import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.EnumSet;
+import java.util.Enumeration;
import java.util.HashMap;
import java.util.List;
-import java.util.Locale;
import java.util.Map;
import jalview.bin.Console;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.bin.argparser.Arg.Opt;
+import jalview.bin.argparser.Arg.Type;
import jalview.util.FileUtils;
+import jalview.util.HttpUtils;
public class ArgParser
{
+ protected static final String SINGLEDASH = "-";
+
protected static final String DOUBLEDASH = "--";
+ public static final char EQUALS = '=';
+
+ public static final String STDOUTFILENAME = "-";
+
protected static final String NEGATESTRING = "no";
- // the default linked id prefix used for no id (not even square braces)
+ /**
+ * the default linked id prefix used for no id (ie when not even square braces
+ * are provided)
+ */
protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
- // the counter added to the default linked id prefix
+ /**
+ * the linkedId string used to match all linkedIds seen so far
+ */
+ protected static final String MATCHALLLINKEDIDS = "*";
+
+ /**
+ * the linkedId string used to match all of the last --open'ed linkedIds
+ */
+ protected static final String MATCHOPENEDLINKEDIDS = "open*";
+
+ /**
+ * the counter added to the default linked id prefix
+ */
private int defaultLinkedIdCounter = 0;
- // the linked id used to increment the idCounter (and use the incremented
- // value)
- private static final String INCREMENTAUTOCOUNTERLINKEDID = "{++n}";
+ /**
+ * the substitution string used to use the defaultLinkedIdCounter
+ */
+ private static final String DEFAULTLINKEDIDCOUNTER = "{}";
+
+ /**
+ * the linked id prefix used for --open files. NOW the same as DEFAULT
+ */
+ protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX;
+
+ /**
+ * the counter used for {n} substitutions
+ */
+ private int linkedIdAutoCounter = 0;
+
+ /**
+ * the linked id substitution string used to increment the idCounter (and use
+ * the incremented value)
+ */
+ private static final String INCREMENTLINKEDIDAUTOCOUNTER = "{++n}";
+
+ /**
+ * the linked id substitution string used to use the idCounter
+ */
+ private static final String LINKEDIDAUTOCOUNTER = "{n}";
+
+ /**
+ * the linked id substitution string used to use the filename extension of
+ * --append or --open
+ */
+ private static final String LINKEDIDEXTENSION = "{extension}";
+
+ /**
+ * the linked id substitution string used to use the base filename of --append
+ */
+ /** or --open */
+ private static final String LINKEDIDBASENAME = "{basename}";
+
+ /**
+ * the linked id substitution string used to use the dir path of --append or
+ * --open
+ */
+ private static final String LINKEDIDDIRNAME = "{dirname}";
- // the linked id used to use the idCounter
- private static final String AUTOCOUNTERLINKEDID = "{n}";
+ /**
+ * the current argfile
+ */
+ private String argFile = null;
- private int idCounter = 0;
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ */
+ /** --argfile name */
+ private static final String ARGFILEBASENAME = "{argfilebasename}";
- // flag to say whether {n} subtitutions in output filenames should be made.
- // Turn on and off with --subs and --nosubs
- private boolean substitutions = false;
+ /**
+ * the linked id substitution string used to use the dir path of the latest
+ * --argfile name
+ */
+ private static final String ARGFILEDIRNAME = "{argfiledirname}";
+
+ /**
+ * flag to say whether {n} subtitutions in output filenames should be made.
+ * Turn on and off with --substitutions and --nosubstitutions Start with it on
+ */
+ private boolean substitutions = true;
+
+ /**
+ * flag to say whether the default linkedId is the current default linked id
+ *
+ * or ALL linkedIds
+ */
+ private boolean allLinkedIds = false;
+
+ /**
+ * flag to say whether the structure arguments should be applied to all
+ * structures with this linked id
+ */
+ private boolean allStructures = false;
protected static final Map<String, Arg> argMap;
protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
- protected List<String> linkedOrder = null;
+ protected List<String> linkedOrder = new ArrayList<>();
+
+ protected List<String> storedLinkedIds = new ArrayList<>();
+
+ protected List<Arg> argList = new ArrayList<>();
+
+ private static final char ARGFILECOMMENT = '#';
+
+ private int argIndex = 0;
+
+ private BootstrapArgs bootstrapArgs = null;
- protected List<Arg> argList;
+ private boolean oldArguments = false;
+
+ private boolean mixedArguments = false;
+
+ /**
+ * saved examples of mixed arguments
+ */
+ private String[] mixedExamples = new String[] { null, null };
static
{
if (argMap.containsKey(argName))
{
Console.warn("Trying to add argument name multiple times: '"
- + argName + "'"); // RESTORE THIS WHEN MERGED
+ + argName + "'");
if (argMap.get(argName) != a)
{
Console.error(
public ArgParser(String[] args)
{
- // Make a mutable new ArrayList so that shell globbing parser works.
