Merge pull request #153 from SynBioDex/revert-152-marpaia/sbol3

Revert "Add support for SBOL3 via SBOL-Converter"

Author: cjmyers

.gitignore

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

README.md

@@ -1,13 +1,10 @@
 # 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 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.
+A web-based validator for SBOL files backed by libSBOLj's validation runtimes. This validator offers support for SBOL2, SBOL1.1, and GenBank.
 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 openjdk21-jre python3-dev build-base linux-headers pcre-dev bash
+RUN apk add nginx openjdk17-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 openjdk21-jre python3-dev build-base linux-headers pcre-dev bash
+RUN apk add nginx openjdk17-jre python3-dev build-base linux-headers pcre-dev bash
 
 WORKDIR /opt/SBOL-Validator
 

src/conversion-form/html/form.html

@@ -71,13 +71,16 @@ <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/libSBOLj.jar

@@ -91,12 +91,13 @@ <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/sbol-converter.jar

@@ -17,24 +17,14 @@
 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 = [
-            line for line in output.strip().split('\n')
-            if line.strip() and line.strip() not in self.STATUS_LINES
-        ]
+        self.errors = output.strip().split('\n')
 
     def decipher(self, output, options):
         if self.check_equality:
@@ -43,24 +33,16 @@ def decipher(self, output, options):
             else:
                 self.equal = True
 
-        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:
+        if "Validation successful, no errors." not in output:
+            self.valid = False
             self.digest_errors(output)
+        else:
+            self.digest_errors(output.strip(u"Validation successful, no errors."))
             self.valid = True
 
-            if options.return_file and os.path.exists(options.output_file):
+            if options.return_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
@@ -80,15 +62,14 @@ def execute(self):
 
 	    # Attempt to run command
         try:
-            command = self.options.command("sbol-converter.jar", self.validation_file, self.diff_file)
+            command = self.options.command("libSBOLj.jar", self.validation_file, self.diff_file)
             logger.info("Running command: %s", " ".join(command))
-            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
+            output = subprocess.check_output(command, universal_newlines=True, stderr=subprocess.STDOUT)
             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)