ExternalResources: lock json file while accessing it

package/debian13/control

@@ -36,6 +36,7 @@ Build-Depends: cython3 (>= 0.23.2),
                python3-sphinx,
                python3-sphinx-copybutton,
                python3-sphinxcontrib.programoutput,
+               python3-filelock,
                xauth,
                xvfb
 Standards-Version: 4.1.3
@@ -74,7 +75,10 @@ Description: Toolbox for X-Ray data analysis - Executables
 Package: python3-silx
 Architecture: any
 Section: python
-Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         ${shlibs:Depends},
+         python3-filelock
 Description: Toolbox for X-Ray data analysis - Python3
  The silx project aims at providing a collection of Python packages to
  support the development of data assessment, reduction and analysis

pyproject.toml

@@ -36,6 +36,7 @@ dependencies = [
    'h5py >= 3',
    'fabio',
    'pydantic >= 2',
+   'filelock',
 ]
 
 [build-system]

src/silx/_version.py

@@ -71,8 +71,8 @@
 
 MAJOR = 3
 MINOR = 0
-MICRO = 1
-RELEV = "final"  # <16
+MICRO = 2
+RELEV = "dev"  # <16
 SERIAL = 0  # <16
 
 date = __date__

src/silx/math/fit/fitmanager.py

@@ -777,10 +777,8 @@ def setdata(self, x, y, sigmay=None, xmin=None, xmax=None):
                     numpy.sqrt(self.ydata) if self.fitconfig["WeightFlag"] else None
                 )
             else:
-                self.sigmay0 = numpy.array(sigmay)
-                self.sigmay = (
-                    numpy.array(sigmay) if self.fitconfig["WeightFlag"] else None
-                )
+                self.fitconfig["WeightFlag"] = True
+                self.sigmay0 = self.sigmay = numpy.array(sigmay)
 
             # take the data between limits, using boolean array indexing
             if (xmin is not None or xmax is not None) and len(self.xdata):
@@ -789,7 +787,14 @@ def setdata(self, x, y, sigmay=None, xmin=None, xmax=None):
                 bool_array = (self.xdata >= xmin) & (self.xdata <= xmax)
                 self.xdata = self.xdata[bool_array]
                 self.ydata = self.ydata[bool_array]
-                self.sigmay = self.sigmay[bool_array] if sigmay is not None else None
+                if sigmay is None:
+                    self.sigmay = (
+                        self.sigmay[bool_array]
+                        if self.fitconfig["WeightFlag"]
+                        else None
+                    )
+                else:
+                    self.sigmay0 = self.sigmay = self.sigmay[bool_array]
 
         self._finite_mask = numpy.logical_and(
             numpy.all(

src/silx/utils/ExternalResources.py

@@ -25,7 +25,7 @@
 
 __authors__ = ["Thomas Vincent", "J. Kieffer"]
 __license__ = "MIT"
-__date__ = "21/12/2021"
+__date__ = "12/05/2026"
 
 
 import hashlib
@@ -34,12 +34,14 @@
 import os
 import sys
 import tarfile
-import threading
 import tempfile
+import threading
+import time
 import unittest
 import urllib.request
 import urllib.error
 import zipfile
+import filelock
 
 logger = logging.getLogger(__name__)
 
@@ -74,6 +76,13 @@ def __init__(self, project, url_base, env_key=None, timeout=60, data_home=None):
         self.all_data = {}
         self.timeout = timeout
         self._data_home = data_home
+        self.testdata = ""
+        self.lock = None
+
+    @property
+    def lockfile(self):
+        """Returns the lockfile path."""
+        return self.testdata + ".lock"
 
     @property
     def data_home(self):
@@ -101,8 +110,14 @@ def data_home(self):
             basename = f"{self.project}_testdata_{name}"
             data_home = os.path.join(tempfile.gettempdir(), basename)
         if not os.path.exists(data_home):
-            os.makedirs(data_home)
+            try:
+                os.makedirs(data_home)
+            except OSError as exc:
+                raise RuntimeError(
+                    f"Unable to create data directory {data_home} ! ({exc})"
+                )
         self._data_home = data_home
+
         return data_home
 
     def get_hash(self, filename=None, data=None):
@@ -126,15 +141,8 @@ def _initialize_data(self):
             with self.sem:
                 if not self._initialized:
                     self.testdata = os.path.join(self.data_home, "all_testdata.json")
-                    if os.path.exists(self.testdata):
-                        with open(self.testdata) as f:
-                            jdata = json.load(f)
-                        if isinstance(jdata, dict):
-                            self.all_data = jdata
-                        else:
-                            # recalculate the hash only if the data was stored as a list
-                            self.all_data = {k: self.get_hash(k) for k in jdata}
-                            self.save_json()
+                    self.lock = filelock.FileLock(self.lockfile, timeout=self.timeout)
+                    self.all_data = self.load_json()
                     self._initialized = True
 
     def getfile(self, filename):
@@ -151,7 +159,34 @@ def getfile(self, filename):
 
         fullfilename = os.path.abspath(os.path.join(self.data_home, filename))
 