- // (When shell file globbing is used, there are a sequence of non-Arg
- // arguments (which are the expanded globbed filenames) that need to be
- // consumed by the --open/--argfile/etc Arg which is most easily done by
- // removing these filenames from the list one at a time. This can't be done
- // with an ArrayList made with only Arrays.asList(String[] args). )
- this(new ArrayList<>(Arrays.asList(args)));
+ this(args, false, null);
}
- public ArgParser(List<String> args)
+ public ArgParser(String[] args, boolean initsubstitutions,
+ BootstrapArgs bsa)
{
- parse(args);
+ /*
+ * Make a mutable new ArrayList so that shell globbing parser works.
+ * (When shell file globbing is used, there are a sequence of non-Arg
+ * arguments (which are the expanded globbed filenames) that need to be
+ * consumed by the --append/--argfile/etc Arg which is most easily done
+ * by removing these filenames from the list one at a time. This can't be
+ * done with an ArrayList made with only Arrays.asList(String[] args) as
+ * that is not mutable. )
+ */
+ this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
+ bsa);
}
- private void parse(List<String> args)
+ public ArgParser(List<String> args, boolean initsubstitutions)
{
- int argIndex = 0;
- boolean initialFilenameArgs = true;
- for (int i = 0; i < args.size(); i++)
- {
- String arg = args.get(i);
+ this(args, initsubstitutions, false, null);
+ }
- // If the first arguments do not start with "--" or "-" or is "open" and
- // is a filename that exists it is probably a file/list of files to open
- // so we fake an Arg.OPEN argument and when adding files only add the
- // single arg[i] and increment the defaultLinkedIdCounter so that each of
- // these files is opened separately.
- if (initialFilenameArgs && !arg.startsWith(DOUBLEDASH)
- && !arg.startsWith("-") && new File(arg).exists())
+ public ArgParser(List<String> args, boolean initsubstitutions,
+ boolean allowPrivate, BootstrapArgs bsa)
+ {
+ // do nothing if there are no "--" args and (some "-" args || >0 arg is
+ // "open")
+ boolean d = false;
+ boolean dd = false;
+ for (String arg : args)
+ {
+ if (arg.startsWith(DOUBLEDASH))
+ {
+ dd = true;
+ if (mixedExamples[1] == null)
+ {
+ mixedExamples[1] = arg;
+ }
+ }
+ else if ((arg.startsWith("-") && !arg.equals(STDOUTFILENAME))
+ || arg.equals("open"))
+ {
+ d = true;
+ if (mixedExamples[0] == null)
+ {
+ mixedExamples[0] = arg;
+ }
+ }
+ }
+ if (d)
+ {
+ if (dd)
{
- arg = DOUBLEDASH + Arg.OPEN.getName();
- Console.debug("Adding argument '" + args.get(i)
- + "' as a file to be opened");
+ mixedArguments = true;
}
else
{
- initialFilenameArgs = false;
+ oldArguments = true;
}
+ }
+
+ if (oldArguments || mixedArguments)
+ {
+ // leave it to the old style -- parse an empty list
+ parse(new ArrayList<String>(), false, false);
+ return;
+ }
+
+ if (bsa != null)
+ this.bootstrapArgs = bsa;
+ else
+ this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+ parse(args, initsubstitutions, allowPrivate);
+ }
+
+ private void parse(List<String> args, boolean initsubstitutions,
+ boolean allowPrivate)
+ {
+ this.substitutions = initsubstitutions;
+
+ /*
+ * If the first argument does not start with "--" or "-" or is not "open",
+ * and is a filename that exists or a URL, it is probably a file/list of
+ * files to open so we insert an Arg.OPEN argument before it. This will
+ * mean the list of files at the start of the arguments are all opened
+ * separately.
