17380144000

Committed 01 Sep 2025 02:12PM UTC coverage: 12.03% (+0.05%) from 11.978%

Build # 17380144000

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor: replace printStackTrace with logger.error for better error handling

Run Details

330 of 3850 branches covered (8.57%)

Branch coverage included in aggregate %.

958 of 6857 relevant lines covered (13.97%)

0.62 hits per line

Source File
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68.06

src/main/java/com/knowledgepixels/nanodash/NanodashPreferences.java

package com.knowledgepixels.nanodash;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.File;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Class to manage Nanodash preferences.
 */
public class NanodashPreferences implements Serializable {

    private static final long serialVersionUID = 1L;
    private static NanodashPreferences obj;
    private static final Logger logger = LoggerFactory.getLogger(NanodashPreferences.class);

    /**
     * Get the singleton instance of NanodashPreferences.
     *
     * @return the NanodashPreferences instance
     */
    public static NanodashPreferences get() {
        if (obj == null) {
            File prefFile = new File(System.getProperty("user.home") + "/.nanopub/nanodash-preferences.yml");
            if (!prefFile.exists()) {
                return new NanodashPreferences();
            }
            ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
            try {
                obj = mapper.readValue(prefFile, NanodashPreferences.class);
            } catch (IOException ex) {
                obj = new NanodashPreferences();
                logger.error("Could not read preferences file, using defaults.", ex);
            }
        }
        return obj;
    }

    private List<String> nanopubActions = new ArrayList<>();
    private boolean readOnlyMode = false;
    private String websiteUrl = "http://localhost:37373/";
    private boolean orcidLoginMode = false;
    private String orcidClientId;
    private String orcidClientSecret;
    private String settingUri;

    /**
     * Return the list of nanopub actions.
     *
     * @return list of nanopub actions
     */
    public List<String> getNanopubActions() {
        String s = System.getenv("NANODASH_NANOPUB_ACTIONS");
        if (!(s == null) && !s.isEmpty()) return Arrays.asList(s.split(" "));
        return nanopubActions;
    }

    /**
     * Set the list of nanopub actions.
     *
     * @param nanopubActions the list of nanopub actions
     */
    public void setNanopubActions(List<String> nanopubActions) {
        this.nanopubActions = nanopubActions;
    }

    /**
     * Check if the application is in read-only mode.
     *
     * @return true if in read-only mode, false otherwise
     */
    public boolean isReadOnlyMode() {
        if ("true".equals(System.getenv("NANODASH_READ_ONLY_MODE"))) return true;
        return readOnlyMode;
    }

    /**
     * Set the read-only mode.
     *
     * @param readOnlyMode true to enable read-only mode, false to disable
     */
    public void setReadOnlyMode(boolean readOnlyMode) {
        this.readOnlyMode = readOnlyMode;
    }

    /**
     * Get the website URL.
     *
     * @return the website URL
     */
    public String getWebsiteUrl() {
        String s = System.getenv("NANODASH_WEBSITE_URL");
        if (!(s == null) && !s.isEmpty()) return s;
        return websiteUrl;
    }

    /**
     * Set the website URL.
     *
     * @param websiteUrl the website URL to set
     */
    public void setWebsiteUrl(String websiteUrl) {
        this.websiteUrl = websiteUrl;
    }

    /**
     * Check if the application is in ORCID login mode.
     *
     * @return true if in ORCID login mode, false otherwise
     */
    public boolean isOrcidLoginMode() {
        if ("true".equals(System.getenv("NANODASH_ORCID_LOGIN_MODE"))) return true;
        return orcidLoginMode;
    }

    /**
     * Set the ORCID login mode.
     *
     * @param orcidLoginMode true to enable ORCID login mode, false to disable
     */
    public void setOrcidLoginMode(boolean orcidLoginMode) {
        this.orcidLoginMode = orcidLoginMode;
    }

    /**
     * Get the ORCID client ID.
     *
     * @return the ORCID client ID
     */
    public String getOrcidClientId() {
        String s = System.getenv("NANOPUB_ORCID_CLIENT_ID");
        if (!(s == null) && !s.isEmpty()) return s;
        return orcidClientId;
    }

    /**
     * Set the ORCID client ID.
     *
     * @param orcidClientId the ORCID client ID to set
     */
    public void setOrcidClientId(String orcidClientId) {
        this.orcidClientId = orcidClientId;
    }

    /**
     * Get the ORCID client secret.
     *
     * @return the ORCID client secret
     */
    public String getOrcidClientSecret() {
        String s = System.getenv("NANOPUB_ORCID_CLIENT_SECRET");
        if (!(s == null) && !s.isEmpty()) return s;
        return orcidClientSecret;
    }

    /**
     * Set the ORCID client secret.
     *
     * @param orcidClientSecret the ORCID client secret to set
     */
    public void setOrcidClientSecret(String orcidClientSecret) {
        this.orcidClientSecret = orcidClientSecret;
    }

    /**
     * Get the setting URI.
     *
     * @return the setting URI
     */
    public String getSettingUri() {
        return settingUri;
    }

    /**
     * Set the setting URI.
     *
     * @param settingUri the setting URI to set
     */
    public void setSettingUri(String settingUri) {
        this.settingUri = settingUri;
    }

