#394

Committed 31 Oct 2025 04:10PM UTC coverage: 57.972% (-1.6%) from 59.538%

Build # #394

Build Type

push

github

Committed by

mr-c

Commit Message

rename package to a namespace that we control

Coverage Stats

7575 of 12994 new or added lines in 261 files covered. (58.3%)

7752 of 13372 relevant lines covered (57.97%)

0.58 hits per line

Source File
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92.42

/src/main/java/org/commonwl/cwlsdk/cwl1_2/utils/Loader.java

package org.commonwl.cwlsdk.cwl1_2.utils;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

public interface Loader<T> {

  T load(
      final Object doc,
      final String baseUri,
      final LoadingOptions loadingOptions,
      final String docRoot);

  default T load(final Object doc, final String baseUri, final LoadingOptions loadingOptions) {
    return load(doc, baseUri, loadingOptions, null);
  }

  default T documentLoad(
      final String doc, final String baseUri, final LoadingOptions loadingOptions) {
    return load(doc, baseUri, loadingOptions);
  }

  default T documentLoad(
      final Map<String, Object> doc_, final String baseUri_, final LoadingOptions loadingOptions_) {
    Map<String, Object> doc = doc_;
    LoadingOptions loadingOptions = loadingOptions_;
    if (doc.containsKey("$namespaces")) {
      final Map<String, String> namespaces = (Map<String, String>) doc.get("$namespaces");
      loadingOptions =
          new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNamespaces(namespaces).build();
      doc = copyWithoutKey(doc, "$namespaces");
    }
    String baseUri = baseUri_;
    if (doc.containsKey("$base")) {
      baseUri = (String) doc.get("$base");
    }
    if (doc.containsKey("$graph")) {
      return load(doc.get("$graph"), baseUri, loadingOptions);
    } else {
      return load(doc, baseUri, loadingOptions, baseUri);
    }
  }

  default T documentLoad(
      final List<Object> doc, final String baseUri, final LoadingOptions loadingOptions) {
    return load(doc, baseUri, loadingOptions);
  }

  default T documentLoadByUrl(final String url, final LoadingOptions loadingOptions) {
    if (loadingOptions.idx.containsKey(url)) {
      Object result = loadingOptions.idx.get(url);
      if (result instanceof String) {
        return documentLoad((String) result, url, loadingOptions);
      } else if (result instanceof Map) {
        return documentLoad((Map<String, Object>) result, url, loadingOptions);
      }
      return load(result, url, loadingOptions);
    }

    final String text = loadingOptions.fetcher.fetchText(url);
    try {
      Map<String, Object> resultMap = YamlUtils.mapFromString(text);
      loadingOptions.idx.put(url, resultMap);
      final LoadingOptionsBuilder urlLoadingOptions =
          new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url);
      return documentLoad(resultMap, url, urlLoadingOptions.build());
    } catch (ClassCastException e) {
      List<Object> resultList = YamlUtils.listFromString(text);
      loadingOptions.idx.put(url, resultList);
      final LoadingOptionsBuilder urlLoadingOptions =
          new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url);
      return documentLoad(resultList, url, urlLoadingOptions.build());
    }
  }

  default T loadField(
      final Object val_, final String baseUri, final LoadingOptions loadingOptions) {
    Object val = val_;
    if (val instanceof Map) {
      Map<String, Object> valMap = (Map<String, Object>) val;
      if (valMap.containsKey("$import")) {
        if (loadingOptions.fileUri == null) {
          throw new ValidationException("Cannot load $import without fileuri");
        }
        return documentLoadByUrl(
            loadingOptions.fetcher.urlJoin(loadingOptions.fileUri, (String) valMap.get("$import")),
            loadingOptions);
      } else if (valMap.containsKey("$include")) {
        if (loadingOptions.fileUri == null) {
          throw new ValidationException("Cannot load $import without fileuri");
        }
        val =
            loadingOptions.fetcher.fetchText(
                loadingOptions.fetcher.urlJoin(
                    loadingOptions.fileUri, (String) valMap.get("$include")));
      }
    }
    return load(val, baseUri, loadingOptions);
  }

  default Map<String, Object> copyWithoutKey(final Map<String, Object> doc, final String key) {
    final Map<String, Object> result = new HashMap();
    for (final Map.Entry<String, Object> entry : doc.entrySet()) {
      if (!entry.getKey().equals(key)) {
        result.put(entry.getKey(), entry.getValue());
      }
    }
    return result;
  }

  static <T> T validateOfJavaType(final Class<T> clazz, final Object doc) {
    if (!clazz.isInstance(doc)) {
      String className = "null";
      if (doc != null) {
        className = doc.getClass().getName();
      }
      final String message =
          String.format(
              "Expected object with Java type of %s but got %s", clazz.getName(), className);
      throw new ValidationException(message);
    }
    return (T) doc;
  }
}