+ */
+ if (args.size() > 0)
+ {
+ String arg0 = args.get(0);
+ if (arg0 != null
+ && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-")
+ && !arg0.equals("open") && (new File(arg0).exists()
+ || HttpUtils.startsWithHttpOrHttps(arg0))))
+ {
+ // insert "--open" at the start
+ args.add(0, Arg.OPEN.argString());
+ }
+ }
+
+ for (int i = 0; i < args.size(); i++)
+ {
+ String arg = args.get(i);
- String argName = null;
- String val = null;
- List<String> vals = null; // for Opt.GLOB only
- String linkedId = null;
+ // look for double-dash, e.g. --arg
if (arg.startsWith(DOUBLEDASH))
{
- int equalPos = arg.indexOf('=');
+ String argName = null;
+ String val = null;
+ List<String> globVals = null; // for Opt.GLOB only
+ SubVals globSubVals = null; // also for use by Opt.GLOB only
+ String linkedId = null;
+ Type type = null;
+
+ // look for equals e.g. --arg=value
+ int equalPos = arg.indexOf(EQUALS);
if (equalPos > -1)
{
argName = arg.substring(DOUBLEDASH.length(), equalPos);
{
argName = arg.substring(DOUBLEDASH.length());
}
+
+ // look for linked ID e.g. --arg[linkedID]
int idOpen = argName.indexOf('[');
int idClose = argName.indexOf(']');
-
if (idOpen > -1 && idClose == argName.length() - 1)
{
linkedId = argName.substring(idOpen + 1, idClose);
argName = argName.substring(0, idOpen);
}
+ // look for type modification e.g. --help-opening
+ int dashPos = argName.indexOf(SINGLEDASH);
+ if (dashPos > -1)
+ {
+ String potentialArgName = argName.substring(0, dashPos);
+ Arg potentialArg = argMap.get(potentialArgName);
+ if (potentialArg != null && potentialArg.hasOption(Opt.HASTYPE))
+ {
+ String typeName = argName.substring(dashPos + 1);
+ try
+ {
+ type = Type.valueOf(typeName);
+ } catch (IllegalArgumentException e)
+ {
+ type = Type.INVALID;
+ }
+ argName = argName.substring(0, dashPos);
+ }
+ }
+
Arg a = argMap.get(argName);
- // check for boolean prepended by "no"
+ // check for boolean prepended by "no" e.g. --nowrap
boolean negated = false;
- if (a == null && argName.startsWith(NEGATESTRING) && argMap
- .containsKey(argName.substring(NEGATESTRING.length())))
+ if (a == null)
{
- argName = argName.substring(NEGATESTRING.length());
- a = argMap.get(argName);
- negated = true;
+ if (argName.startsWith(NEGATESTRING) && argMap
+ .containsKey(argName.substring(NEGATESTRING.length())))
+ {
+ argName = argName.substring(NEGATESTRING.length());
+ a = argMap.get(argName);
+ negated = true;
+ }
+ else
+ {
+ // after all other args, look for Opt.PREFIXKEV args if still not
+ // found
+ for (Arg potentialArg : EnumSet.allOf(Arg.class))
+ {
+ if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+ && argName.startsWith(potentialArg.getName())
+ && equalPos > -1)
+ {
+ val = argName.substring(potentialArg.getName().length())
+ + EQUALS + val;
+ argName = argName.substring(0,
+ potentialArg.getName().length());
+ a = potentialArg;
+ break;
+ }
+ }
+ }
}
// check for config errors
if (a == null)
{
// arg not found
- Console.error("Argument '" + arg + "' not recognised. Ignoring.");
+ Console.error("Argument '" + arg + "' not recognised. Exiting.");
+ Jalview.exit(
+ "Invalid argument used." + System.lineSeparator() + "Use"
+ + System.lineSeparator() + "jalview "
+ + Arg.HELP.argString() + System.lineSeparator()
+ + "for a usage statement.",
+ ExitCode.INVALID_ARGUMENT);
+ continue;
+ }
+ if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
+ {
+ Console.error(
+ "Argument '" + a.argString() + "' is private. Ignoring.");
continue;
}
if (!a.hasOption(Opt.BOOLEAN) && negated)
{
// used "no" with a non-boolean option
- Console.error("Argument '--" + NEGATESTRING + argName
+ Console.error("Argument '" + DOUBLEDASH + NEGATESTRING + argName
+ "' not a boolean option. Ignoring.");
continue;
}
if (!a.hasOption(Opt.STRING) && equalPos > -1)
{
// set --argname=value when arg does not accept values
- Console.error("Argument '--" + argName
+ Console.error("Argument '" + a.argString()
+ "' does not expect a value (given as '" + arg
+ "'). Ignoring.");
continue;
if (!a.hasOption(Opt.LINKED) && linkedId != null)
{
// set --argname[linkedId] when arg does not use linkedIds
- Console.error("Argument '--" + argName
+ Console.error("Argument '" + a.argString()
+ "' does not expect a linked id (given as '" + arg
+ "'). Ignoring.");
continue;
}
- if (a.hasOption(Opt.STRING) && equalPos == -1)
+ // String value(s)
+ if (a.hasOption(Opt.STRING))
{
- // take next arg as value if required, and '=' was not found
- // if (!argE.hasMoreElements())
- if (i + 1 >= args.size())
- {
- // no value to take for arg, which wants a value
- Console.error("Argument '" + a.getName()
- + "' requires a value, none given. Ignoring.");
- continue;
- }
- // deal with bash globs here (--arg val* is expanded before reaching
- // the JVM). Note that SubVals cannot be used in this case.
- // If using the --arg=val then the glob is preserved and Java globs
- // will be used later. SubVals can be used.
- if (a.hasOption(Opt.GLOB))
+ if (equalPos >= 0)
{
- // if this is the first argument with a file list at the start of
- // the args we add filenames from index i instead of i+1
- // and assume they should be opened separately
- if (initialFilenameArgs)
+ if (a.hasOption(Opt.GLOB))
{
- val = args.get(i);
- defaultLinkedIdCounter++;
+ // strip off and save the SubVals to be added individually later
+ globSubVals = new SubVals(val);
+ // make substitutions before looking for files
+ String fileGlob = makeSubstitutions(globSubVals.getContent(),
+ linkedId);
+ globVals = FileUtils.getFilenamesFromGlob(fileGlob);
}
else
{
- vals = getShellGlobbedFilenameValues(a, args, i + 1);
+ // val is already set -- will be saved in the ArgValue later in
+ // the normal way
}
}
else
{
- val = args.get(i + 1);
+ // There is no "=" so value is next arg or args (possibly shell
+ // glob-expanded)
+ if (i + 1 >= args.size())
+ {
+ // no value to take for arg, which wants a value
+ Console.error("Argument '" + a.getName()
+ + "' requires a value, none given. Ignoring.");
+ continue;
+ }
+ // deal with bash globs here (--arg val* is expanded before reaching
+ // the JVM). Note that SubVals cannot be used in this case.
