Examples of Stage1Output

Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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        final StringBuilder bldr = new StringBuilder();

        stageOutput("Validating " + file);
        long t1 = currentTimeMillis();

        final Stage1Output output;
        if (isBELScript(file)) {
            output = p1.stage1BELValidation(file);
        } else {
            output = p1.stage1XBELValidation(file);
        }

        if (output.hasValidationErrors()) {
            for (final ValidationError error : output.getValidationErrors()) {
                stageError(error.getUserFacingMessage());
            }
            return null;
        }

        if (output.hasConversionError()) {
            stageError(output.getConversionError().getUserFacingMessage());
            return null;
        }

        if (output.getSymbolWarning() != null) {
            stageWarning(output.getSymbolWarning().getUserFacingMessage());
        }

        long t2 = currentTimeMillis();
        markTime(bldr, t1, t2);
        markEndStage(bldr);
        stageOutput(bldr.toString());
        return output.getDocument();
    }
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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            failUsage();
        }

        stageOutput("Processing protein families");
        long t1 = currentTimeMillis();
        final Stage1Output output;
        if (pfamType == BEL) {
            output = p1.stage1BELValidation(pfamResource);
        } else {
            output = p1.stage1XBELValidation(pfamResource);
        }

        if (output.hasValidationErrors()) {
            for (final ValidationError error : output.getValidationErrors()) {
                stageError(error.getUserFacingMessage());
            }
            bail(NO_VALID_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.hasConversionError()) {
            stageError(output.getConversionError().getUserFacingMessage());
            bail(NO_CONVERTED_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document pfDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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        }

        stageOutput("Processing named complexes");
        long t1 = currentTimeMillis();

        final Stage1Output output;
        if (ncType == BEL) {
            output = p1.stage1BELValidation(ncFile);
        } else {
            output = p1.stage1XBELValidation(ncFile);
        }

        if (output.hasValidationErrors()) {
            for (final ValidationError error : output.getValidationErrors()) {
                stageError(error.getUserFacingMessage());
            }
            bail(NO_VALID_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.hasConversionError()) {
            stageError(output.getConversionError().getUserFacingMessage());
            bail(NO_CONVERTED_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document ncDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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        }

        stageOutput("Processing gene scaffolding");
        long t1 = currentTimeMillis();

        final Stage1Output output;
        if (gsType == BEL) {
            output = p1.stage1BELValidation(gsFile);
        } else {
            output = p1.stage1XBELValidation(gsFile);
        }

        if (output.hasValidationErrors()) {
            for (final ValidationError error : output.getValidationErrors()) {
                stageError(error.getUserFacingMessage());
            }
            bail(NO_VALID_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.hasConversionError()) {
            stageError(output.getConversionError().getUserFacingMessage());
            bail(NO_CONVERTED_DOCUMENTS);
            return pn; // Dead code
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        long t2 = currentTimeMillis();
        Document gsDoc = output.getDocument();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        stageOutput(bldr.toString());
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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        } catch (ResourceDownloadError e) {
            e.printStackTrace();
            return null;
        }

        final Stage1Output output;
        if (type == BEL) {
            output = p1.stage1BELValidation(res);
        } else {
            output = p1.stage1XBELValidation(res);
        }

        if (output.hasValidationErrors()) {
            for (final ValidationError error : output.getValidationErrors()) {
                stageError(error.getUserFacingMessage());
            }
            bail(NO_VALID_DOCUMENTS);
            return null; // Dead code
        }
        if (output.hasConversionError()) {
            stageError(output.getConversionError().getUserFacingMessage());
            bail(NO_CONVERTED_DOCUMENTS);
            return null; // Dead code
        }
        if (output.getSymbolWarning() != null) {
            stageError(output.getSymbolWarning().getUserFacingMessage());
        }
        Document doc = output.getDocument();
        return doc;
    }
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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        }

        // read in BEL document and compile to proto network
        final File doc = new File(DOC_PATH);
        assertThat("test BEL document cannot be read", doc.canRead(), is(true));
        Stage1Output p1s1 = p1.stage1BELValidation(doc);
        final ProtoNetworkBuilder bldr = new ProtoNetworkBuilder(p1s1.getDocument());
        pn = bldr.buildProtoNetwork();

        // Create system configuration, BELFRAMEWORK_HOME must be set.
        try {
            createSystemConfiguration();
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Examples of org.openbel.framework.compiler.DefaultPhaseOne.Stage1Output

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            File xbelFile = new File(asPath(
                    testAssetDirectory.getAbsolutePath(), xbelFilePath));

            try {
                Stage1Output s1o = phaseOne.stage1XBELValidation(xbelFile);
                phaseOne.stage2NamespaceCompilation(s1o.getDocument());
                phaseOne.stage3SymbolVerification(s1o.getDocument());
                phaseOne.stage4SemanticVerification(s1o.getDocument());
                ProtoNetwork pn = phaseOne.stage5Building(s1o.getDocument());
                phaseOne.stage6Expansion(s1o.getDocument(), pn, true);

                // assert proto network is valid.
                assertNotNull(pn);
            } catch (ResourceDownloadError e) {
                e.printStackTrace();
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