13853363634

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

Build # 13853363634

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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.

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80.85

/api/src/main/java/org/openmrs/obs/handler/BinaryDataHandler.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.IOException;
import java.io.InputStream;
import java.io.UncheckedIOException;

import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
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"
 * 
 * @since 1.5
 */
@Component
public class BinaryDataHandler extends AbstractHandler implements ComplexObsHandler {
        
        /** Views supported by this handler */
        private static final String[] supportedViews = { ComplexObsHandler.RAW_VIEW, };
        
        private static final Logger log = LoggerFactory.getLogger(BinaryDataHandler.class);
        
        /**
         * Constructor initializes formats for alternative file names to protect from unintentionally
         * overwriting existing files.
         */
        public BinaryDataHandler() {
                super();
        }
        
        /**
         * Currently supports the following views: org.openmrs.obs.ComplexObsHandler#RAW_VIEW
         * 
         * @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;
                
                // Raw view (i.e. the file as is)
                if (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 in = storageService.getData(key)){
                                complexData = new ComplexData(originalFilename, IOUtils.toByteArray(in));
                        }
                        catch (IOException e) {
                                log.error("Trying to read file: {}", key, e);
                        }
                } 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");
                
                injectMissingMetadata(key, complexData);
                obs.setComplexData(complexData);
                
                return obs;
        }
        
        /**
         * @see org.openmrs.obs.ComplexObsHandler#getSupportedViews()
         */
        @Override
        public String[] getSupportedViews() {
                return supportedViews;
        }
        
        /**
         * TODO should this support a StringReader too?
         * 
         * @see org.openmrs.obs.ComplexObsHandler#saveObs(org.openmrs.Obs)
         */
        @Override
        public Obs saveObs(Obs obs) throws APIException {
                // Get the buffered file  from the ComplexData.
                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 {
                        Object data = obs.getComplexData().getData();
                        ObjectMetadata metadata = new ObjectMetadata();
                        if (data instanceof byte[]) {
                                metadata.setLength((long) ((byte[]) data).length);        
                        }
                        metadata.setFilename(obs.getComplexData().getTitle());
                        
                        String key = storageService.saveData(outputStream -> {
                                if (data instanceof byte[]) {
                                        IOUtils.write((byte[]) data, outputStream);
                                } else if (InputStream.class.isAssignableFrom(data.getClass())) {
                                        IOUtils.copy((InputStream) data, outputStream);
                                }
                                outputStream.flush();
                        }, metadata, getObsDir());

                        // Set the Title and URI for the valueComplex
                        obs.setValueComplex(StringUtils.defaultIfBlank(obs.getComplexData().getTitle(), key) + " file |" + key);

                        // Remove the ComplexData from the Obs
                        obs.setComplexData(null);
                } catch (IOException e) {
                        throw new UncheckedIOException(e);
                }
                