+ // If using the --arg=val then the glob is preserved and Java globs
+ // will be used later. SubVals can be used.
+ if (a.hasOption(Opt.GLOB))
+ {
+ // if this is the first argument with a file list at the start of
+ // the args we add filenames from index i instead of i+1
+ globVals = getShellGlobbedFilenameValues(a, args, i + 1);
+ }
+ else
+ {
+ val = args.get(i + 1);
+ }
}
}
// make NOACTION adjustments
// default and auto counter increments
- if (a == Arg.INCREMENT)
- {
- defaultLinkedIdCounter++;
- }
- else if (a == Arg.NPP)
+ if (a == Arg.NPP)
{
- idCounter++;
+ linkedIdAutoCounter++;
}
else if (a == Arg.SUBSTITUTIONS)
{
substitutions = !negated;
}
+ else if (a == Arg.SETARGFILE)
+ {
+ argFile = val;
+ }
+ else if (a == Arg.UNSETARGFILE)
+ {
+ argFile = null;
+ }
+ else if (a == Arg.ALL)
+ {
+ allLinkedIds = !negated;
+ }
+ else if (a == Arg.ALLSTRUCTURES)
+ {
+ allStructures = !negated;
+ }
+
+ if (a.hasOption(Opt.STORED))
+ {
+ // reset the lastOpenedLinkedIds list
+ this.storedLinkedIds = new ArrayList<>();
+ }
+
+ // this is probably only Arg.NEW and Arg.OPEN
+ if (a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
+ {
+ // use the next default prefixed OPENLINKEDID
+ defaultLinkedId(true);
+ }
String autoCounterString = null;
- boolean usingAutoCounterLinkedId = false;
- String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
- .append(Integer.toString(defaultLinkedIdCounter))
- .toString();
+ String defaultLinkedId = defaultLinkedId(false);
boolean usingDefaultLinkedId = false;
if (a.hasOption(Opt.LINKED))
{
if (linkedId == null)
{
- // use default linkedId for linked arguments
- linkedId = defaultLinkedId;
- usingDefaultLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
- }
- else if (linkedId.equals(AUTOCOUNTERLINKEDID))
- {
- // turn {n} to the autoCounter
- autoCounterString = Integer.toString(idCounter);
- linkedId = autoCounterString;
- usingAutoCounterLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
+ if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID)
+ && val.contains(MATCHALLLINKEDIDS))
+ {
+ // --output=*.ext is shorthand for --output {basename}.ext
+ // --output=*/*.ext is shorthand for
+ // --output {dirname}/{basename}.ext
+ // (or --image=*.ext)
+ linkedId = allLinkedIds ? MATCHALLLINKEDIDS
+ : MATCHOPENEDLINKEDIDS;
+ val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS,
+ LINKEDIDDIRNAME, LINKEDIDBASENAME);
+ }
+ else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID))
+ {
+ linkedId = MATCHALLLINKEDIDS;
+ }
+ else if (a.hasOption(Opt.ALLOWMULTIID)
+ && this.storedLinkedIds != null
+ && this.storedLinkedIds.size() > 0)
+ {
+ linkedId = MATCHOPENEDLINKEDIDS;
+ }
+ else
+ {
+ // use default linkedId for linked arguments
+ linkedId = defaultLinkedId;
+ usingDefaultLinkedId = true;
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
}
- else if (linkedId.equals(INCREMENTAUTOCOUNTERLINKEDID))
+ else
{
- // turn {++n} to the incremented autoCounter
- autoCounterString = Integer.toString(++idCounter);
- linkedId = autoCounterString;
- usingAutoCounterLinkedId = true;
- Console.debug(
- "Changing linkedId to '" + linkedId + "' from " + arg);
+ if (linkedId.contains(LINKEDIDAUTOCOUNTER))
+ {
+ // turn {n} to the autoCounter
+ autoCounterString = Integer.toString(linkedIdAutoCounter);
+ linkedId = linkedId.replace(LINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
+ if (linkedId.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ {
+ // turn {++n} to the incremented autoCounter
+ autoCounterString = Integer.toString(++linkedIdAutoCounter);
+ linkedId = linkedId.replace(INCREMENTLINKEDIDAUTOCOUNTER,
+ autoCounterString);
+ Console.debug("Changing linkedId to '" + linkedId + "' from "
