13853363634

Committed 14 Mar 2025 09:10AM UTC coverage: 65.081% (+0.1%) from 64.959%

Build # 13853363634

Build Type

push

github

Committed by

web-flow

Commit Message

TRUNK-6304 Refactor code to use Storage Service (#4944)

* TRUNK-6300 Add Storage Service

* TRUNK-6304 Refactor code to use Storage Service

Run Details

319 of 401 new or added lines in 13 files covered. (79.55%)

17 existing lines in 4 files now uncovered.

23407 of 35966 relevant lines covered (65.08%)

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71.88

/api/src/main/java/org/openmrs/obs/handler/TextHandler.java

/**
 * This Source Code Form is subject to the terms of the Mozilla Public License,
 * v. 2.0. If a copy of the MPL was not distributed with this file, You can
 * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
 * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
 *
 * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
 * graphic logo is a trademark of OpenMRS Inc.
 */
package org.openmrs.obs.handler;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.Reader;
import java.io.UncheckedIOException;
import java.nio.charset.StandardCharsets;

import org.apache.commons.io.IOUtils;
import org.openmrs.Obs;
import org.openmrs.api.APIException;
import org.openmrs.api.storage.ObjectMetadata;
import org.openmrs.obs.ComplexData;
import org.openmrs.obs.ComplexObsHandler;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import org.springframework.util.Assert;

/**
 * Handler for storing files for complex obs to the file system. Files are stored in the location
 * specified by the global property: "obs.complex_obs_dir"
 * The in coming data are either char[] or java.io.Reader
 *
 */
@Component
public class TextHandler extends AbstractHandler implements ComplexObsHandler {
        
        /** Views supported by this handler */
        private static final String[] supportedViews = { ComplexObsHandler.TEXT_VIEW, ComplexObsHandler.RAW_VIEW,
                ComplexObsHandler.URI_VIEW };
        
        private static final Logger log = LoggerFactory.getLogger(TextHandler.class);
        
        /**
         * Constructor initializes formats for alternative file names to protect from unintentionally
         * overwriting existing files.
         */
        public TextHandler() {
                super();
        }
        
        /**
         * 
         * 
         * @see org.openmrs.obs.ComplexObsHandler#getObs(org.openmrs.Obs, java.lang.String)
         */
        @Override
        public Obs getObs(Obs obs, String view) {
                String key = parseDataKey(obs);
                
                log.debug("value complex: {}", obs.getValueComplex());
                log.debug("file path: {}", key);
                ComplexData complexData = null;
                
                if (ComplexObsHandler.TEXT_VIEW.equals(view) || ComplexObsHandler.RAW_VIEW.equals(view)) {
                        // to handle problem with downloading/saving files with blank spaces or commas in their names
                        // also need to remove the "file" text appended to the end of the file name
                        String[] names = obs.getValueComplex().split("\\|");
                        String originalFilename = names[0];
                        originalFilename = originalFilename.replaceAll(",", "")
                                .replaceAll(" ", "").replaceAll("file$", "");
                        
                        try (InputStream is = storageService.getData(key)){
                                complexData = ComplexObsHandler.RAW_VIEW.equals(view) ? new ComplexData(originalFilename, 
                                        IOUtils.toByteArray(is)) : new ComplexData(originalFilename, 
                                        IOUtils.toString(is, StandardCharsets.UTF_8));
                        }
                        catch (IOException e) {
                                log.error("Trying to read file: {}", key, e);
                        }
                } else if (ComplexObsHandler.URI_VIEW.equals(view)) {
                        complexData = new ComplexData(parseDataTitle(obs), key);
                } else {
                        // No other view supported
                        // NOTE: if adding support for another view, don't forget to update supportedViews list above
                        return null;
                }
                Assert.notNull(complexData, "Complex data must not be null");
                
                // Get the Mime Type and set it
                ObjectMetadata metadata;
                try {
                        metadata = storageService.getMetadata(key);
                } catch (IOException e) {
                        throw new UncheckedIOException(e);
                }
                String mimeType = metadata.getMimeType();
                mimeType = !(mimeType.equals("application/octet-stream")) ? mimeType : "text/plain";
                complexData.setMimeType(mimeType);
                complexData.setLength(metadata.getLength());
                obs.setComplexData(complexData);
                
                return obs;
        }
        
        /**
         * @see org.openmrs.obs.ComplexObsHandler#getSupportedViews()
         */
        @Override
        public String[] getSupportedViews() {
                return supportedViews;
        }
        
        /**
         * 
         * 
         * @see org.openmrs.obs.ComplexObsHandler#saveObs(org.openmrs.Obs)
         */
        @Override
        public Obs saveObs(Obs obs) throws APIException {
                ComplexData complexData = obs.getComplexData();
                if (complexData == null) {
                        log.error("Cannot save complex data where obsId={} because its ComplexData is null.", obs.getObsId());
                        return obs;
                }
                try {
                        String assignedKey = storageService.saveData((out) -> {
                                BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8));

                                Object data = obs.getComplexData().getData();
                                if (data instanceof char[]) {
                                        writer.write((char[]) data);
                                } else if (Reader.class.isAssignableFrom(data.getClass())) {
                                        try (Reader reader = new BufferedReader((Reader) data)){
                                                IOUtils.copy(reader, writer);
                                        }
                                        catch (IOException e) {
                                                throw new APIException("Obs.error.unable.convert.complex.data", new Object[] { "Reader" }, e);
                                        }
                                } else if (InputStream.class.isAssignableFrom(data.getClass())) {
                                        try (Reader reader = new BufferedReader(new InputStreamReader((InputStream) data, 
                                                StandardCharsets.UTF_8))) {
                                                IOUtils.copy(reader, writer);
                                        }
                                        catch (IOException e) {
                                                throw new APIException("Obs.error.unable.convert.complex.data", new Object[] { "input stream" }, e);
                                        }
                                }
                                writer.flush();
                        }, ObjectMetadata.builder().setFilename(obs.getComplexData().getTitle()).build(),  getObsDir());
                        
                        // Set the Title and URI for the valueComplex
                        obs.setValueComplex(obs.getComplexData().getTitle() + " file |" + assignedKey);
                        
                        // Remove the ComplexData from the Obs
                        obs.setComplexData(null);
                        
                }
                catch (IOException ioe) {
                        throw new APIException("Obs.error.trying.write.complex", null, ioe);
                }
                
