#1694

Committed 30 Sep 2024 10:51AM UTC coverage: 70.306% (-0.5%) from 70.811%

Build # #1694

Build Type

push

github

Committed by

mr-c

Commit Message

detect non-Workflow CWL documents and give a better error message

Run Details

2 of 19 new or added lines in 4 files covered. (10.53%)

106 existing lines in 4 files now uncovered.

1700 of 2418 relevant lines covered (70.31%)

0.7 hits per line

Source File
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96.43

/src/main/java/org/commonwl/view/workflow/WorkflowFormValidator.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.commonwl.view.workflow;

import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.commons.lang.StringUtils;
import org.commonwl.view.git.GitDetails;
import org.springframework.stereotype.Component;
import org.springframework.validation.Errors;
import org.springframework.validation.ValidationUtils;

/** Runs validation on the workflow form from the main page */
@Component
public class WorkflowFormValidator {

  // URL validation for cwl files on github.com
  private static final String GITHUB_CWL_REGEX =
      "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
  private static final Pattern githubCwlPattern = Pattern.compile(GITHUB_CWL_REGEX);

  // URL validation for directories on github.com
  private static final String GITHUB_DIR_REGEX =
      "^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree|blob)\\/([^/]+)\\/?(.*)?)?$";
  private static final Pattern githubDirPattern = Pattern.compile(GITHUB_DIR_REGEX);

  // URL validation for cwl files on gitlab.com
  private static final String GITLAB_CWL_REGEX =
      "^https?:\\/\\/gitlab\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
  private static final Pattern gitlabCwlPattern = Pattern.compile(GITLAB_CWL_REGEX);

  // URL validation for directories on gitlab.com
  private static final String GITLAB_DIR_REGEX =
      "^https?:\\/\\/gitlab\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree|blob)\\/([^/]+)\\/?(.*)?)?$";
  private static final Pattern gitlabDirPattern = Pattern.compile(GITLAB_DIR_REGEX);

  // Generic Git URL validation
  private static final String GIT_REPO_REGEX =
      "^((git|ssh|http(s)?)|(git@[\\w\\.]+))(:(//)?)([\\w\\.@\\:/\\-~]+)(\\.git)(/)?$";
  private static final Pattern gitRepoPattern = Pattern.compile(GIT_REPO_REGEX);

  /**
   * Validates a WorkflowForm to ensure the URL is not empty and links to a cwl file
   *
   * @param form The given WorkflowForm
   * @param e Any errors from validation
   */
  public GitDetails validateAndParse(WorkflowForm form, Errors e) {
    ValidationUtils.rejectIfEmptyOrWhitespace(e, "url", "url.emptyOrWhitespace");

    // If not null and isn't just whitespace
    if (!e.hasErrors()) {

      // Override if specific branch or path is given in the form
      String repoUrl = null;
      String branch = null;
      String path = null;
      String packedId = null;
      if (!isEmptyOrWhitespace(form.getBranch())) {
        branch = form.getBranch();
      }
      if (!isEmptyOrWhitespace(form.getPath())) {
        path = form.getPath();
      }
      if (!isEmptyOrWhitespace(form.getPackedId())) {
        packedId = form.getPackedId();
      }

      // github.com URL
      Matcher m = githubCwlPattern.matcher(form.getUrl());
      if (m.find()) {
        repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
        if (branch == null) branch = m.group(3);
        if (path == null) path = m.group(4);
      }

      // gitlab.com URL
      m = gitlabCwlPattern.matcher(form.getUrl());
      if (m.find()) {
        repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
        if (branch == null) branch = m.group(3);
        if (path == null) path = m.group(4);
      }

      // github.com Dir URL
      m = githubDirPattern.matcher(form.getUrl());
      if (m.find() && !m.group(2).endsWith(".git")) {
        repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";
        if (branch == null) branch = m.group(3);
        if (path == null) path = m.group(4);
      }

      // gitlab.com Dir URL
      m = gitlabDirPattern.matcher(form.getUrl());
      if (m.find() && !m.group(2).endsWith(".git")) {
        repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";
        if (branch == null) branch = m.group(3);
        if (path == null) path = m.group(4);
      }