+ + arg);
+ }
}
}
- if (!linkedArgs.containsKey(linkedId))
- linkedArgs.put(linkedId, new ArgValuesMap());
-
- // do not continue for NOACTION args
+ // do not continue in this block for NOACTION args
if (a.hasOption(Opt.NOACTION))
continue;
- ArgValuesMap avm = linkedArgs.get(linkedId);
+ ArgValuesMap avm = getOrCreateLinkedArgValuesMap(linkedId);
// not dealing with both NODUPLICATEVALUES and GLOB
if (a.hasOption(Opt.NODUPLICATEVALUES) && avm.hasValue(a, val))
{
- Console.error("Argument '--" + argName
+ Console.error("Argument '" + a.argString()
+ "' cannot contain a duplicate value ('" + val
+ "'). Ignoring this and subsequent occurrences.");
continue;
}
// check for unique id
- SubVals sv = ArgParser.getSubVals(val);
- String id = sv.get(ArgValues.ID);
+ SubVals subvals = new SubVals(val);
+ boolean addNewSubVals = false;
+ String id = subvals.get(ArgValues.ID);
if (id != null && avm.hasId(a, id))
{
- Console.error("Argument '--" + argName + "' has a duplicate id ('"
- + id + "'). Ignoring.");
+ Console.error("Argument '" + a.argString()
+ + "' has a duplicate id ('" + id + "'). Ignoring.");
continue;
}
- ArgValues avs = avm.getOrCreateArgValues(a);
- if (avs == null)
+ // set allstructures to all non-primary structure options in this linked
+ // id if --allstructures has been set
+ if (allStructures && (a.getType() == Type.STRUCTURE
+ // || a.getType() == Type.STRUCTUREIMAGE)
+ ) && !a.hasOption(Opt.PRIMARY))
{
- avs = new ArgValues(a);
+ if (!subvals.has(Arg.ALLSTRUCTURES.getName()))
+ // && !subvals.has("structureid"))
+ {
+ subvals.put(Arg.ALLSTRUCTURES.getName(), "true");
+ addNewSubVals = true;
+ }
}
- boolean argIndexIncremented = false;
- // store appropriate value
+ ArgValues avs = avm.getOrCreateArgValues(a);
+
+ // store appropriate String value(s)
if (a.hasOption(Opt.STRING))
{
- if (a.hasOption(Opt.GLOB) && vals != null && vals.size() > 0)
+ if (a.hasOption(Opt.GLOB) && globVals != null
+ && globVals.size() > 0)
{
- for (String v : vals)
+ Enumeration<String> gve = Collections.enumeration(globVals);
+ while (gve.hasMoreElements())
{
- avs.addValue(makeSubstitutions(v), argIndex++);
- argIndexIncremented = true;
+ String v = gve.nextElement();
+ SubVals vsv = new SubVals(globSubVals, v);
+ addValue(linkedId, type, avs, vsv, v, argIndex++, true);
+ // if we're using defaultLinkedId and the arg increments the
+ // counter:
+ if (gve.hasMoreElements() && usingDefaultLinkedId
+ && a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
+ {
+ // increment the default linkedId
+ linkedId = defaultLinkedId(true);
+ // get new avm and avs
+ avm = linkedArgs.get(linkedId);
+ avs = avm.getOrCreateArgValues(a);
+ }
}
}
else
{
- avs.addValue(makeSubstitutions(val), argIndex);
+ // addValue(linkedId, type, avs, val, argIndex, true);
+ addValue(linkedId, type, avs, addNewSubVals ? subvals : null,
+ val, argIndex, true);
}
}
else if (a.hasOption(Opt.BOOLEAN))
{
- avs.setBoolean(!negated, argIndex);
- avs.setNegated(negated);
+ setBoolean(linkedId, type, avs, !negated, argIndex);
+ setNegated(linkedId, avs, negated);
}
else if (a.hasOption(Opt.UNARY))
{
- avs.setBoolean(true, argIndex);
+ setBoolean(linkedId, type, avs, true, argIndex);
}
- avs.incrementCount();
- if (!argIndexIncremented)
- argIndex++;
- // store in appropriate place
- if (a.hasOption(Opt.LINKED))
+ // remove the '*' or 'open*' linkedId that should be empty if it was
+ // created
+ if ((MATCHALLLINKEDIDS.equals(linkedId)
+ || MATCHOPENEDLINKEDIDS.equals(linkedId))
+ && linkedArgs.containsKey(linkedId))
{
- // allow a default linked id for single usage
- if (linkedId == null)
- linkedId = defaultLinkedId;
- // store the order of linkedIds
- if (linkedOrder == null)