1	package org.commonwl.cwlsdk.cwl1_2.utils;
2
3	import java.util.HashMap;
4	import java.util.List;
5	import java.util.Map;
6
7	public interface Loader<T> {
8
9	T load(
10	final Object doc,
11	final String baseUri,
12	final LoadingOptions loadingOptions,
13	final String docRoot);
14
15	default T load(final Object doc, final String baseUri, final LoadingOptions loadingOptions) {
16	return load(doc, baseUri, loadingOptions, null);	1✔
17	}
18
19	default T documentLoad(
20	final String doc, final String baseUri, final LoadingOptions loadingOptions) {
NEW 21	return load(doc, baseUri, loadingOptions);	×
22	}
23
24	default T documentLoad(
25	final Map<String, Object> doc_, final String baseUri_, final LoadingOptions loadingOptions_) {
26	Map<String, Object> doc = doc_;	1✔
27	LoadingOptions loadingOptions = loadingOptions_;	1✔
28	if (doc.containsKey("$namespaces")) {	1✔
29	final Map<String, String> namespaces = (Map<String, String>) doc.get("$namespaces");	1✔
30	loadingOptions =	1✔
31	new LoadingOptionsBuilder().copiedFrom(loadingOptions).setNamespaces(namespaces).build();	1✔
32	doc = copyWithoutKey(doc, "$namespaces");	1✔
33	}
34	String baseUri = baseUri_;	1✔
35	if (doc.containsKey("$base")) {	1✔
NEW 36	baseUri = (String) doc.get("$base");	×
37	}
38	if (doc.containsKey("$graph")) {	1✔
39	return load(doc.get("$graph"), baseUri, loadingOptions);	1✔
40	} else {
41	return load(doc, baseUri, loadingOptions, baseUri);	1✔
42	}
43	}
44
45	default T documentLoad(
46	final List<Object> doc, final String baseUri, final LoadingOptions loadingOptions) {
47	return load(doc, baseUri, loadingOptions);	1✔
48	}
49
50	default T documentLoadByUrl(final String url, final LoadingOptions loadingOptions) {
51	if (loadingOptions.idx.containsKey(url)) {	1✔
52	Object result = loadingOptions.idx.get(url);	1✔
53	if (result instanceof String) {	1✔
NEW 54	return documentLoad((String) result, url, loadingOptions);	×
55	} else if (result instanceof Map) {	1✔
56	return documentLoad((Map<String, Object>) result, url, loadingOptions);	1✔
57	}
58	return load(result, url, loadingOptions);	1✔
59	}
60
61	final String text = loadingOptions.fetcher.fetchText(url);	1✔
62	try {
63	Map<String, Object> resultMap = YamlUtils.mapFromString(text);	1✔
64	loadingOptions.idx.put(url, resultMap);	1✔
65	final LoadingOptionsBuilder urlLoadingOptions =	1✔
66	new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url);	1✔
67	return documentLoad(resultMap, url, urlLoadingOptions.build());	1✔
68	} catch (ClassCastException e) {	1✔
69	List<Object> resultList = YamlUtils.listFromString(text);	1✔
70	loadingOptions.idx.put(url, resultList);	1✔
71	final LoadingOptionsBuilder urlLoadingOptions =	1✔
72	new LoadingOptionsBuilder().copiedFrom(loadingOptions).setFileUri(url);	1✔
73	return documentLoad(resultList, url, urlLoadingOptions.build());	1✔
74	}
75	}
76
77	default T loadField(
78	final Object val_, final String baseUri, final LoadingOptions loadingOptions) {
79	Object val = val_;	1✔
80	if (val instanceof Map) {	1✔
81	Map<String, Object> valMap = (Map<String, Object>) val;	1✔
82	if (valMap.containsKey("$import")) {	1✔
83	if (loadingOptions.fileUri == null) {	1✔
NEW 84	throw new ValidationException("Cannot load $import without fileuri");	×
85	}
86	return documentLoadByUrl(	1✔
87	loadingOptions.fetcher.urlJoin(loadingOptions.fileUri, (String) valMap.get("$import")),	1✔
88	loadingOptions);
89	} else if (valMap.containsKey("$include")) {	1✔
90	if (loadingOptions.fileUri == null) {	1✔
NEW 91	throw new ValidationException("Cannot load $import without fileuri");	×
92	}
93	val =	1✔
94	loadingOptions.fetcher.fetchText(	1✔
95	loadingOptions.fetcher.urlJoin(	1✔
96	loadingOptions.fileUri, (String) valMap.get("$include")));	1✔
97	}
98	}
99	return load(val, baseUri, loadingOptions);	1✔
100	}
101
102	default Map<String, Object> copyWithoutKey(final Map<String, Object> doc, final String key) {
103	final Map<String, Object> result = new HashMap();	1✔
104	for (final Map.Entry<String, Object> entry : doc.entrySet()) {	1✔
105	if (!entry.getKey().equals(key)) {	1✔
106	result.put(entry.getKey(), entry.getValue());	1✔
107	}
108	}	1✔
109	return result;	1✔
110	}
111
112	static <T> T validateOfJavaType(final Class<T> clazz, final Object doc) {
113	if (!clazz.isInstance(doc)) {	1✔
114	String className = "null";	1✔
115	if (doc != null) {	1✔
116	className = doc.getClass().getName();	1✔
117	}
118	final String message =	1✔
119	String.format(	1✔
120	"Expected object with Java type of %s but got %s", clazz.getName(), className);	1✔
121	throw new ValidationException(message);	1✔
122	}
123	return (T) doc;	1✔
124	}
125	}

common-workflow-language / cwljava / #394

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