      // Split off packed ID if present
      if (repoUrl != null) {
        GitDetails details = new GitDetails(repoUrl, branch, path);
        if (packedId != null) {
          details.setPackedId(packedId);
        } else {
          String[] pathSplit = path.split("#");
          if (pathSplit.length > 1) {
            details.setPath(pathSplit[pathSplit.length - 2]);
            details.setPackedId(pathSplit[pathSplit.length - 1]);
          }
        }
        return details;
      }

      // General Git details if didn't match the above
      ValidationUtils.rejectIfEmptyOrWhitespace(e, "branch", "branch.emptyOrWhitespace");
      if (!e.hasErrors()) {
        m = gitRepoPattern.matcher(form.getUrl());
        if (m.find()) {
          GitDetails details = new GitDetails(form.getUrl(), form.getBranch(), form.getPath());
          details.setPackedId(form.getPackedId());
          return details;
        }
      }
    }

    // Errors will stop this being used anyway
    return null;
  }

  /**
   * Checks if a string is empty or whitespace
   *
   * @param str The string to be checked
   * @return Whether the string is empty or whitespace
   */
  private boolean isEmptyOrWhitespace(String str) {
    return (str == null || str.length() == 0 || StringUtils.isWhitespace(str));
  }
}

1	/*
2	* Licensed to the Apache Software Foundation (ASF) under one
3	* or more contributor license agreements. See the NOTICE file
4	* distributed with this work for additional information
5	* regarding copyright ownership. The ASF licenses this file
6	* to you under the Apache License, Version 2.0 (the
7	* "License"); you may not use this file except in compliance
8	* with the License. You may obtain a copy of the License at
9	*
10	* http://www.apache.org/licenses/LICENSE-2.0
11	*
12	* Unless required by applicable law or agreed to in writing,
13	* software distributed under the License is distributed on an
14	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
15	* KIND, either express or implied. See the License for the
16	* specific language governing permissions and limitations
17	* under the License.
18	*/
19
20	package org.commonwl.view.workflow;
21
22	import java.util.regex.Matcher;
23	import java.util.regex.Pattern;
24	import org.apache.commons.lang.StringUtils;
25	import org.commonwl.view.git.GitDetails;
26	import org.springframework.stereotype.Component;
27	import org.springframework.validation.Errors;
28	import org.springframework.validation.ValidationUtils;
29
30	/** Runs validation on the workflow form from the main page */
31	@Component
32	public class WorkflowFormValidator {	1✔
33
34	// URL validation for cwl files on github.com
35	private static final String GITHUB_CWL_REGEX =
36	"^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree\|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
37	private static final Pattern githubCwlPattern = Pattern.compile(GITHUB_CWL_REGEX);	1✔
38
39	// URL validation for directories on github.com
40	private static final String GITHUB_DIR_REGEX =
41	"^https?:\\/\\/github\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree\|blob)\\/([^/]+)\\/?(.*)?)?$";
42	private static final Pattern githubDirPattern = Pattern.compile(GITHUB_DIR_REGEX);	1✔
43
44	// URL validation for cwl files on gitlab.com
45	private static final String GITLAB_CWL_REGEX =
46	"^https?:\\/\\/gitlab\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:tree\|blob)\\/([^/]+)(?:\\/(.+\\.cwl))$";
47	private static final Pattern gitlabCwlPattern = Pattern.compile(GITLAB_CWL_REGEX);	1✔
48
49	// URL validation for directories on gitlab.com
50	private static final String GITLAB_DIR_REGEX =
51	"^https?:\\/\\/gitlab\\.com\\/([A-Za-z0-9_.-]+)\\/([A-Za-z0-9_.-]+)\\/?(?:(?:tree\|blob)\\/([^/]+)\\/?(.*)?)?$";