- linkedOrder = new ArrayList<>();
- if (!linkedOrder.contains(linkedId))
- linkedOrder.add(linkedId);
- }
-
- // store arg in the list of args used
- if (argList == null)
- argList = new ArrayList<>();
- if (!argList.contains(a))
- argList.add(a);
+ linkedArgs.remove(linkedId);
+ }
}
}
}
- private String makeSubstitutions(String val)
+ private void finaliseStoringArgValue(String linkedId, ArgValues avs)
{
- if (!this.substitutions)
+ Arg a = avs.arg();
+ incrementCount(linkedId, avs);
+ argIndex++;
+
+ // store in appropriate place
+ if (a.hasOption(Opt.LINKED))
+ {
+ // store the order of linkedIds
+ if (!linkedOrder.contains(linkedId))
+ linkedOrder.add(linkedId);
+ }
+
+ // store arg in the list of args used
+ if (!argList.contains(a))
+ argList.add(a);
+ }
+
+ private String defaultLinkedId(boolean increment)
+ {
+ String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
+ .append(Integer.toString(defaultLinkedIdCounter)).toString();
+ if (increment)
+ {
+ while (linkedArgs.containsKey(defaultLinkedId))
+ {
+ defaultLinkedIdCounter++;
+ defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
+ .append(Integer.toString(defaultLinkedIdCounter))
+ .toString();
+ }
+ }
+ getOrCreateLinkedArgValuesMap(defaultLinkedId);
+ return defaultLinkedId;
+ }
+
+ public String makeSubstitutions(String val, String linkedId)
+ {
+ if (!this.substitutions || val == null)
return val;
String subvals;
subvals = "";
rest = val;
}
- rest.replace(AUTOCOUNTERLINKEDID, String.valueOf(idCounter));
- rest.replace(INCREMENTAUTOCOUNTERLINKEDID, String.valueOf(++idCounter));
- rest.replace("{}", String.valueOf(defaultLinkedIdCounter));
+ if (rest.contains(LINKEDIDAUTOCOUNTER))
+ rest = rest.replace(LINKEDIDAUTOCOUNTER,
+ String.valueOf(linkedIdAutoCounter));
+ if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+ rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER,
+ String.valueOf(++linkedIdAutoCounter));
+ if (rest.contains(DEFAULTLINKEDIDCOUNTER))
+ rest = rest.replace(DEFAULTLINKEDIDCOUNTER,
+ String.valueOf(defaultLinkedIdCounter));
+ ArgValuesMap avm = linkedArgs.get(linkedId);
+ if (avm != null)
+ {
+ if (rest.contains(LINKEDIDBASENAME))
+ {
+ rest = rest.replace(LINKEDIDBASENAME, avm.getBasename());
+ }
+ if (rest.contains(LINKEDIDEXTENSION))
+ {
+ rest = rest.replace(LINKEDIDEXTENSION, avm.getExtension());
+ }
+ if (rest.contains(LINKEDIDDIRNAME))
+ {
+ rest = rest.replace(LINKEDIDDIRNAME, avm.getDirname());
+ }
+ }
+ if (argFile != null)
+ {
+ if (rest.contains(ARGFILEBASENAME))
+ {
+ rest = rest.replace(ARGFILEBASENAME,
+ FileUtils.getBasename(new File(argFile)));
+ }
+ if (rest.contains(ARGFILEDIRNAME))
+ {
+ rest = rest.replace(ARGFILEDIRNAME,
+ FileUtils.getDirname(new File(argFile)));
+ }
+ }
return new StringBuilder(subvals).append(rest).toString();
}
/*
* A helper method to take a list of String args where we're expecting
* {"--previousargs", "--arg", "file1", "file2", "file3", "--otheroptionsornot"}
- * and the index of the globbed arg, here 1. It returns a
- * List<String> {"file1", "file2", "file3"}
- * *and remove these from the original list object* so that processing
- * can continue from where it has left off, e.g. args has become
- * {"--previousargs", "--arg", "--otheroptionsornot"}
- * so the next increment carries on from the next --arg if available.
+ * and the index of the globbed arg, here 1. It returns a List<String> {"file1",
+ * "file2", "file3"} *and remove these from the original list object* so that
+ * processing can continue from where it has left off, e.g. args has become
+ * {"--previousargs", "--arg", "--otheroptionsornot"} so the next increment
+ * carries on from the next --arg if available.
