Mercurial > hg > orthanc-tests
annotate Tests/Toolbox.py @ 735:be8f174d3c9d find-refactoring tip
tools/find: Limit and Since are now forbidden when filtering on DICOM tags that are not stored in DB
| author | Alain Mazy <am@orthanc.team> |
|---|---|
| date | Thu, 24 Oct 2024 15:08:59 +0200 |
| parents | 0322fda1834e |
| children | d2ac1c6588db |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/python |
| 2 | |
| 1 | 3 # Orthanc - A Lightweight, RESTful DICOM Store |
| 73 | 4 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
| 1 | 5 # Department, University Hospital of Liege, Belgium |
|
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6 # Copyright (C) 2017-2023 Osimis S.A., Belgium |
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7 # Copyright (C) 2024-2024 Orthanc Team SRL, Belgium |
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8 # Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 1 | 9 # |
| 10 # This program is free software: you can redistribute it and/or | |
| 11 # modify it under the terms of the GNU General Public License as | |
| 12 # published by the Free Software Foundation, either version 3 of the | |
| 13 # License, or (at your option) any later version. | |
| 14 # | |
| 15 # This program is distributed in the hope that it will be useful, but | |
| 16 # WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 18 # General Public License for more details. | |
| 19 # | |
| 20 # You should have received a copy of the GNU General Public License | |
| 21 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 0 | 22 |
| 23 | |
| 24 import hashlib | |
| 25 import httplib2 | |
| 26 import json | |
| 4 | 27 import os |
| 1 | 28 import re |
| 4 | 29 import signal |
| 1 | 30 import subprocess |
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31 import tempfile |
| 4 | 32 import threading |
| 83 | 33 import sys |
| 0 | 34 import time |
| 1 | 35 import zipfile |
| 0 | 36 |
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37 from xml.dom import minidom |
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38 |
| 304 | 39 from PIL import Image, ImageChops |
| 40 import math | |
| 41 import operator | |
| 42 | |
| 83 | 43 |
| 44 if (sys.version_info >= (3, 0)): | |
| 45 from urllib.parse import urlencode | |
| 46 from io import StringIO | |
| 47 from io import BytesIO | |
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48 from urllib.parse import unquote |
| 83 | 49 |
| 50 else: | |
| 51 from urllib import urlencode | |
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52 from urlparse import unquote |
| 83 | 53 |
| 54 # http://stackoverflow.com/a/1313868/881731 | |
| 55 try: | |
| 56 from cStringIO import StringIO | |
| 57 except: | |
| 58 from StringIO import StringIO | |
| 3 | 59 |
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60 |
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61 def DecodeJson(s): |
| 83 | 62 t = s |
| 63 | |
| 64 if (sys.version_info >= (3, 0)): | |
| 65 try: | |
| 66 t = s.decode() | |
| 67 except: | |
| 68 pass | |
| 69 | |
| 70 try: | |
| 71 return json.loads(t) | |
| 72 except: | |
| 73 return t | |
| 0 | 74 |
| 75 | |
| 13 | 76 def DefineOrthanc(server = 'localhost', |
| 77 restPort = 8042, | |
| 1 | 78 username = None, |
| 79 password = None, | |
| 80 aet = 'ORTHANC', | |
| 81 dicomPort = 4242): | |
| 13 | 82 #m = re.match(r'(http|https)://([^:]+):([^@]+)@([^@]+)', url) |
| 83 #if m != None: | |
| 84 # url = m.groups()[0] + '://' + m.groups()[3] | |
| 85 # username = m.groups()[1] | |
| 86 # password = m.groups()[2] | |
| 0 | 87 |
| 13 | 88 #if not url.endswith('/'): |
| 89 # url += '/' | |
| 0 | 90 |
| 1 | 91 return { |
| 13 | 92 'Server' : server, |
| 93 'Url' : 'http://%s:%d/' % (server, restPort), | |
| 1 | 94 'Username' : username, |
| 95 'Password' : password, | |
| 96 'DicomAet' : aet, | |
| 97 'DicomPort' : dicomPort | |
| 98 } | |
| 0 | 99 |
| 100 | |
| 101 def _SetupCredentials(orthanc, http): | |
| 1 | 102 if (orthanc['Username'] != None and |
| 103 orthanc['Password'] != None): | |
| 104 http.add_credentials(orthanc['Username'], orthanc['Password']) | |
| 0 | 105 |
| 28 | 106 def DoGetRaw(orthanc, uri, data = {}, body = None, headers = {}): |
| 0 | 107 d = '' |
| 108 if len(data.keys()) > 0: | |
| 109 d = '?' + urlencode(data) | |
| 110 | |
| 111 http = httplib2.Http() | |
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112 http.follow_redirects = False |
| 0 | 113 _SetupCredentials(orthanc, http) |
| 114 | |
| 1 | 115 resp, content = http.request(orthanc['Url'] + uri + d, 'GET', body = body, |
| 0 | 116 headers = headers) |
| 28 | 117 return (resp, content) |
| 118 | |
| 119 | |
| 120 def DoGet(orthanc, uri, data = {}, body = None, headers = {}): | |
| 121 (resp, content) = DoGetRaw(orthanc, uri, data = data, body = body, headers = headers) | |
| 122 | |
| 0 | 123 if not (resp.status in [ 200 ]): |
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124 raise Exception(resp.status, resp) |
| 0 | 125 else: |
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126 return DecodeJson(content) |
| 0 | 127 |
| 128 def _DoPutOrPost(orthanc, uri, method, data, contentType, headers): | |
| 129 http = httplib2.Http() | |
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130 http.follow_redirects = False |
| 0 | 131 _SetupCredentials(orthanc, http) |
| 132 | |
| 83 | 133 if isinstance(data, (str, bytearray, bytes)): |
| 0 | 134 body = data |
| 135 if len(contentType) != 0: | |
| 136 headers['content-type'] = contentType | |
| 137 else: | |
| 138 body = json.dumps(data) | |
| 139 headers['content-type'] = 'application/json' | |
| 140 | |
| 141 headers['expect'] = '' | |
| 142 | |
| 1 | 143 resp, content = http.request(orthanc['Url'] + uri, method, |
| 0 | 144 body = body, |
| 145 headers = headers) | |
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146 return (resp, content) |
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147 |
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148 def DoDeleteRaw(orthanc, uri, headers = {}): |
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149 http = httplib2.Http() |
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150 http.follow_redirects = False |
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151 _SetupCredentials(orthanc, http) |
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152 |
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153 resp, content = http.request(orthanc['Url'] + uri, 'DELETE', headers = headers) |
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154 return (resp, content) |
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155 |
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156 def DoDelete(orthanc, uri, headers = {}): |
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157 (resp, content) = DoDeleteRaw(orthanc, uri, headers) |
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158 if not (resp.status in [ 200 ]): |
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159 raise Exception(resp.status, resp) |
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160 else: |
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161 return DecodeJson(content) |
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162 |
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163 def DoPutRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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164 return _DoPutOrPost(orthanc, uri, 'PUT', data, contentType, headers) |
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165 |
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166 def DoPut(orthanc, uri, data = {}, contentType = '', headers = {}): |
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167 (resp, content) = DoPutRaw(orthanc, uri, data, contentType, headers) |
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168 if not (resp.status in [ 200, 201, 302 ]): |
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169 raise Exception(resp.status, resp) |
| 0 | 170 else: |
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171 return DecodeJson(content) |
| 0 | 172 |
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173 def DoPostRaw(orthanc, uri, data = {}, contentType = '', headers = {}): |
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174 return _DoPutOrPost(orthanc, uri, 'POST', data, contentType, headers) |
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175 |
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176 def DoPost(orthanc, uri, data = {}, contentType = '', headers = {}): |
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177 (resp, content) = DoPostRaw(orthanc, uri, data, contentType, headers) |
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178 if not (resp.status in [ 200, 201, 302 ]): |
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179 raise Exception(resp.status, resp) |
| 0 | 180 else: |
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181 return DecodeJson(content) |
| 0 | 182 |
| 13 | 183 def GetDatabasePath(filename): |
| 184 return os.path.join(os.path.dirname(__file__), '..', 'Database', filename) | |
| 185 | |
| 0 | 186 def UploadInstance(orthanc, filename): |
| 83 | 187 with open(GetDatabasePath(filename), 'rb') as f: |
| 188 d = f.read() | |
| 189 | |
| 0 | 190 return DoPost(orthanc, '/instances', d, 'application/dicom') |
| 191 | |
| 192 def UploadFolder(orthanc, path): | |
| 13 | 193 for i in os.listdir(GetDatabasePath(path)): |
| 1 | 194 try: |
| 195 UploadInstance(orthanc, os.path.join(path, i)) | |
| 196 except: | |
| 197 pass | |
| 0 | 198 |
| 199 def DropOrthanc(orthanc): | |
| 200 # Reset the Lua callbacks | |
| 201 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance(instanceId, tags, metadata) end', 'application/lua') | |
| 202 | |
| 203 DoDelete(orthanc, '/exports') | |
| 204 | |
| 205 for s in DoGet(orthanc, '/patients'): | |
| 206 DoDelete(orthanc, '/patients/%s' % s) | |
| 207 | |
| 174 | 208 def InstallLuaScriptFromPath(orthanc, path): |
| 209 with open(GetDatabasePath(path), 'r') as f: | |
| 210 InstallLuaScript(orthanc, f.read()) | |
| 211 | |
| 212 def InstallLuaScript(orthanc, script): | |
| 213 DoPost(orthanc, '/tools/execute-script', script, 'application/lua') | |
| 214 | |
| 215 def UninstallLuaCallbacks(orthanc): | |
| 216 DoPost(orthanc, '/tools/execute-script', 'function OnStoredInstance() end', 'application/lua') | |
| 217 InstallLuaScriptFromPath(orthanc, 'Lua/TransferSyntaxEnable.lua') | |
| 218 | |
| 219 | |
| 0 | 220 def ComputeMD5(data): |
| 221 m = hashlib.md5() | |
| 222 m.update(data) | |
| 223 return m.hexdigest() | |
| 224 | |
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225 def UncompressImage(data): |
| 83 | 226 if (sys.version_info >= (3, 0)): |
| 227 return Image.open(BytesIO(data)) | |
| 228 else: | |
| 229 return Image.open(StringIO(data)) | |
| 0 | 230 |
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231 def GetImage(orthanc, uri, headers = {}): |
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232 # http://www.pythonware.com/library/pil/handbook/introduction.htm |
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233 return UncompressImage(DoGet(orthanc, uri, headers = headers)) |
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234 |
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235 def ParseArchive(s): |
| 0 | 236 # http://stackoverflow.com/a/1313868/881731 |
| 83 | 237 if (sys.version_info >= (3, 0)): |
| 238 return zipfile.ZipFile(BytesIO(s), "r") | |
| 239 else: | |
| 240 return zipfile.ZipFile(StringIO(s), "r") | |
| 0 | 241 |
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242 def GetArchive(orthanc, uri): |
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243 return ParseArchive(DoGet(orthanc, uri)) |
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244 |
| 192 | 245 def PostArchive(orthanc, uri, body): |
| 246 # http://stackoverflow.com/a/1313868/881731 | |
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247 return ParseArchive(DoPost(orthanc, uri, body)) |
| 192 | 248 |
| 1 | 249 def IsDefinedInLua(orthanc, name): |
| 0 | 250 s = DoPost(orthanc, '/tools/execute-script', 'print(type(%s))' % name, 'application/lua') |
| 251 return (s.strip() != 'nil') | |
| 252 | |
| 1 | 253 def WaitEmpty(orthanc): |
| 0 | 254 while True: |
| 1 | 255 if len(DoGet(orthanc, '/instances')) == 0: |
| 0 | 256 return |
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257 time.sleep(0.01) |
| 0 | 258 |
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259 def WaitJobDone(orthanc, job): |
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260 while True: |
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261 s = DoGet(orthanc, '/jobs/%s' % job) ['State'] |
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262 |
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263 if s == 'Success': |
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264 return True |
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265 elif s == 'Failure': |
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266 return False |
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267 |
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268 time.sleep(0.01) |
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269 |
| 138 | 270 def MonitorJob(orthanc, func): # "func" is a lambda |
| 271 a = set(DoGet(orthanc, '/jobs')) | |
| 272 func() | |
| 273 b = set(DoGet(orthanc, '/jobs')) | |
| 274 | |
| 275 diff = list(b - a) | |
| 276 if len(diff) != 1: | |
| 277 print('No job was created!') | |
| 278 return False | |
| 279 else: | |
| 280 return WaitJobDone(orthanc, diff[0]) | |
| 281 | |
|
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282 def MonitorJob2(orthanc, func): # "func" is a lambda |
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283 a = set(DoGet(orthanc, '/jobs')) |
| 181 | 284 job = func() |
|
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285 b = set(DoGet(orthanc, '/jobs')) |
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286 |
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287 diff = list(b - a) |
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288 if len(diff) != 1: |
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289 print('No job was created!') |
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290 return None |
| 181 | 291 elif (not 'ID' in job or |
| 292 diff[0] != job['ID']): | |
| 293 print('Mismatch in the job ID') | |
| 294 return None | |
|
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295 elif WaitJobDone(orthanc, diff[0]): |
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296 return diff[0] |
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297 else: |
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298 print('Error while executing the job') |
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299 return None |
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300 |
| 220 | 301 def WaitAllNewJobsDone(orthanc, func): # "func" is a lambda |
| 302 a = set(DoGet(orthanc, '/jobs')) | |
| 303 func() | |
| 304 | |
| 305 first = True | |
| 306 | |
| 307 while True: | |
| 308 b = set(DoGet(orthanc, '/jobs')) | |
| 309 | |
| 310 diff = list(b - a) | |
| 311 if len(diff) == 0: | |
| 312 if first: | |
| 313 raise Exception('No job was created') | |
| 314 else: | |
| 315 return # We're done | |
| 316 else: | |
| 317 first = False | |
| 318 | |
| 319 if WaitJobDone(orthanc, diff[0]): | |
| 320 a.add(diff[0]) | |
| 321 else: | |
| 322 raise Exception('Error while executing the job') | |
| 323 | |
| 324 | |
| 1 | 325 def GetDockerHostAddress(): |
| 326 route = subprocess.check_output([ '/sbin/ip', 'route' ]) | |
| 327 m = re.search(r'default via ([0-9.]+)', route) | |
| 328 if m == None: | |
| 329 return 'localhost' | |
| 330 else: | |
| 331 return m.groups()[0] | |
| 4 | 332 |
|
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333 def FindExecutable(name): |
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334 p = os.path.join('/usr/local/bin', name) |
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335 if os.path.isfile(p): |
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336 return p |
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337 |
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338 p = os.path.join('/usr/local/sbin', name) |
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339 if os.path.isfile(p): |
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340 return p |
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341 |
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342 return name |
| 4 | 343 |
| 173 | 344 def IsOrthancVersionAbove(orthanc, major, minor, revision): |
| 345 v = DoGet(orthanc, '/system')['Version'] | |
| 346 | |
| 703 | 347 if v.startswith('mainline'): |
| 173 | 348 return True |
| 349 else: | |
| 350 tmp = v.split('.') | |
| 351 a = int(tmp[0]) | |
| 352 b = int(tmp[1]) | |
| 353 c = int(tmp[2]) | |
| 354 return (a > major or | |
| 355 (a == major and b > minor) or | |
| 356 (a == major and b == minor and c >= revision)) | |
| 4 | 357 |
| 693 | 358 |
| 359 def HasExtendedFind(orthanc): | |
| 360 v = DoGet(orthanc, '/system') | |
| 361 | |
| 362 if 'Capabilities' in v and 'HasExtendedFind' in v['Capabilities']: | |
| 363 return v['Capabilities']['HasExtendedFind'] | |
| 364 return False | |
| 365 | |
| 366 | |
| 367 def HasExtendedChanges(orthanc): | |
| 368 v = DoGet(orthanc, '/system') | |
| 369 | |
| 370 if 'Capabilities' in v and 'HasExtendedChanges' in v['Capabilities']: | |
| 371 return v['Capabilities']['HasExtendedChanges'] | |
| 372 return False | |
| 373 | |
| 374 | |
| 375 def GetStorageAccessesCount(orthanc): | |
| 376 mm = DoGetRaw(orthanc, "/tools/metrics-prometheus")[1] | |
| 377 | |
| 378 if (sys.version_info >= (3, 0)): | |
| 379 try: | |
| 380 mm = mm.decode() | |
| 381 except: | |
| 382 pass | |
| 383 | |
| 384 mm = [x.split(" ") for x in mm.split("\n")] | |
| 385 | |
| 386 count = 0 | |
| 387 for m in mm: | |
| 388 if m[0] == 'orthanc_storage_cache_hit_count': | |
| 389 count += int(m[1]) | |
| 390 if m[0] == 'orthanc_storage_cache_miss_count': | |
| 391 count += int(m[1]) | |
| 392 | |
| 393 # print("storage access count = %s" % count) | |
| 394 return count | |
| 395 | |
| 396 | |
| 532 | 397 def IsPluginVersionAbove(orthanc, plugin, major, minor, revision): |
| 398 v = DoGet(orthanc, '/plugins/%s' % plugin)['Version'] | |
| 399 | |
| 711 | 400 if v.startswith('mainline'): |
| 532 | 401 return True |
| 402 else: | |
| 403 tmp = v.split('.') | |
| 404 if len(tmp) >= 3: | |
| 405 a = int(tmp[0]) | |
| 406 b = int(tmp[1]) | |
| 407 c = int(tmp[2]) | |
| 408 return (a > major or | |
| 409 (a == major and b > minor) or | |
| 410 (a == major and b == minor and c >= revision)) | |
| 411 elif len(tmp) >= 2: | |
| 412 a = int(tmp[0]) | |
| 413 b = int(tmp[1]) | |
| 414 return (a > major or | |
| 415 (a == major and b > minor)) | |
| 416 else: | |
| 417 return False | |
| 4 | 418 |
| 419 class ExternalCommandThread: | |
| 420 @staticmethod | |
| 421 def ExternalCommandFunction(arg, stop_event, command, env): | |
|
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422 with open(os.devnull, 'w') as devnull: |
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423 external = subprocess.Popen(command, env = env, stderr = devnull) |
| 4 | 424 |
|
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425 while (not stop_event.is_set()): |
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426 error = external.poll() |
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427 if error != None: |
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428 # http://stackoverflow.com/a/1489838/881731 |
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429 os._exit(-1) |
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430 stop_event.wait(0.1) |
| 4 | 431 |
| 83 | 432 print('Stopping the external command') |
| 4 | 433 external.terminate() |
| 9 | 434 external.communicate() # Wait for the command to stop |
| 4 | 435 |
| 436 def __init__(self, command, env = None): | |
| 437 self.thread_stop = threading.Event() | |
| 438 self.thread = threading.Thread(target = self.ExternalCommandFunction, | |
| 439 args = (10, self.thread_stop, command, env)) | |
| 9 | 440 #self.daemon = True |
| 4 | 441 self.thread.start() |
| 442 | |
| 443 def stop(self): | |
| 444 self.thread_stop.set() | |
| 445 self.thread.join() | |
| 220 | 446 |
| 447 | |
|
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448 def AssertAlmostEqualRecursive(self, a, b, places = 7, ignoreKeys = []): |
| 220 | 449 if type(a) is dict: |
| 450 self.assertTrue(type(b) is dict) | |
| 451 self.assertEqual(a.keys(), b.keys()) | |
| 452 for key, value in a.items(): | |
|
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453 if not key in ignoreKeys: |
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454 AssertAlmostEqualRecursive(self, a[key], b[key], places) |
| 220 | 455 |
| 456 elif type(a) is list: | |
| 457 self.assertTrue(type(b) is list) | |
| 458 self.assertEqual(len(a), len(b)) | |
| 459 for i in range(len(a)): | |
| 460 AssertAlmostEqualRecursive(self, a[i], b[i], places) | |
| 461 | |
| 462 else: | |
| 463 self.assertAlmostEqual(a, b, places = places) | |
|
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464 |
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465 |
| 543 | 466 def GetTransferSyntax(dicom, encoding='utf-8'): |
|
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467 with tempfile.NamedTemporaryFile(delete = True) as f: |
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468 f.write(dicom) |
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469 f.flush() |
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470 |
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471 with open(os.devnull, 'w') as devnull: |
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472 data = subprocess.check_output([ FindExecutable('dcm2xml'), f.name ], |
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473 stderr = devnull) |
| 543 | 474 return re.search('<data-set xfer="(.*?)"', data.decode(encoding)).group(1) |
| 304 | 475 |
| 476 | |
| 477 def HasGdcmPlugin(orthanc): | |
| 478 plugins = DoGet(orthanc, '/plugins') | |
| 479 return ('gdcm' in plugins) | |
| 480 | |
| 481 | |
| 482 def _GetMaxImageDifference(im1, im2): | |
| 483 h = ImageChops.difference(im1, im2).histogram() | |
| 484 | |
| 485 if len(h) < 256: | |
| 486 raise Exception() | |
| 487 | |
| 488 i = len(h) - 1 | |
| 489 while h[i] == 0: | |
| 490 i -= 1 | |
| 491 | |
| 492 return i | |
| 493 | |
| 494 | |
| 495 def GetMaxImageDifference(im1, im2): | |
| 496 if im1.mode != im2.mode: | |
| 497 raise Exception('Incompatible image modes') | |
| 498 | |
| 499 if im1.mode == 'RGB': | |
| 500 red1, green1, blue1 = im1.split() | |
| 501 red2, green2, blue2 = im2.split() | |
| 502 return max([ _GetMaxImageDifference(red1, red2), | |
| 503 _GetMaxImageDifference(green1, green2), | |
| 504 _GetMaxImageDifference(blue1, blue2) ]) | |
| 505 else: | |
| 506 return _GetMaxImageDifference(im1, im2) | |
|
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507 |
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508 |
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509 def DoPropFind(orthanc, uri, depth): |
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510 http = httplib2.Http() |
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511 http.follow_redirects = False |
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512 _SetupCredentials(orthanc, http) |
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513 |
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514 resp, content = http.request(orthanc['Url'] + uri, 'PROPFIND', headers = { 'Depth' : str(depth) }) |
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515 |
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516 if not (resp.status in [ 207 ]): |
