Merge pull request #180 from qbicsoftware/development

Release 2.2.0

README.md

@@ -102,11 +102,11 @@ When using the application, you can either:
 1. enter your password interactively `--password`
 2. enter the name of a system property containing your password `--password:prop my.awesome.property`
 ```bash
-java -jar -Dmy.awesome.property=ABCDEFG postman.jar -u qbc001a --password:prop my.awesome.property
+java -jar -Dmy.awesome.property=ABCDEFG postman.jar -u qbc001a --password:prop my.awesome.property @path/to/config.txt 
 ```
 3. enter the name of an environment variable containing your password `--password:env MY_PASSWORD`. Make sure to *not* use the `$` sign before the environment variable (as in bash variables) otherwise the password is not recognized (`--password:env $MY_PASSWORD` will fail)
 ```bash
-MY_PASSWORD=ABCDEFG java -jar postman.jar -u qbc001a --password:env MY_PASSWORD
+MY_PASSWORD=ABCDEFG java -jar postman.jar -u qbc001a --password:env MY_PASSWORD @path/to/config.txt 
 ```
 ### How to provide QBiC identifiers
 To specify which data you want to list or download, you need to provide us with QBiC identifiers. 
@@ -128,7 +128,7 @@ QSTTS001AB
 QSTTS002BC
 ```
 ```bash
-java -jar postman.jar -f myids.txt
+java -jar postman.jar -f myids.txt @path/to/config.txt 
 ```
 
 ### How to filter files by suffix
@@ -138,17 +138,36 @@ Multiple suffixes can be provided separated by a comma. A suffix does not have t
 
 If you only want to download `fastq` and `fastq.gz` files you can run postman with 
 ```bash
-java -jar postman.jar -s .fastq,.fastq.gz
+java -jar postman.jar -s .fastq,.fastq.gz @path/to/config.txt 
+```
+
+### How to filter by regular expression
+Both the `download` and the `list` command allow you to filter files using [a regular expression](https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html). 
+When filtering with a regular expression pattern, the path of the file as well as the filename are matched against the pattern. Only matching files are included in the output.
+
+If you only want to download files containing `test` in their path or in their name, you can run postman with
+```bash
+java -jar postman.jar --pattern ".*test.*" @path/to/config.txt 
+```
+Although this can be used to filter for suffixes as well, please use the `--suffix` option. 
+
+Instead of
+```bash
+java -jar postman.jar --pattern".*\.fastq\.gz" @path/to/config.txt 
+```
+do
+```bash
+java -jar postman.jar -s .fastq.gz @path/to/config.txt 
 ```
 
 ## `list`
 ```txt
 Usage: postman-cli list [-hV] [--exact-filesize] [--with-checksum]
-                        [--without-header] [--format=<outputFormat>] -u=<user>
-                        [-s=<suffix>[,<suffix>...]]... (--password:
-                        env=<environment-variable> | --password:
-                        prop=<system-property> | --password) (-f=<filePath> |
-                        SAMPLE_IDENTIFIER...)
+                        [--without-header] [--format=<format>]
+                        [--pattern=<regex_pattern>] -u=<user> [-s=<suffix>[,
+                        <suffix>...]]... (--password:env=<environment-variable>
+                        | --password:prop=<system-property> | --password)
+                        (-f=<filePath> | SAMPLE_IDENTIFIER...)
 