*/
protected static List<String> getShellGlobbedFilenameValues(Arg a,
List<String> args, int i)
List<String> vals = new ArrayList<>();
while (i < args.size() && !args.get(i).startsWith(DOUBLEDASH))
{
- vals.add(args.remove(i));
+ vals.add(FileUtils.substituteHomeDir(args.remove(i)));
if (!a.hasOption(Opt.GLOB))
break;
}
return vals;
}
+ public BootstrapArgs getBootstrapArgs()
+ {
+ return bootstrapArgs;
+ }
+
public boolean isSet(Arg a)
{
- return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
+ return a.hasOption(Opt.LINKED) ? isSetAtAll(a) : isSet(null, a);
+ }
+
+ public boolean isSetAtAll(Arg a)
+ {
+ for (String linkedId : linkedOrder)
+ {
+ if (isSet(linkedId, a))
+ return true;
+ }
+ return false;
}
public boolean isSet(String linkedId, Arg a)
return avm == null ? false : avm.containsArg(a);
}
- public boolean getBool(Arg a)
+ public boolean getBoolean(Arg a)
{
if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
{
return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
}
- public List<String> linkedIds()
+ public List<String> getLinkedIds()
{
return linkedOrder;
}
- public ArgValuesMap linkedArgs(String id)
+ public ArgValuesMap getLinkedArgs(String id)
{
return linkedArgs.get(id);
}
StringBuilder sb = new StringBuilder();
sb.append("UNLINKED\n");
sb.append(argValuesMapToString(linkedArgs.get(null)));
- if (linkedIds() != null)
+ if (getLinkedIds() != null)
{
sb.append("LINKED\n");
- for (String id : linkedIds())
+ for (String id : getLinkedIds())
{
// already listed these as UNLINKED args
if (id == null)
continue;
- ArgValuesMap avm = linkedArgs(id);
+ ArgValuesMap avm = getLinkedArgs(id);
sb.append("ID: '").append(id).append("'\n");
sb.append(argValuesMapToString(avm));
}
return sb.toString();
}
- public static SubVals getSubVals(String item)
- {
- return new SubVals(item);
- }
-
- public static ArgParser parseArgFiles(List<String> argFilenameGlobs)
+ public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<File> argFiles = new ArrayList<>();
argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
}
- return parseArgFileList(argFiles);
+ return parseArgFileList(argFiles, initsubstitutions, bsa);
}
- public static ArgParser parseArgFileList(List<File> argFiles)
+ public static ArgParser parseArgFileList(List<File> argFiles,
+ boolean initsubstitutions, BootstrapArgs bsa)
{
List<String> argsList = new ArrayList<>();
for (File argFile : argFiles)
{
if (!argFile.exists())
{
- String message = DOUBLEDASH
- + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
+ String message = Arg.ARGFILE.argString() + EQUALS + "\""
+ argFile.getPath() + "\": File does not exist.";
- Jalview.exit(message, 2);
+ Jalview.exit(message, ExitCode.FILE_NOT_FOUND);
}
try
{
- argsList.addAll(Files.readAllLines(Paths.get(argFile.getPath())));
+ String setargfile = new StringBuilder(Arg.SETARGFILE.argString())
+ .append(EQUALS).append(argFile.getCanonicalPath())
+ .toString();
+ argsList.add(setargfile);
+ argsList.addAll(readArgFile(argFile));
+ argsList.add(Arg.UNSETARGFILE.argString());
} catch (IOException e)
{
- String message = DOUBLEDASH
- + Arg.ARGFILE.name().toLowerCase(Locale.ROOT) + "=\""
- + argFile.getPath() + "\": File could not be read.";
- Jalview.exit(message, 3);
+ String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ + "\": File could not be read.";
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
+ }
+ }
+ // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
+ // --unsetargfile
+ return new ArgParser(argsList, initsubstitutions, true, bsa);
+ }
+
+ protected static List<String> readArgFile(File argFile)
+ {
+ List<String> args = new ArrayList<>();
+ if (argFile != null && argFile.exists())
+ {
+ try
+ {
+ for (String line : Files.readAllLines(Paths.get(argFile.getPath())))
+ {
+ if (line != null && line.length() > 0
+ && line.charAt(0) != ARGFILECOMMENT)
+ args.add(line);
+ }
+ } catch (IOException e)
+ {
+ String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
+ + "\": File could not be read.";
+ Console.debug(message, e);
+ Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
+ }
+ }
+ return args;
+ }
+
+ // the following methods look for the "*" linkedId and add the argvalue to all
+ // linkedId ArgValues if it does.
+ /**
+ * This version inserts the subvals sv into all created values
+ */
+ private void addValue(String linkedId, Type type, ArgValues avs,
+ SubVals sv, String v, int argIndex, boolean doSubs)
+ {
+ this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false,
+ argIndex, doSubs);
+ }
+
+ private void setBoolean(String linkedId, Type type, ArgValues avs,
+ boolean b, int argIndex)
+ {
+ this.argValueOperation(Op.SETBOOLEAN, linkedId, type, avs, null, null,
+ b, argIndex, false);
+ }
+
+ private void setNegated(String linkedId, ArgValues avs, boolean b)
+ {
+ this.argValueOperation(Op.SETNEGATED, linkedId, null, avs, null, null,
+ b, 0, false);
+ }
+
+ private void incrementCount(String linkedId, ArgValues avs)
+ {
+ this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null,
+ null, false, 0, false);
+ }
+
+ private enum Op
+ {
+ ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
+ }
+
+ private void argValueOperation(Op op, String linkedId, Type type,
+ ArgValues avs, SubVals sv, String v, boolean b, int argIndex,
+ boolean doSubs)
+ {
+ // default to merge subvals if subvals are provided
+ argValueOperation(op, linkedId, type, avs, sv, true, v, b, argIndex,
+ doSubs);
+ }
+
+ /**
+ * The following operations look for the "*" and "open*" linkedIds and add the
+ * argvalue to all appropriate linkedId ArgValues if it does. If subvals are
+ * supplied, they are inserted into all new set values.