}

1	package com.knowledgepixels.nanodash;
2
3	import com.fasterxml.jackson.databind.ObjectMapper;
4	import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
5	import org.slf4j.Logger;
6	import org.slf4j.LoggerFactory;
7
8	import java.io.File;
9	import java.io.IOException;
10	import java.io.Serializable;
11	import java.util.ArrayList;
12	import java.util.Arrays;
13	import java.util.List;
14
15	/**
16	* Class to manage Nanodash preferences.
17	*/
18	public class NanodashPreferences implements Serializable {	2✔
19
20	private static final long serialVersionUID = 1L;
21	private static NanodashPreferences obj;
22	private static final Logger logger = LoggerFactory.getLogger(NanodashPreferences.class);	4✔
23
24	/**
25	* Get the singleton instance of NanodashPreferences.
26	*
27	* @return the NanodashPreferences instance
28	*/
29	public static NanodashPreferences get() {
30	if (obj == null) {	2!
31	File prefFile = new File(System.getProperty("user.home") + "/.nanopub/nanodash-preferences.yml");	7✔
32	if (!prefFile.exists()) {	3!
33	return new NanodashPreferences();	4✔
34	}
35	ObjectMapper mapper = new ObjectMapper(new YAMLFactory());	×
36	try {
37	obj = mapper.readValue(prefFile, NanodashPreferences.class);	×
38	} catch (IOException ex) {	×
39	obj = new NanodashPreferences();	×
40	logger.error("Could not read preferences file, using defaults.", ex);	×
41	}	×
42	}
43	return obj;	×
44	}
45
46	private List<String> nanopubActions = new ArrayList<>();	5✔
47	private boolean readOnlyMode = false;	3✔
48	private String websiteUrl = "http://localhost:37373/";	3✔
49	private boolean orcidLoginMode = false;	4✔
50	private String orcidClientId;
51	private String orcidClientSecret;
52	private String settingUri;
53
54	/**
55	* Return the list of nanopub actions.
56	*
57	* @return list of nanopub actions
58	*/
59	public List<String> getNanopubActions() {
60	String s = System.getenv("NANODASH_NANOPUB_ACTIONS");	3✔
61	if (!(s == null) && !s.isEmpty()) return Arrays.asList(s.split(" "));	2!
62	return nanopubActions;	3✔
63	}
64
65	/**
66	* Set the list of nanopub actions.
67	*
68	* @param nanopubActions the list of nanopub actions
69	*/
70	public void setNanopubActions(List<String> nanopubActions) {
71	this.nanopubActions = nanopubActions;	3✔
72	}	1✔
73
74	/**
75	* Check if the application is in read-only mode.
76	*
77	* @return true if in read-only mode, false otherwise
78	*/
79	public boolean isReadOnlyMode() {
80	if ("true".equals(System.getenv("NANODASH_READ_ONLY_MODE"))) return true;	5!
81	return readOnlyMode;	3✔
82	}
83
84	/**
85	* Set the read-only mode.
86	*
87	* @param readOnlyMode true to enable read-only mode, false to disable
88	*/
89	public void setReadOnlyMode(boolean readOnlyMode) {
90	this.readOnlyMode = readOnlyMode;	3✔
91	}	1✔
92
93	/**
94	* Get the website URL.
95	*
96	* @return the website URL
97	*/
98	public String getWebsiteUrl() {
99	String s = System.getenv("NANODASH_WEBSITE_URL");	3✔
100	if (!(s == null) && !s.isEmpty()) return s;	2!
101	return websiteUrl;	3✔
102	}
103
104	/**
105	* Set the website URL.
106	*
107	* @param websiteUrl the website URL to set
108	*/
109	public void setWebsiteUrl(String websiteUrl) {
110	this.websiteUrl = websiteUrl;	3✔
111	}	1✔
112
113	/**
114	* Check if the application is in ORCID login mode.
115	*
116	* @return true if in ORCID login mode, false otherwise
117	*/
118	public boolean isOrcidLoginMode() {
119	if ("true".equals(System.getenv("NANODASH_ORCID_LOGIN_MODE"))) return true;	5!
120	return orcidLoginMode;	3✔
121	}
122
123	/**
124	* Set the ORCID login mode.
125	*
126	* @param orcidLoginMode true to enable ORCID login mode, false to disable
127	*/
128	public void setOrcidLoginMode(boolean orcidLoginMode) {
129	this.orcidLoginMode = orcidLoginMode;	3✔
130	}	1✔
131
132	/**
133	* Get the ORCID client ID.
134	*
135	* @return the ORCID client ID
136	*/
137	public String getOrcidClientId() {
138	String s = System.getenv("NANOPUB_ORCID_CLIENT_ID");	3✔
139	if (!(s == null) && !s.isEmpty()) return s;	2!
140	return orcidClientId;	3✔
141	}
142
143	/**
144	* Set the ORCID client ID.
145	*
146	* @param orcidClientId the ORCID client ID to set
147	*/
148	public void setOrcidClientId(String orcidClientId) {
149	this.orcidClientId = orcidClientId;	3✔
150	}	1✔
151
152	/**
153	* Get the ORCID client secret.
154	*
155	* @return the ORCID client secret
156	*/
157	public String getOrcidClientSecret() {
158	String s = System.getenv("NANOPUB_ORCID_CLIENT_SECRET");	3✔
159	if (!(s == null) && !s.isEmpty()) return s;	2!
160	return orcidClientSecret;	3✔
161	}
162
163	/**
164	* Set the ORCID client secret.
165	*
166	* @param orcidClientSecret the ORCID client secret to set
167	*/
168	public void setOrcidClientSecret(String orcidClientSecret) {
169	this.orcidClientSecret = orcidClientSecret;	3✔
170	}	1✔
171
172	/**
173	* Get the setting URI.
174	*
175	* @return the setting URI
176	*/
177	public String getSettingUri() {
178	return settingUri;	3✔
179	}
180
181	/**
182	* Set the setting URI.
183	*
184	* @param settingUri the setting URI to set
185	*/
186	public void setSettingUri(String settingUri) {
187	this.settingUri = settingUri;	3✔
188	}	1✔
189
190	}

knowledgepixels / nanodash / 17380144000

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