source: java/main/src/main/java/com/framsticks/parsers/F0Parser.java @ 98

package com.framsticks.parsers;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.List;

import com.framsticks.model.Model;
import com.framsticks.model.f0.Schema;

import static com.framsticks.params.SimpleAbstractAccess.*;

import com.framsticks.params.Flags;
import com.framsticks.params.Param;
import com.framsticks.params.PrimitiveParam;
import com.framsticks.util.FramsticksException;
import com.framsticks.util.io.Encoding;
import com.framsticks.util.lang.Containers;
import com.framsticks.util.lang.Pair;
import com.framsticks.util.lang.Strings;
import org.apache.log4j.Logger;

import com.framsticks.params.FramsClass;
import com.framsticks.params.AccessInterface;

/**
 * The class Parser is used to parse genotype encoded in f0 representation.
 */
public class F0Parser {

        private final static Logger log = Logger.getLogger(F0Parser.class);

        /** The schema proper for f0 representation. */
        protected final Schema schema;
        protected final InputStream is;
        protected final List<AccessInterface> result = new ArrayList<AccessInterface>();
        int lineNumber = 0;

        public F0Parser(Schema schema, InputStream is) {
                assert schema != null;
                assert is != null;
                this.schema = schema;
                this.is = is;
        }

        protected AccessInterface processLine(String line) {
                try {

                        Pair<String, String> p = Strings.splitIntoPair(line, ':', "");
                        String classId = p.first.trim();
                        FramsClass framsClass = schema.getFramsClass(classId);
                        if (framsClass == null) {
                                throw new Exception("unknown class id: " + classId);
                        }
                        AccessInterface access = schema.getRegistry().createAccess(classId, framsClass);
                        access.select(access.createAccessee());
                        for (Exception e : loadFromLine(access, p.second)) {
                                warn(lineNumber, "however entry was added", e);
                        }
                        return access;
                } catch (Exception e) {
                        warn(lineNumber, "entry was not added", e);
                }
                return null;
        }

        /**
         * Parses the stream with genotype in f0 representation. The correctness of
         * genotype is checked. IO and syntax exceptions interrupts parsing and no
         * result is returned. Other exceptions, connected with schema validation
         * cause that certain object or it's parameter is ignored (appropriate
         * communicate informs user about it). Inappropriate values in numeric
         * fields (bigger than maximum or smaller than minimum values) are
         * communicated by warnings and set to minimum / maximum value.
         *
         * @return the list
         * @throws IOException
         *             Signals that an I/O exception has occurred.
         * @throws ParseException
         *             the parse exception
         */
        public List<AccessInterface> parse() {

                try (InputStreamReader reader = new InputStreamReader(is, Encoding.getDefaultCharset())) {
                        BufferedReader br = new BufferedReader(reader);
                        while (br.ready()) {
                                ++lineNumber;
                                String line = br.readLine();
                                line = (line == null ? "" : line.trim());
                                if (lineNumber == 1) {
                                        if (!"//0".equals(line)) {
                                                log.warn("stream should begin with \"//0\" in the first line");
                                        } else {
                                                continue;
                                        }
                                }
                                if (line.equals("")) {
                                        continue;
                                }
                                if (line.startsWith("#")) {
                                        continue;
                                }
                                AccessInterface access = processLine(line);
                                if (access != null) {
                                        result.add(access);
                                }
                        }

                        /** If no 'm' (Model) line was found, than simulate it on the beginning of the result.*/
                        if (result.isEmpty() || !(result.get(0) instanceof Model)) {
                                result.add(0, processLine("m:"));
                        }
                } catch (IOException e) {
                        throw new FramsticksException().msg("failed to parse f0").arg("parser", this).arg("schema", schema).cause(e);
                }

                return result;
        }

        private static void warn(int lineNumber, String message, Exception e) {
                log.warn("in line " + lineNumber + " the following error occurred (" + message + "): " + e);
        }

