SBOL2" id="sbol20" checked="checked" /> Output SBOL 2

src/validation-form/html/form.html

@@ -91,13 +91,12 @@ <h3 class="panel-title">
 							</div>
 							<div class="panel-body">
 								<div class="form-group" id="fileOptions">
-									<!-- <div class="radio">
+									<div class="radio">
 										<label>
 											<input type="radio" name="output" value="SBOL3" id="sbol32" /> Output SBOL 3
 											<br />
 										</label>
 									</div>
-                                                                        -->
 									<div class="radio">
 										<label>
 											<input type="radio" name="output" value="SBOL2" id="sbol20" checked="checked" /> Output SBOL 2

src/validator/validator.py

@@ -17,14 +17,24 @@
 logger = logging.getLogger(__name__)
 
 class ValidationResult:
+    # Status lines the SBOL-Converter prints that are not validation errors and should
+    # not surface to the user (e.g. among a comparison's differences).
+    STATUS_LINES = frozenset([
+        "Validation successful, no errors.",
+        "Either Validate or Convert to/from SBOL2",
+    ])
+
     def __init__(self, output_file, equality):
         self.check_equality = equality
         self.output_file = output_file
         self.valid = False
         self.errors = []
 
     def digest_errors(self, output):
-        self.errors = output.strip().split('\n')
+        self.errors = [
+            line for line in output.strip().split('\n')
+            if line.strip() and line.strip() not in self.STATUS_LINES
+        ]
 
     def decipher(self, output, options):
         if self.check_equality:
@@ -33,16 +43,24 @@ def decipher(self, output, options):
             else:
                 self.equal = True
 
-        if "Validation successful, no errors." not in output:
-            self.valid = False
+        succeeded = "Validation successful, no errors." in output
+
+        # The SBOL-Converter is silent on a successful conversion (e.g. SBOL2<->SBOL3)
+        # and exits non-zero on any error, so reaching this point with a written
+        # output file signals success even without the validation message.
+        if not succeeded and options.return_file:
+            succeeded = os.path.exists(options.output_file) and os.path.getsize(options.output_file) > 0
+
+        if succeeded:
             self.digest_errors(output)
-        else:
-            self.digest_errors(output.strip(u"Validation successful, no errors."))
             self.valid = True
 
-            if options.return_file:
+            if options.return_file and os.path.exists(options.output_file):
                 with open(options.output_file, 'r') as file:
                     self.result = file.read()
+        else:
+            self.valid = False
+            self.digest_errors(output)
 
     def broken_validation_request(self, command):
         self.valid = False
@@ -62,14 +80,15 @@ def execute(self):
 
 	    # Attempt to run command
         try:
-            command = self.options.command("libSBOLj.jar", self.validation_file, self.diff_file)
+            command = self.options.command("sbol-converter.jar", self.validation_file, self.diff_file)
             logger.info("Running command: %s", " ".join(command))
-            output = subprocess.check_output(command, universal_newlines=True, stderr=subprocess.STDOUT)
+            try:
+                output = subprocess.check_output(command, universal_newlines=True, stderr=subprocess.STDOUT)
+            except subprocess.CalledProcessError as exception:
+                # The SBOL-Converter exits non-zero both for an invalid document and when a
+                # comparison finds differences; decipher classifies each from the output.
+                output = exception.output
             result.decipher(output, self.options)
-        except subprocess.CalledProcessError as exception:
-            #If the command fails, the file is not valid.
-            result.valid = False
-            result.errors += [exception.output, ]
         except ValueError as ve:
             print(traceback.print_tb(ve.__traceback__))
             result.broken_validation_request(command)