 Description:
 lists all the datasets found for the given identifiers
@@ -169,6 +188,8 @@ Options:
   -s, --suffix=<suffix>[,<suffix>...]
                              only include files ending with one of these
                                (case-insensitive) suffixes
+      --pattern=<regex_pattern>
+                             only include files with paths matching this pattern
       --with-checksum        list the crc32 checksum for each file
       --exact-filesize       use exact byte count instead of unit suffixes:
                                Byte, Kilobyte, Megabyte, Gigabyte, Terabyte and
@@ -220,8 +241,9 @@ NGSQSTTS015A0 (20211026111452695-847006)	NGSQSTTS015A0	2021-10-26T09:14:53.14381
 
 ```txt
 Usage: postman-cli download [-hV] [--ignore-subdirectories] [-o=<outputPath>]
-                            -u=<user> [-s=<suffix>[,<suffix>...]]...
-                            (--password:env=<environment-variable> | --password:
+                            [--pattern=<regex_pattern>] -u=<user> [-s=<suffix>[,
+                            <suffix>...]]... (--password:
+                            env=<environment-variable> | --password:
                             prop=<system-property> | --password) (-f=<filePath>
                             | SAMPLE_IDENTIFIER...)
 
@@ -244,6 +266,8 @@ Options:
   -s, --suffix=<suffix>[,<suffix>...]
                              only include files ending with one of these
                                (case-insensitive) suffixes
+      --pattern=<regex_pattern>
+                             only include files with paths matching this pattern
   -o, --output-dir=<outputPath>
                              specify where to write the downloaded data
       --ignore-subdirectories
@@ -252,7 +276,7 @@ Options:
                                with files with equal names are not addressed
   -h, --help                 Show this help message and exit.
   -V, --version              Print version information and exit.
-
+  
 Optional: specify a config file by running postman with '@/path/to/config.txt'.
 A detailed documentation can be found at https://github.com/qbicsoftware/postman-cli#readme.
 ```

src/main/java/life/qbic/qpostman/common/DefaultExceptionHandler.java

@@ -2,6 +2,7 @@
 
 import java.nio.file.Path;
 import java.util.Optional;
+import life.qbic.qpostman.common.functions.FileFilter.MalformedPatternException;
 import life.qbic.qpostman.common.options.AuthenticationOptions.NoPasswordException;
 import life.qbic.qpostman.common.options.SampleIdentifierOptions.IdentityFileEmptyException;
 import life.qbic.qpostman.common.options.SampleIdentifierOptions.IdentityFileNotFoundException;
@@ -49,6 +50,13 @@ private void logError(RuntimeException e) {
       log.error(
           "Please provide at least 5 letters for your sample identifiers. The following sample identifiers are to short: "
               + toShortSampleIdsException.getIdentifiers());
+    } else if (e instanceof MalformedPatternException malformedPatternException) {
+      log.error(
+          "The pattern %s is malformed:%s".formatted(malformedPatternException.getPatternString(),
+              malformedPatternException.getErrorDescription()));
+      log.debug(
+          "The pattern %s is malformed:%s".formatted(malformedPatternException.getPatternString(),
+              malformedPatternException.getErrorDescription()), malformedPatternException);
     } else {
       log.error("Something went wrong. For more detailed output see " + Path.of(LOG_PATH, "postman.log").toAbsolutePath());
       log.debug(e.getMessage(), e);

src/main/java/life/qbic/qpostman/common/functions/FileFilter.java

@@ -1,31 +1,74 @@
 package life.qbic.qpostman.common.functions;
 
+import static java.util.Objects.isNull;
+import static java.util.Objects.nonNull;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.function.Predicate;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
 import life.qbic.qpostman.common.structures.DataFile;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 /**
  * A class implementing the {@link Predicate} interface and providing file filtering functionality based on suffixes.
  */
 public class FileFilter implements Predicate<DataFile> {
+    private static final Logger log = LogManager.getLogger(FileFilter.class);
 
     private final List<String> suffixes;
     private final boolean caseSensitive;
+    private final Pattern pattern;
 
     public static FileFilter create() {
-        return new FileFilter(new ArrayList<>(), false);
+        return new FileFilter(new ArrayList<>(), false, null);
     }
 
