Nonrandomparameters

api/src/main/java/org/fairdatapipeline/api/CodeRepo.java

@@ -1,6 +1,5 @@
 package org.fairdatapipeline.api;
 
-import java.net.URL;
 import java.util.List;
 import org.fairdatapipeline.dataregistry.restclient.APIURL;
 
@@ -15,7 +14,7 @@ class CodeRepo {
 
   CodeRepo(
       String latest_commit,
-      URL repo_url,
+      String repo_url,
       String description,
       List<APIURL> authors,
       Coderun coderun) {

api/src/main/java/org/fairdatapipeline/api/Coderun.java

@@ -3,9 +3,7 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.net.MalformedURLException;
 import java.net.URI;
-import java.net.URL;
 import java.nio.file.*;
 import java.time.LocalDateTime;
 import java.util.*;
@@ -237,18 +235,11 @@ private void prepare_code_run() {
     this.registryCode_run.setSubmission_script(this.script_object.getUrl());
     String latest_commit = this.config.run_metadata().latest_commit().orElse("");
     String remote_repo = this.config.run_metadata().remote_repo().orElse("");
-    URL remote_repo_url;
-    try {
-      remote_repo_url = new URL(remote_repo);
-    } catch (MalformedURLException e) {
-      throw (new ConfigException(
-          "Remote repo must be a valid URL; (" + remote_repo + " isn't)", e));
-    }
 
     this.codeRepo =
         new CodeRepo(
             latest_commit,
-            remote_repo_url,
+            remote_repo,
             "Analysis / processing script location",
             this.authors,
             this);

api/src/main/java/org/fairdatapipeline/api/Object_component_read.java

@@ -4,8 +4,14 @@
 import java.nio.file.Path;
 import java.util.List;
 import org.fairdatapipeline.distribution.Distribution;
+import org.fairdatapipeline.distribution.ImmutableDistribution;
+import org.fairdatapipeline.estimate.ImmutableEstimate;
 import org.fairdatapipeline.file.CleanableFileChannel;
+import org.fairdatapipeline.parameters.ImmutableBoolList;
+import org.fairdatapipeline.parameters.ImmutableNumberList;
+import org.fairdatapipeline.parameters.ImmutableStringList;
 import org.fairdatapipeline.parameters.ReadComponent;
+import org.fairdatapipeline.samples.ImmutableSamples;
 
 /**
  * This represents an object_component to read from (or raise issues with) An object_component
@@ -77,7 +83,11 @@
     } catch (IOException e) {
       throw (new RuntimeException("readEstimate() -- IOException trying to read from file", e));
     }
-    return data.getEstimate();
+    if (!(data instanceof ImmutableEstimate)) {
+      throw (new RuntimeException(
+          "readEstimate() -- this objComponent (" + this.component_name + ") is not an estimate"));
+    }
+    return ((ImmutableEstimate) data).getEstimate();
   }
 
   /**
@@ -93,7 +103,70 @@
       throw (new RuntimeException(
           "readDistribution() -- IOException trying to read from file.", e));
     }
-    return data.getDistribution();
+    if (!(data instanceof ImmutableDistribution)) {
+      throw (new RuntimeException(
+          "readDistribution() -- this objComponent ("
+              + this.component_name
+              + ") is not a distribution"));
+    }
+    return ((ImmutableDistribution) data).getDistribution();
+  }
+
+  /**
+   * read the Bools that were stored as this component in a TOML file.
+   *
+   * @return the Bools object
+   */
+  public List<Boolean> readBools() {
+    ReadComponent data;
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      data = this.dp.coderun.parameterDataReader.read(fileChannel, this.component_name);
+    } catch (IOException e) {
+      throw (new RuntimeException("readBools() -- IOException trying to read from file.", e));
+    }
+    if (!(data instanceof ImmutableBoolList)) {
+      throw (new RuntimeException(
+          "readBools() -- this objComponent (" + this.component_name + ") is not a BoolList"));
+    }
+    return ((ImmutableBoolList) data).getBools();
+  }
+
+  /**
+   * read the Strings that were stored as this component in a TOML file.
+   *
+   * @return the Strings object
+   */
+  public List<String> readStrings() {
+    ReadComponent data;
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      data = this.dp.coderun.parameterDataReader.read(fileChannel, this.component_name);
+    } catch (IOException e) {
+      throw (new RuntimeException("readStrings() -- IOException trying to read from file.", e));
+    }
+    if (!(data instanceof ImmutableStringList)) {
+      throw (new RuntimeException(
+          "readStrings() -- this objComponent (" + this.component_name + ") is not a StringList"));
+    }
+    return ((ImmutableStringList) data).getStrings();
+  }
+
+  /**
+   * read the Numbers that were stored as this component in a TOML file.
+   *
+   * @return the Numbers object
+   */
+  public List<Number> readNumbers() {
+    ReadComponent data;
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      data = this.dp.coderun.parameterDataReader.read(fileChannel, this.component_name);
+    } catch (IOException e) {
+      throw (new RuntimeException("readStrings() -- IOException trying to read from file.", e));
+    }
+    if (!(data instanceof ImmutableNumberList)) {
+      throw (new RuntimeException(
+          "readNumbers() -- this objComponent (" + this.component_name + ") is not a NumberList"));
+    }
+    return ((ImmutableNumberList) data).getNumbers();
   }
 