+ *
+ * @param op
+ * The ArgParser.Op operation
+ * @param linkedId
+ * The String linkedId from the ArgValuesMap
+ * @param type
+ * The Arg.Type to attach to this ArgValue
+ * @param avs
+ * The ArgValues for this linkedId
+ * @param sv
+ * Use these SubVals on the ArgValue
+ * @param merge
+ * Merge the SubVals with any existing on the value. False will
+ * replace unless sv is null
+ * @param v
+ * The value of the ArgValue (may contain subvals).
+ * @param b
+ * The boolean value of the ArgValue.
+ * @param argIndex
+ * The argIndex for the ArgValue.
+ * @param doSubs
+ * Whether to perform substitutions on the subvals and value.
+ */
+ private void argValueOperation(Op op, String linkedId, Type type,
+ ArgValues avs, SubVals sv, boolean merge, String v, boolean b,
+ int argIndex, boolean doSubs)
+ {
+ Arg a = avs.arg();
+
+ List<String> wildcardLinkedIds = null;
+ if (a.hasOption(Opt.ALLOWMULTIID))
+ {
+ switch (linkedId)
+ {
+ case MATCHALLLINKEDIDS:
+ wildcardLinkedIds = getLinkedIds();
+ break;
+ case MATCHOPENEDLINKEDIDS:
+ wildcardLinkedIds = this.storedLinkedIds;
+ break;
+ }
+ }
+
+ // if we're not a wildcard linkedId and the arg is marked to be stored, add
+ // to storedLinkedIds
+ if (linkedId != null && wildcardLinkedIds == null
+ && a.hasOption(Opt.STORED)
+ && !storedLinkedIds.contains(linkedId))
+ {
+ storedLinkedIds.add(linkedId);
+ }
+
+ // if we are a wildcard linkedId, apply the arg and value to all appropriate
+ // linkedIds
+ if (wildcardLinkedIds != null)
+ {
+ for (String id : wildcardLinkedIds)
+ {
+ // skip incorrectly stored wildcard ids!
+ if (id == null || MATCHALLLINKEDIDS.equals(id)
+ || MATCHOPENEDLINKEDIDS.equals(id))
+ {
+ continue;
+ }
+ ArgValuesMap avm = linkedArgs.get(id);
+ // don't set an output if there isn't an input
+ if (a.hasOption(Opt.REQUIREINPUT)
+ && !avm.hasArgWithOption(Opt.INPUT))
+ continue;
+
+ ArgValues tavs = avm.getOrCreateArgValues(a);
+ switch (op)
+ {
+
+ case ADDVALUE:
+ String val = v;
+ if (sv != null)
+ {
+ if (doSubs)
+ {
+ sv = new SubVals(sv, val, merge);
+ val = makeSubstitutions(sv.getContent(), id);
+ }
+ tavs.addValue(sv, type, val, argIndex, true);
+ }
+ else
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, id);
+ }
+ tavs.addValue(type, val, argIndex, true);
+ }
+ finaliseStoringArgValue(id, tavs);
+ break;
+
+ case SETBOOLEAN:
+ tavs.setBoolean(type, b, argIndex, true);
+ finaliseStoringArgValue(id, tavs);
+ break;
+
+ case SETNEGATED:
+ tavs.setNegated(b, true);
+ break;
+
+ case INCREMENTCOUNT:
+ tavs.incrementCount();
+ break;
+
+ default:
+ break;
+
+ }
+
+ }
+ }
+ else // no wildcard linkedId -- do it simpler
+ {
+ switch (op)
+ {
+ case ADDVALUE:
+ String val = v;
+ if (sv != null)
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, linkedId);
+ sv = new SubVals(sv, val);
+ }
+ avs.addValue(sv, type, val, argIndex, false);
+ }
+ else
+ {
+ if (doSubs)
+ {
+ val = makeSubstitutions(v, linkedId);
+ }
+ avs.addValue(type, val, argIndex, false);
+ }
+ finaliseStoringArgValue(linkedId, avs);
+ break;
+
+ case SETBOOLEAN:
+ avs.setBoolean(type, b, argIndex, false);
+ finaliseStoringArgValue(linkedId, avs);
+ break;
+
+ case SETNEGATED:
+ avs.setNegated(b, false);
+ break;
+
+ case INCREMENTCOUNT:
+ avs.incrementCount();
+ break;
+
+ default:
+ break;
}
}
- return new ArgParser(argsList);
+ }
+
+ private ArgValuesMap getOrCreateLinkedArgValuesMap(String linkedId)
+ {
+ if (linkedArgs.containsKey(linkedId)
+ && linkedArgs.get(linkedId) != null)
+ return linkedArgs.get(linkedId);
+
+ linkedArgs.put(linkedId, new ArgValuesMap(linkedId));
+ return linkedArgs.get(linkedId);
+ }
+
+ public boolean isOldStyle()
+ {
+ return oldArguments;
+ }
+
+ public boolean isMixedStyle()
+ {
+ return mixedArguments;
+ }
+
+ public String[] getMixedExamples()
+ {
+ return mixedExamples;
}
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff