Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/schema_salad/java/main_utils/LoadingOptions.java @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 package ${package}.utils;
2
3 import java.net.URI;
4 import java.util.ArrayList;
5 import java.util.Arrays;
6 import java.util.List;
7 import java.util.Map;
8
9 public class LoadingOptions {
10 Fetcher fetcher;
11 String fileUri;
12 Map<String, String> namespaces;
13 List<String> schemas;
14 Map<String, Map<String, Object>> idx;
15 Map<String, String> vocab;
16 Map<String, String> rvocab;
17
18 LoadingOptions(
19 final Fetcher fetcher,
20 final String fileUri,
21 final Map<String, String> namespaces,
22 final List<String> schemas,
23 final Map<String, Map<String, Object>> idx) {
24 this.fetcher = fetcher;
25 this.fileUri = fileUri;
26 this.namespaces = namespaces;
27 this.schemas = schemas;
28 this.idx = idx;
29
30 if (namespaces != null) {
31 this.vocab = (Map<String, String>) ConstantMaps.vocab.clone();
32 this.rvocab = (Map<String, String>) ConstantMaps.rvocab.clone();
33 for (Map.Entry<String, String> namespaceEntry : namespaces.entrySet()) {
34 this.vocab.put(namespaceEntry.getKey(), namespaceEntry.getValue());
35 this.rvocab.put(namespaceEntry.getValue(), namespaceEntry.getKey());
36 }
37 } else {
38 this.vocab = (Map<String, String>) ConstantMaps.vocab;
39 this.rvocab = (Map<String, String>) ConstantMaps.rvocab;
40 }
41 }
42
43 public String expandUrl(
44 String url_,
45 final String baseUrl,
46 final boolean scopedId,
47 final boolean vocabTerm,
48 final Integer scopedRef) {
49 // NOT CONVERTING this - doesn't match type declaration
50 // if not isinstance(url, string_types):
51 // return url
52 String url = url_;
53 if (url.equals("@id") || url.equals("@type")) {
54 return url;
55 }
56
57 if (vocabTerm && this.vocab.containsKey(url)) {
58 return url;
59 }
60
61 if (!this.vocab.isEmpty() && url.contains(":")) {
62 String prefix = url.split(":", 1)[0];
63 if (this.vocab.containsKey(prefix)) {
64 url = this.vocab.get(prefix) + url.substring(prefix.length() + 1);
65 }
66 }
67
68 Uris.UriSplit split = Uris.split(url);
69 final String scheme = split.scheme;
70 final boolean hasFragment = stringHasContent(split.fragment);
71 if (scheme != null
72 && ((scheme.length() > 0
73 && (scheme.equals("http") || scheme.equals("https") || scheme.equals("file")))
74 || url.startsWith("$(")
75 || url.startsWith("${"))) {
76 // pass
77 } else if (scopedId && !hasFragment) {
78 final Uris.UriSplit splitbase = Uris.split(baseUrl);
79 final String frg;
80 if (stringHasContent(splitbase.fragment)) {
81 frg = splitbase.fragment + "/" + split.path;
82 } else {
83 frg = split.path;
84 }
85 String pt;
86 if (!splitbase.path.equals("")) {
87 pt = splitbase.path;
88 } else {
89 pt = "/";
90 }
91 url = Uris.unsplit(splitbase.scheme, splitbase.netloc, pt, splitbase.query, frg);
92 } else if (scopedRef != null && !hasFragment) {
93 final Uris.UriSplit splitbase = Uris.split(baseUrl);
94 final ArrayList<String> sp = new ArrayList(Arrays.asList(splitbase.fragment.split("/")));
95 int n = scopedRef;
96 while (n > 0 && sp.size() > 0) {
97 sp.remove(0);
98 n -= 1;
99 }
100 sp.add(url);
101 final String fragment = String.join("/", sp);
102 url = Uris.unsplit(splitbase.scheme, splitbase.netloc, splitbase.path, splitbase.query, fragment);
103 } else {
104 url = this.fetcher.urlJoin(baseUrl, url);
105 }
106
107 if (vocabTerm) {
108 split = Uris.split(url);
109 if (stringHasContent(split.scheme)) {
110 if (this.rvocab.containsKey(url)) {
111 return this.rvocab.get(url);
112 }
113 } else {
114 throw new ValidationException("Term '{}' not in vocabulary".format(url));
115 }
116 }
117 return url;
118 }
119
120 static boolean stringHasContent(final String s) {
121 return s != null && s.length() > 0;
122 }
123 }