52	private static final Pattern gitlabDirPattern = Pattern.compile(GITLAB_DIR_REGEX);	1✔
53
54	// Generic Git URL validation
55	private static final String GIT_REPO_REGEX =
56	"^((git\|ssh\|http(s)?)\|(git@[\\w\\.]+))(:(//)?)([\\w\\.@\\:/\\-~]+)(\\.git)(/)?$";
57	private static final Pattern gitRepoPattern = Pattern.compile(GIT_REPO_REGEX);	1✔
58
59	/**
60	* Validates a WorkflowForm to ensure the URL is not empty and links to a cwl file
61	*
62	* @param form The given WorkflowForm
63	* @param e Any errors from validation
64	*/
65	public GitDetails validateAndParse(WorkflowForm form, Errors e) {
66	ValidationUtils.rejectIfEmptyOrWhitespace(e, "url", "url.emptyOrWhitespace");	1✔
67
68	// If not null and isn't just whitespace
69	if (!e.hasErrors()) {	1✔
70
71	// Override if specific branch or path is given in the form
72	String repoUrl = null;	1✔
73	String branch = null;	1✔
74	String path = null;	1✔
75	String packedId = null;	1✔
76	if (!isEmptyOrWhitespace(form.getBranch())) {	1✔
77	branch = form.getBranch();	1✔
78	}
79	if (!isEmptyOrWhitespace(form.getPath())) {	1✔
80	path = form.getPath();	1✔
81	}
82	if (!isEmptyOrWhitespace(form.getPackedId())) {	1✔
UNCOV 83	packedId = form.getPackedId();	×
84	}
85
86	// github.com URL
87	Matcher m = githubCwlPattern.matcher(form.getUrl());	1✔
88	if (m.find()) {	1✔
89	repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";	1✔
90	if (branch == null) branch = m.group(3);	1✔
91	if (path == null) path = m.group(4);	1✔
92	}
93
94	// gitlab.com URL
95	m = gitlabCwlPattern.matcher(form.getUrl());	1✔
96	if (m.find()) {	1✔
97	repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";	1✔
98	if (branch == null) branch = m.group(3);	1✔
99	if (path == null) path = m.group(4);	1✔
100	}
101
102	// github.com Dir URL
103	m = githubDirPattern.matcher(form.getUrl());	1✔
104	if (m.find() && !m.group(2).endsWith(".git")) {	1✔
105	repoUrl = "https://github.com/" + m.group(1) + "/" + m.group(2) + ".git";	1✔
106	if (branch == null) branch = m.group(3);	1✔
107	if (path == null) path = m.group(4);	1✔
108	}
109
110	// gitlab.com Dir URL
111	m = gitlabDirPattern.matcher(form.getUrl());	1✔
112	if (m.find() && !m.group(2).endsWith(".git")) {	1✔
113	repoUrl = "https://gitlab.com/" + m.group(1) + "/" + m.group(2) + ".git";	1✔
114	if (branch == null) branch = m.group(3);	1✔
115	if (path == null) path = m.group(4);	1✔
116	}
117
118	// Split off packed ID if present
119	if (repoUrl != null) {	1✔
120	GitDetails details = new GitDetails(repoUrl, branch, path);	1✔
121	if (packedId != null) {	1✔
UNCOV 122	details.setPackedId(packedId);	×
123	} else {
124	String[] pathSplit = path.split("#");	1✔
125	if (pathSplit.length > 1) {	1✔
126	details.setPath(pathSplit[pathSplit.length - 2]);	1✔
127	details.setPackedId(pathSplit[pathSplit.length - 1]);	1✔
128	}
129	}
130	return details;	1✔
131	}
132
133	// General Git details if didn't match the above
134	ValidationUtils.rejectIfEmptyOrWhitespace(e, "branch", "branch.emptyOrWhitespace");	1✔
135	if (!e.hasErrors()) {	1✔
136	m = gitRepoPattern.matcher(form.getUrl());	1✔
137	if (m.find()) {	1✔
138	GitDetails details = new GitDetails(form.getUrl(), form.getBranch(), form.getPath());	1✔
139	details.setPackedId(form.getPackedId());	1✔
140	return details;	1✔
141	}
142	}
143	}
144
145	// Errors will stop this being used anyway
146	return null;	1✔
147	}
148
149	/**
150	* Checks if a string is empty or whitespace
151	*
152	* @param str The string to be checked
153	* @return Whether the string is empty or whitespace
154	*/
155	private boolean isEmptyOrWhitespace(String str) {
156	return (str == null \|\| str.length() == 0 \|\| StringUtils.isWhitespace(str));	1✔
157	}
158	}

common-workflow-language / cwlviewer / #1694

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