     public FileFilter withSuffixes(List<String> suffixes) {
         var temp = new ArrayList<>(this.suffixes);
         temp.addAll(suffixes);
-        return new FileFilter(temp, caseSensitive);
+        return new FileFilter(temp, caseSensitive, pattern);
+    }
+
+    public FileFilter withPattern(String pattern) {
+        if (isNull(pattern)) {
+            return new FileFilter(suffixes, caseSensitive, null);
+        }
+        Pattern compiledPattern = null;
+        try {
+            compiledPattern = Pattern.compile(pattern);
+        } catch (PatternSyntaxException e) {
+            throw new MalformedPatternException(e, pattern, e.getMessage());
+        }
+        return new FileFilter(suffixes, caseSensitive, compiledPattern);
+    }
+
+    public static class MalformedPatternException extends RuntimeException {
+
+        private final String patternString;
+        private final String errorDescription;
+        public MalformedPatternException(Throwable cause, String patternString,
+            String errorDescription) {
+            super(cause);
+          this.patternString = patternString;
+          this.errorDescription = errorDescription;
+        }
+
+        public String getPatternString() {
+            return patternString;
+        }
+
+        public String getErrorDescription() {
+            return errorDescription;
+        }
     }
 
-    private FileFilter(List<String> suffixes, boolean caseSensitive) {
+    private FileFilter(List<String> suffixes, boolean caseSensitive, Pattern pattern) {
         this.suffixes = suffixes;
         this.caseSensitive = caseSensitive;
+        this.pattern = pattern;
     }
 
     @Override
@@ -35,6 +78,9 @@ public boolean test(DataFile dataFile) {
             result &= suffixes.stream()
                     .anyMatch(suffix -> hasSuffix(dataFile.fileName(), suffix));
         }
+        if (nonNull(pattern)) {
+            result &= pattern.matcher(dataFile.filePath()).matches();
+        }
         return result;
     }
 

src/main/java/life/qbic/qpostman/common/options/FilterOptions.java

@@ -12,6 +12,11 @@ public class FilterOptions {
             paramLabel = "<suffix>")
     public List<String> suffixes = new ArrayList<>(0);
 
+    @CommandLine.Option(names = {"--pattern"},
+        description= "only include files with paths matching this pattern",
+        paramLabel = "<regex_pattern>")
+    public String pattern = null;
+
     @Override
     public String toString() {
         return new StringJoiner(", ", FilterOptions.class.getSimpleName() + "[", "]")

src/main/java/life/qbic/qpostman/download/DownloadCommand.java

@@ -94,7 +94,8 @@ private Functions functions() {
         IApplicationServerApi applicationServerApi = ServerFactory.applicationServer(serverOptions.as_url, serverOptions.timeoutInMillis);
         OpenBisSessionProvider.init(applicationServerApi, authenticationOptions.user, new String(authenticationOptions.getPassword()));
         SearchDataSets searchDataSets = new SearchDataSets(applicationServerApi);
-        FileFilter myAwesomeFileFilter = FileFilter.create().withSuffixes(filterOptions.suffixes);
+        FileFilter myAwesomeFileFilter = FileFilter.create().withSuffixes(filterOptions.suffixes)
+            .withPattern(filterOptions.pattern);
         WriteFileToDisk writeFileToDisk = new WriteFileToDisk(dataStoreServerApis().toArray(IDataStoreServerApi[]::new)[0],
             downloadOptions.bufferSize, Path.of(downloadOptions.outputPath), downloadOptions.successiveDownloadAttempts,
             downloadOptions.ignoreSubDirectories);

src/main/java/life/qbic/qpostman/list/ListCommand.java

@@ -90,7 +90,8 @@ private Functions setupFunctions() {
             serverOptions.dss_urls, serverOptions.timeoutInMillis);
         SearchDataSets searchDataSets = new SearchDataSets(applicationServerApi);
         FileFilter myAwesomeFileFilter = FileFilter.create()
-            .withSuffixes(filterOptions.suffixes);
+            .withSuffixes(filterOptions.suffixes)
+            .withPattern(filterOptions.pattern);
         SearchFiles searchFiles = new SearchFiles(dataStoreServerApis, number -> {});
         FindSourceSample findSourceSample = new FindSourceSample(serverOptions.sourceSampleType);