        /** Breaks string into entries.*/
        public List<Entry> breakIntoEntries(String parameters) throws Exception {
                // tokenize
                boolean inQuotes = false;
                char previousChar = ',';
                List<Entry> result = new ArrayList<Entry>();
                StringBuilder stringBuilder = new StringBuilder();
                String key = null;
                if (parameters.trim().length() > 0) {
                        for (char currentChar : parameters.toCharArray()) {
                                if (!inQuotes && (currentChar == '=') && (key == null)) {
                                        key = stringBuilder.toString().trim();
                                        stringBuilder = new StringBuilder();
                                } else if (!inQuotes && currentChar == ',') {
                                        if (previousChar == ',') {
                                                result.add(new Entry(key, null));
                                        } else {
                                                result.add(new Entry(key, stringBuilder.toString().trim()));
                                        }
                                        stringBuilder = new StringBuilder();
                                        key = null;
                                } else if (currentChar == '"') {
                                        if (previousChar == '\\') {
                                                stringBuilder.deleteCharAt(stringBuilder.length() - 1);
                                                stringBuilder.append(currentChar);
                                        } else {
                                                inQuotes = !inQuotes;
                                        }
                                } else {
                                        stringBuilder.append(currentChar);
                                }

                                previousChar = currentChar;
                        }

                        result.add(new Entry(key, stringBuilder.toString().trim()));

                        if (inQuotes) {
                                throw new Exception("Double quotes expected while end of line met");
                        }
                }
                return result;
        }

        public List<Exception> loadFromLine(AccessInterface access, String parameters) throws Exception {

                List<Entry> entries = breakIntoEntries(parameters);

                List<Exception> exceptions = new ArrayList<Exception>();

                List<Param> paramsL = new ArrayList<>();

                for (Param param : access.getParams()) {
                        paramsL.add(param);
                }

                Param[] params = paramsL.toArray(new Param[] {null});
                if (params.length == 0) {
                        return exceptions;
                }
                for (PrimitiveParam<?> p : Containers.filterInstanceof(paramsL, PrimitiveParam.class)) {
                        Object def = p.getDef(Object.class);
                        if (def != null) {
                                access.set(p, def);
                        }
                }

                int number = -1;
                Integer nextParamNumber = 0;
                for (Entry pair : entries) {
                        ++number;
                        try {
                                Param currentParam;
                                if (pair.key != null) {
                                        currentParam = access.getParam(pair.key);
                                        if (currentParam == null) {
                                                nextParamNumber = null;
                                                throw new Exception("no parameter with such id: " + pair.key);
                                        }
                                } else {
                                        if (nextParamNumber == null || ((params[nextParamNumber].getFlags() & Flags.CANOMITNAME) == 0)) {
                                                nextParamNumber = null;
                                                throw new Exception(
                                                                "parameter with offset: "
                                                                                + number
                                                                                + " is not set, "
                                                                                + "because it's definition or definition of the previous param "
                                                                                + "does not contain flag, which allows to skip the name (flag 1024)");
                                        }
                                        currentParam = params[nextParamNumber];
                                }
                                if (currentParam != null) {
                                        if (pair.value != null) {
                                                PrimitiveParam<?> vp = (PrimitiveParam<?>) currentParam;
                                                int setFlag = access.set(vp, pair.value);
                                                if ((setFlag & Flags.PSET_HITMIN) != 0) {
                                                        exceptions.add(createBoundaryHitException(access, vp, pair.value, Flags.PSET_HITMIN));
                                                }

                                                if ((setFlag & Flags.PSET_HITMAX) != 0) {
                                                        exceptions.add(createBoundaryHitException(access, vp, pair.value, Flags.PSET_HITMAX));
                                                }

                                                if ((setFlag & Flags.PSET_RONLY) != 0) {
                                                        throw (new Exception("tried to set a read-only attribute \""
                                                                + currentParam.getId()
                                                                + "\" in class \"" + access.getId() + "\""));
                                                }
                                        }
                                        nextParamNumber = null;
                                        for (int j = params.length - 1; j > 0; --j) {
                                                if (params[j - 1] == currentParam) {
                                                        nextParamNumber = j;
                                                }
                                        }
                                }

                        } catch (Exception e) {
                                exceptions.add(e);
                        }
                }
                return exceptions;
        }

        private static Exception createBoundaryHitException(AccessInterface access, PrimitiveParam<?> param, String value, int flag) {
                boolean minimum = (flag & Flags.PSET_HITMIN) != 0;
                String boundary = (minimum ? param.getMin(Object.class) : param.getMax(Object.class)).toString();
                String name =  (minimum ? "minimum" : "maximum");
                return new Exception("Tried to set attribute \""
                                + param.getId()
                                + "\" in class \""
                                + access.getId()
                                + "\" to value which exceeds " + name + " ("
                                + value
                                + "), truncated to: "
                                + boundary);
        }
}