                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.IOException;
13	import java.io.InputStream;
14	import java.io.UncheckedIOException;
15
16	import org.apache.commons.io.IOUtils;
17	import org.apache.commons.lang3.StringUtils;
18	import org.openmrs.Obs;
19	import org.openmrs.api.APIException;
20	import org.openmrs.api.storage.ObjectMetadata;
21	import org.openmrs.obs.ComplexData;
22	import org.openmrs.obs.ComplexObsHandler;
23	import org.slf4j.Logger;
24	import org.slf4j.LoggerFactory;
25	import org.springframework.stereotype.Component;
26	import org.springframework.util.Assert;
27
28	/**
29	* Handler for storing files for complex obs to the file system. Files are stored in the location
30	* specified by the global property: "obs.complex_obs_dir"
31	*
32	* @since 1.5
33	*/
34	@Component
35	public class BinaryDataHandler extends AbstractHandler implements ComplexObsHandler {
36
37	/** Views supported by this handler */
38	private static final String[] supportedViews = { ComplexObsHandler.RAW_VIEW, };	1✔
39
40	private static final Logger log = LoggerFactory.getLogger(BinaryDataHandler.class);	1✔
41
42	/**
43	* Constructor initializes formats for alternative file names to protect from unintentionally
44	* overwriting existing files.
45	*/
46	public BinaryDataHandler() {
47	super();	1✔
48	}	1✔
49
50	/**
51	* Currently supports the following views: org.openmrs.obs.ComplexObsHandler#RAW_VIEW
52	*
53	* @see org.openmrs.obs.ComplexObsHandler#getObs(org.openmrs.Obs, java.lang.String)
54	*/
55	@Override
56	public Obs getObs(Obs obs, String view) {
57	String key = parseDataKey(obs);	1✔
58
59	log.debug("value complex: {}", obs.getValueComplex());	1✔
60	log.debug("file path: {}", key);	1✔
61	ComplexData complexData = null;	1✔
62
63	// Raw view (i.e. the file as is)
64	if (ComplexObsHandler.RAW_VIEW.equals(view)) {	1✔
65	// to handle problem with downloading/saving files with blank spaces or commas in their names
66	// also need to remove the "file" text appended to the end of the file name
67	String[] names = obs.getValueComplex().split("\\\|");	1✔
68	String originalFilename = names[0];	1✔
69	originalFilename = originalFilename.replaceAll(",", "")	1✔
70	.replaceAll(" ", "").replaceAll("file$", "");	1✔
71
72	try (InputStream in = storageService.getData(key)){	1✔
73	complexData = new ComplexData(originalFilename, IOUtils.toByteArray(in));	1✔
74	}
75	catch (IOException e) {	×
NEW 76	log.error("Trying to read file: {}", key, e);	×
77	}	1✔
78	} else {	1✔
79	// No other view supported
80	// NOTE: if adding support for another view, don't forget to update supportedViews list above
81	return null;	×
82	}
83
84	Assert.notNull(complexData, "Complex data must not be null");	1✔
85
86	injectMissingMetadata(key, complexData);	1✔
87	obs.setComplexData(complexData);	1✔
88
89	return obs;	1✔
90	}
91
92	/**
93	* @see org.openmrs.obs.ComplexObsHandler#getSupportedViews()
94	*/
95	@Override
96	public String[] getSupportedViews() {
97	return supportedViews;	1✔
98	}
99
100	/**
101	* TODO should this support a StringReader too?
102	*
103	* @see org.openmrs.obs.ComplexObsHandler#saveObs(org.openmrs.Obs)
104	*/
105	@Override
106	public Obs saveObs(Obs obs) throws APIException {
107	// Get the buffered file from the ComplexData.
108	ComplexData complexData = obs.getComplexData();	1✔
109	if (complexData == null) {	1✔
NEW 110	log.error("Cannot save complex data where obsId={} because its ComplexData is null.", obs.getObsId());	×
111	return obs;	×
112	}
113	try {
114	Object data = obs.getComplexData().getData();	1✔
115	ObjectMetadata metadata = new ObjectMetadata();	1✔
116	if (data instanceof byte[]) {	1✔
117	metadata.setLength((long) ((byte[]) data).length);	1✔
118	}
119	metadata.setFilename(obs.getComplexData().getTitle());	1✔
120
121	String key = storageService.saveData(outputStream -> {	1✔
122	if (data instanceof byte[]) {	1✔
123	IOUtils.write((byte[]) data, outputStream);	1✔
NEW 124	} else if (InputStream.class.isAssignableFrom(data.getClass())) {	×
NEW 125	IOUtils.copy((InputStream) data, outputStream);	×
126	}
127	outputStream.flush();	1✔
128	}, metadata, getObsDir());	1✔
129
130	// Set the Title and URI for the valueComplex
131	obs.setValueComplex(StringUtils.defaultIfBlank(obs.getComplexData().getTitle(), key) + " file \|" + key);	1✔
132
133	// Remove the ComplexData from the Obs
134	obs.setComplexData(null);	1✔
NEW 135	} catch (IOException e) {	×
NEW 136	throw new UncheckedIOException(e);	×
137	}	1✔
138
139	return obs;	1✔
140	}
141
142	}

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