-        if not os.path.isfile(fullfilename):
+        if os.path.isfile(fullfilename):
+            if filename not in self.all_data:
+                """File already exists but is not in the list of known files"""
+                time_out = time.perf_counter() + self.timeout
+                while time.perf_counter() < time_out:
+                    dico = self.load_json()
+                    if filename in dico:
+                        dico.update(self.all_data)
+                        self.all_data = dico
+                        break
+                    time.sleep(1)
+                else:
+                    logger.warning(
+                        f"Timeout! Filename {filename} not present in all_data:{os.linesep}{json.dumps(self.all_data, indent=2)}"
+                    )
+                    os.remove(fullfilename)
+                    return self.getfile(filename)
+
+            h = self.hash()
+            with open(fullfilename, mode="rb") as fd:
+                h.update(fd.read())
+
+            if h.hexdigest() != self.all_data[filename]:
+                logger.warning(f"Detected corrupted file {fullfilename} !")
+                self.all_data.pop(filename)
+                os.unlink(fullfilename)
+                return self.getfile(filename)
+        else:
             logger.debug(
                 "Trying to download file %s, timeout set to %ss",
                 filename,
@@ -174,53 +209,68 @@ def getfile(self, filename):
                 data = opener(
                     f"{self.url_base}/{filename}", data=None, timeout=self.timeout
                 ).read()
-                logger.info("File %s successfully downloaded.", filename)
+                logger.info(f"File {filename} successfully downloaded.")
             except urllib.error.URLError:
                 raise unittest.SkipTest("network unreachable.")
 
-            if not os.path.isdir(os.path.dirname(fullfilename)):
-                # Create sub-directory if needed
-                os.makedirs(os.path.dirname(fullfilename))
+            dirname = os.path.dirname(fullfilename)
+            if not os.path.isdir(dirname):
+                """Create sub-directory if needed"""
+                os.makedirs(dirname)
 
             try:
                 with open(fullfilename, mode="wb") as outfile:
                     outfile.write(data)
             except OSError:
-                raise OSError("unable to write downloaded \
-                    data to disk at %s" % self.data_home)
+                raise OSError(f"unable to write downloaded \
+                    data to disk at {fullfilename}")
 
-            if not os.path.isfile(fullfilename):
+            if os.path.isfile(fullfilename):
+                self.all_data[filename] = self.get_hash(data=data)
+                self.save_json()
+            else:
                 raise RuntimeError("""Could not automatically download test files %s!
                     If you are behind a firewall, please set both environment variable
                      http_proxy and https_proxy.
                     This even works under windows !
                     Otherwise please try to download the files manually from
                     %s/%s""" % (filename, self.url_base, filename))
-            else:
-                self.all_data[filename] = self.get_hash(data=data)
-                self.save_json()
-
-        else:
-            h = self.hash()
-            with open(fullfilename, mode="rb") as fd:
-                h.update(fd.read())
-            if h.hexdigest() != self.all_data[filename]:
-                logger.warning(f"Detected corruped file {fullfilename}")
-                self.all_data.pop(filename)
-                os.unlink(fullfilename)
-                return self.getfile(filename)
-
         return fullfilename
 
+    def load_json(self) -> dict:
+        """Loads the JSON file containing the list of files and their hashes"""
+        all_data = {}
+        if self.testdata and os.path.exists(self.testdata):
+            try:
+                with self.lock:
+                    with open(self.testdata) as f:
+                        jdata = json.load(f)
+            except filelock.Timeout:
+                logger.error("Unable to lock JSON file")
+                jdata = {}
+            if isinstance(jdata, dict):
+                all_data = jdata
+            else:
+                # recalculate the hash only if the data was stored as a list
+                all_data = {k: self.get_hash(k) for k in jdata}
+        return all_data
+
     def save_json(self):
-        file_list = list(self.all_data.keys())
+        """Saves the JSON file containing the list of files and their hashes"""
+        dico = self.load_json()
+        dico.update(self.all_data)
+        file_list = list(dico.keys())
         file_list.sort()
-        dico = {i: self.all_data[i] for i in file_list}
+        dico = {i: dico[i] for i in file_list}  # reorder items
+
         try:
-            with open(self.testdata, "w") as fp:
-                json.dump(dico, fp, indent=4)
+            with self.lock:
+                with open(self.testdata, "w") as fp:
+                    json.dump(dico, fp, indent=4)
+        except filelock.Timeout:
+            logger.error("Unable to lock JSON file")
         except OSError:
-            logger.info("Unable to save JSON dict")
+            logger.error("Unable to save JSON dict")
 
     def getdir(self, dirname):
         """Downloads the requested tarball from the server