   /**
@@ -108,7 +181,11 @@
     } catch (IOException e) {
       throw (new RuntimeException("readSamples() -- IOException trying to read from file.", e));
     }
-    return data.getSamples();
+    if (!(data instanceof ImmutableSamples)) {
+      throw (new RuntimeException(
+          "readSamples() -- this objComponent (" + this.component_name + ") is not a samples"));
+    }
+    return ((ImmutableSamples) data).getSamples();
   }
 
   void register_me_in_registry() {

api/src/main/java/org/fairdatapipeline/api/Object_component_write.java

@@ -7,6 +7,9 @@
 import org.fairdatapipeline.distribution.Distribution;
 import org.fairdatapipeline.estimate.ImmutableEstimate;
 import org.fairdatapipeline.file.CleanableFileChannel;
+import org.fairdatapipeline.parameters.BoolList;
+import org.fairdatapipeline.parameters.NumberList;
+import org.fairdatapipeline.parameters.StringList;
 import org.fairdatapipeline.samples.Samples;
 
 /**
@@ -64,6 +67,9 @@
    * @param estimateNumber the number to write.
    */
   public void writeEstimate(Number estimateNumber) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
     var estimate =
         ImmutableEstimate.builder().internalValue(estimateNumber).rng(this.dp.coderun.rng).build();
 
@@ -72,6 +78,7 @@
     } catch (IOException e) {
       throw (new RuntimeException("writeEstimate() -- IOException trying to write to file.", e));
     }
+    this.been_used = true;
   }
 
   /**
@@ -80,12 +87,67 @@
    * @param distribution the Distribution to write
    */
   public void writeDistribution(Distribution distribution) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
     try (CleanableFileChannel fileChannel = this.getFileChannel()) {
       this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, distribution);
     } catch (IOException e) {
       throw (new RuntimeException(
           "writeDistribution() -- IOException trying to write to file.", e));
     }
+    this.been_used = true;
+  }
+
+  /**
+   * write a BoolList, as this named component in the data product.
+   *
+   * @param bools the Booleans to write
+   */
+  public void writeBools(BoolList bools) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, bools);
+    } catch (IOException e) {
+      throw (new RuntimeException("writeBools() -- IOException trying to write to file.", e));
+    }
+    this.been_used = true;
+  }
+
+  /**
+   * write a StringList, as this named component in the data product.
+   *
+   * @param strings the Strings to write
+   */
+  public void writeStrings(StringList strings) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, strings);
+    } catch (IOException e) {
+      throw (new RuntimeException("writeStrings() -- IOException trying to write to file.", e));
+    }
+    this.been_used = true;
+  }
+
+  /**
+   * write NumberList, as this named component in the data product.
+   *
+   * @param numbers the Numbers to write
+   */
+  public void writeNumbers(NumberList numbers) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
+    try (CleanableFileChannel fileChannel = this.getFileChannel()) {
+      this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, numbers);
+    } catch (IOException e) {
+      throw (new RuntimeException("writeStrings() -- IOException trying to write to file.", e));
+    }
+    this.been_used = true;
   }
 
   /**
@@ -94,11 +156,15 @@
    * @param samples a Samples object containing the samples
    */
   public void writeSamples(Samples samples) {
+    if (this.been_used) {
+      throw (new RuntimeException("obj component already written"));
+    }
     try (CleanableFileChannel fileChannel = this.getFileChannel()) {
       this.dp.coderun.parameterDataWriter.write(fileChannel, this.component_name, samples);
     } catch (IOException e) {
       throw (new RuntimeException("writeSamples() -- IOException trying to write to file.", e));
     }
+    this.been_used = true;
   }
 
   void register_me_in_code_run() {

api/src/main/java/org/fairdatapipeline/api/Storage_location.java

@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 import java.net.URI;
-import java.net.URL;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Map;
@@ -14,6 +13,7 @@
 /** This is used to store a file or a remote repo to the registry as a RegistryStorage_location. */
 class Storage_location {
   private static final Logger logger = LoggerFactory.getLogger(Storage_location.class);
+
   RegistryStorage_location registryStorage_location;
 