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517 raise Exception(resp.status, resp) |
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518 else: |
|
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519 xml = minidom.parseString(content) |
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520 |
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521 if (xml.documentElement.nodeName != 'D:multistatus' or |
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522 xml.documentElement.attributes['xmlns:D'].value != 'DAV:'): |
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523 raise Exception() |
|
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524 |
|
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525 result = {} |
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526 |
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527 for i in xml.documentElement.childNodes: |
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528 if i.nodeType == minidom.Node.ELEMENT_NODE: |
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529 if i.nodeName != 'D:response': |
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530 raise Exception() |
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531 href = None |
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532 prop = None |
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533 for j in i.childNodes: |
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534 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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535 if j.nodeName == 'D:href': |
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536 if href == None: |
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537 href = unquote(j.firstChild.nodeValue) |
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538 else: |
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539 raise Exception() |
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540 elif j.nodeName == 'D:propstat': |
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541 for k in j.childNodes: |
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542 if k.nodeName == 'D:status': |
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543 if k.firstChild.nodeValue != 'HTTP/1.1 200 OK': |
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544 raise Exception() |
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545 elif k.nodeType == minidom.Node.ELEMENT_NODE: |
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546 if (k.nodeName != 'D:prop' or |
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547 prop != None): |
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548 raise Exception() |
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549 prop = k |
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550 else: |
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551 raise Exception() |
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552 if href == None or prop == None: |
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553 raise Exception() |
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554 |
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555 info = {} |
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556 |
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557 for j in prop.childNodes: |
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558 if j.nodeType == minidom.Node.ELEMENT_NODE: |
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559 if j.nodeName == 'D:displayname': |
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560 info['displayname'] = j.firstChild.nodeValue if j.firstChild != None else '' |
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561 elif j.nodeName == 'D:creationdate': |
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562 info['creationdate'] = j.firstChild.nodeValue |
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563 elif j.nodeName == 'D:getlastmodified': |
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564 info['lastmodified'] = j.firstChild.nodeValue |
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565 elif j.nodeName == 'D:resourcetype': |
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566 k = j.getElementsByTagName('D:collection') |
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567 info['folder'] = (len(k) == 1) |
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568 |
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569 result[href] = info |
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570 elif i.nodeType != minidom.Node.TEXT_NODE: |
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571 raise Exception() |
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572 |
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573 return result |