                return obs;
        }
        
}

1	/**
2	* This Source Code Form is subject to the terms of the Mozilla Public License,
3	* v. 2.0. If a copy of the MPL was not distributed with this file, You can
4	* obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
5	* the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
6	*
7	* Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
8	* graphic logo is a trademark of OpenMRS Inc.
9	*/
10	package org.openmrs.obs.handler;
11
12	import java.io.BufferedReader;
13	import java.io.BufferedWriter;
14	import java.io.IOException;
15	import java.io.InputStream;
16	import java.io.InputStreamReader;
17	import java.io.OutputStreamWriter;
18	import java.io.Reader;
19	import java.io.UncheckedIOException;
20	import java.nio.charset.StandardCharsets;
21
22	import org.apache.commons.io.IOUtils;
23	import org.openmrs.Obs;
24	import org.openmrs.api.APIException;
25	import org.openmrs.api.storage.ObjectMetadata;
26	import org.openmrs.obs.ComplexData;
27	import org.openmrs.obs.ComplexObsHandler;
28	import org.slf4j.Logger;
29	import org.slf4j.LoggerFactory;
30	import org.springframework.stereotype.Component;
31	import org.springframework.util.Assert;
32
33	/**
34	* Handler for storing files for complex obs to the file system. Files are stored in the location
35	* specified by the global property: "obs.complex_obs_dir"
36	* The in coming data are either char[] or java.io.Reader
37	*
38	*/
39	@Component
40	public class TextHandler extends AbstractHandler implements ComplexObsHandler {
41
42	/** Views supported by this handler */
43	private static final String[] supportedViews = { ComplexObsHandler.TEXT_VIEW, ComplexObsHandler.RAW_VIEW,	1✔
44	ComplexObsHandler.URI_VIEW };
45
46	private static final Logger log = LoggerFactory.getLogger(TextHandler.class);	1✔
47
48	/**
49	* Constructor initializes formats for alternative file names to protect from unintentionally
50	* overwriting existing files.
51	*/
52	public TextHandler() {
53	super();	1✔
54	}	1✔
55
56	/**
57	*
58	*
59	* @see org.openmrs.obs.ComplexObsHandler#getObs(org.openmrs.Obs, java.lang.String)
60	*/
61	@Override
62	public Obs getObs(Obs obs, String view) {
63	String key = parseDataKey(obs);	1✔
64
65	log.debug("value complex: {}", obs.getValueComplex());	1✔
66	log.debug("file path: {}", key);	1✔
67	ComplexData complexData = null;	1✔
68
69	if (ComplexObsHandler.TEXT_VIEW.equals(view) \|\| ComplexObsHandler.RAW_VIEW.equals(view)) {	1✔
70	// to handle problem with downloading/saving files with blank spaces or commas in their names
71	// also need to remove the "file" text appended to the end of the file name
72	String[] names = obs.getValueComplex().split("\\\|");	1✔
73	String originalFilename = names[0];	1✔
74	originalFilename = originalFilename.replaceAll(",", "")	1✔
75	.replaceAll(" ", "").replaceAll("file$", "");	1✔
76
77	try (InputStream is = storageService.getData(key)){	1✔
78	complexData = ComplexObsHandler.RAW_VIEW.equals(view) ? new ComplexData(originalFilename,	1✔
79	IOUtils.toByteArray(is)) : new ComplexData(originalFilename,	1✔
80	IOUtils.toString(is, StandardCharsets.UTF_8));	1✔
81	}
82	catch (IOException e) {	×
NEW 83	log.error("Trying to read file: {}", key, e);	×
84	}	1✔
85	} else if (ComplexObsHandler.URI_VIEW.equals(view)) {	1✔
NEW 86	complexData = new ComplexData(parseDataTitle(obs), key);	×
87	} else {
88	// No other view supported
89	// NOTE: if adding support for another view, don't forget to update supportedViews list above
90	return null;	×
91	}
92	Assert.notNull(complexData, "Complex data must not be null");	1✔
93
94	// Get the Mime Type and set it
95	ObjectMetadata metadata;
96	try {
97	metadata = storageService.getMetadata(key);	1✔
NEW 98	} catch (IOException e) {	×
NEW 99	throw new UncheckedIOException(e);	×
100	}	1✔
101	String mimeType = metadata.getMimeType();	1✔
102	mimeType = !(mimeType.equals("application/octet-stream")) ? mimeType : "text/plain";	1✔
103	complexData.setMimeType(mimeType);	1✔
104	complexData.setLength(metadata.getLength());	1✔
105	obs.setComplexData(complexData);	1✔
106
107	return obs;	1✔
108	}
109
110	/**
111	* @see org.openmrs.obs.ComplexObsHandler#getSupportedViews()
112	*/
113	@Override
114	public String[] getSupportedViews() {
115	return supportedViews;	1✔
116	}
117
118	/**
119	*
120	*
121	* @see org.openmrs.obs.ComplexObsHandler#saveObs(org.openmrs.Obs)
122	*/
123	@Override
124	public Obs saveObs(Obs obs) throws APIException {
125	ComplexData complexData = obs.getComplexData();	1✔
126	if (complexData == null) {	1✔
NEW 127	log.error("Cannot save complex data where obsId={} because its ComplexData is null.", obs.getObsId());	×
128	return obs;	×
129	}
130	try {
131	String assignedKey = storageService.saveData((out) -> {	1✔
132	BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(out, StandardCharsets.UTF_8));	1✔
133
134	Object data = obs.getComplexData().getData();	1✔
135	if (data instanceof char[]) {	1✔
NEW 136	writer.write((char[]) data);	×
137	} else if (Reader.class.isAssignableFrom(data.getClass())) {	1✔
138	try (Reader reader = new BufferedReader((Reader) data)){	1✔
139	IOUtils.copy(reader, writer);	1✔
140	}
NEW 141	catch (IOException e) {	×
NEW 142	throw new APIException("Obs.error.unable.convert.complex.data", new Object[] { "Reader" }, e);	×
143	}	1✔
144	} else if (InputStream.class.isAssignableFrom(data.getClass())) {	1✔
NEW 145	try (Reader reader = new BufferedReader(new InputStreamReader((InputStream) data,	×
146	StandardCharsets.UTF_8))) {
NEW 147	IOUtils.copy(reader, writer);	×
148	}
NEW 149	catch (IOException e) {	×
NEW 150	throw new APIException("Obs.error.unable.convert.complex.data", new Object[] { "input stream" }, e);	×
UNCOV 151	}	×
152	}
153	writer.flush();	1✔
154	}, ObjectMetadata.builder().setFilename(obs.getComplexData().getTitle()).build(), getObsDir());	1✔
155
156	// Set the Title and URI for the valueComplex
157	obs.setValueComplex(obs.getComplexData().getTitle() + " file \|" + assignedKey);	1✔
158
159	// Remove the ComplexData from the Obs
160	obs.setComplexData(null);	1✔
161
162	}
163	catch (IOException ioe) {	×
164	throw new APIException("Obs.error.trying.write.complex", null, ioe);	×
165	}	1✔
166
167	return obs;	1✔
168	}
169
170	}

openmrs / openmrs-core / 13853363634

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