   /**
@@ -25,8 +25,8 @@ class Storage_location {
    *     we will use the existing one instead of storing this one.
    * @param coderun link back to the Coderun that created us.
    */
-  Storage_location(URL remote_repo, String latest_commit, Coderun coderun) {
-    String[] split_repo = Storage_root.url_to_root(remote_repo);
+  Storage_location(String remote_repo, String latest_commit, Coderun coderun) {
+    String[] split_repo = Storage_root.gitrepo_to_root(remote_repo);
     Storage_root storage_root = new Storage_root(URI.create(split_repo[0]), coderun.restClient);
     create_storagelocation(latest_commit, storage_root, coderun, split_repo[1], null);
   }

api/src/main/java/org/fairdatapipeline/api/Storage_root.java

@@ -1,15 +1,21 @@
 package org.fairdatapipeline.api;
 
 import java.net.URI;
-import java.net.URL;
 import java.nio.file.Path;
 import java.util.Collections;
+import java.util.Objects;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import org.fairdatapipeline.dataregistry.content.RegistryStorage_root;
 import org.fairdatapipeline.dataregistry.restclient.APIURL;
 import org.fairdatapipeline.dataregistry.restclient.RestClient;
 
 /** Retrieve or create the RegistryStorage_root with a given 'root'. */
 class Storage_root {
+  private static Pattern git_repo_url =
+      Pattern.compile("(\\w+://)(.+@)*([\\w\\d\\.]+)(:[\\d]+){0,1}/*(.*)");
+  private static Pattern git_repo_file = Pattern.compile("file://(.*)");
+  private static Pattern git_repo_ssh = Pattern.compile("(.+@)([\\w\\d\\.]+):(.*)");
   RegistryStorage_root registryStorage_root;
 
   /**
@@ -47,15 +53,27 @@ Path getPath() {
   }
 
   /**
-   * split the repository URL into a storage root (proto://authority/ part) and path (/xxx/xxx) part
+   * split the repository location into a storage root HTTPS: proto://authority/path/to/stuff
+   * becomes proto://authority AND /path/to/stuff SSH: [email protected]:bboskamp/BTv.git becomes
+   * [email protected] AND /bboskamp/BTv.git
    *
-   * @param url the URL to split up into scheme/authority and path.
+   * @param repo_location the repository location string to split up into scheme/authority and path.
    * @return string array of length 2.
    */
-  static String[] url_to_root(URL url) {
-    String path = url.getPath().substring(1);
-    String scheme_and_authority_part =
-        url.toString().substring(0, url.toString().length() - path.length());
-    return new String[] {scheme_and_authority_part, path};
+  static String[] gitrepo_to_root(String repo_location) {
+    Matcher m1 = git_repo_url.matcher(repo_location);
+    if (m1.find())
+      return new String[] {
+        Objects.toString(m1.group(1), "")
+            + Objects.toString(m1.group(2), "")
+            + Objects.toString(m1.group(3), "")
+            + Objects.toString(m1.group(4), ""),
+        m1.group(5)
+      };
+    m1 = git_repo_file.matcher(repo_location);
+    if (m1.find()) return new String[] {"file://", m1.group(1)};
+    m1 = git_repo_ssh.matcher(repo_location);
+    if (m1.find()) return new String[] {m1.group(1) + m1.group(2), m1.group(3)};
+    return new String[] {};
   }
 }

api/src/main/java/org/fairdatapipeline/distribution/Distribution.java

@@ -18,7 +18,7 @@
 import org.apache.commons.math3.distribution.RealDistribution;
 import org.apache.commons.math3.distribution.UniformRealDistribution;
 import org.apache.commons.math3.random.EmpiricalDistribution;
-import org.fairdatapipeline.parameters.Component;
+import org.fairdatapipeline.parameters.RngComponent;
 import org.immutables.value.Value.Auxiliary;
 import org.immutables.value.Value.Check;
 import org.immutables.value.Value.Immutable;
@@ -33,7 +33,7 @@
  TODO support other distributions:
  https://github.com/ScottishCovidResponse/SCRCIssueTracking/issues/671
 */
-public interface Distribution extends Component {
+public interface Distribution extends RngComponent {
   enum DistributionType {
     gamma(),
     exponential(),

api/src/main/java/org/fairdatapipeline/estimate/Estimate.java

@@ -6,14 +6,14 @@
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import java.util.List;
 import org.fairdatapipeline.distribution.Distribution;
-import org.fairdatapipeline.parameters.Component;
+import org.fairdatapipeline.parameters.RngComponent;
 import org.immutables.value.Value.Immutable;
 
 /** a component to store a plain simple single Number */
 @Immutable
 @JsonDeserialize
 @JsonSerialize
-public interface Estimate extends Component {
+public interface Estimate extends RngComponent {
   /** @return Number - the value that is stored in this component */
   @JsonProperty("value")
   Number internalValue();