WIP: backup

compile_java_code.sh

@@ -9,15 +9,15 @@
 set -x
 set -e
 
-JDK_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home
-# JDK_HOME=/Library/Java/JavaVirtualMachines/openjdk-12.0.2.jdk/Contents/Home/
 #JDK_HOME=/Users/uweschmitt/Downloads/jdk-11.0.2.jdk/Contents/Home/
+#JDK_HOME=/Library/Java/JavaVirtualMachines/openjdk-12.0.2.jdk/Contents/Home/
+JDK_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home
 
 JAVAC=${JDK_HOME}/bin/javac
 JAR=${JDK_HOME}/bin/jar
 
-MZMINE_JARS=~/Projects/mzmine2/build/MZmine-2.52-macOS/lib  # /mzmine2-2.52.jar
-MZMINE_JARS=~/Downloads/MZmine-2.51-macOS/lib
+#MZMINE_JARS=~/Downloads/MZmine-2.51-macOS/lib
+#MZMINE_JARS=~/Projects/mzmine2/build/MZmine-2.52-macOS/lib  # /mzmine2-2.52.jar
 MZMINE_JARS=$(cat ~/.emzed.ext.mzmine2/mzmine2/mzmine2_home)/lib
 echo ${MZMINE_JARS}
 cd mzm/java
@@ -27,5 +27,5 @@ BUILD_ROOT=$(mktemp -d)/ch/ethz/emzed
 mkdir -p ${BUILD_ROOT}
 cp *.java ${BUILD_ROOT}
 
-${JAVAC} -Xlint:unchecked -cp ${MZMINE_JARS}'/*' ${BUILD_ROOT}/*.java
+${JAVAC} -Xlint:unchecked -cp "${MZMINE_JARS}/*" ${BUILD_ROOT}/*.java
 ${JAR} cf extensions.jar ${BUILD_ROOT}/../../../ch

emzed/ext/mzmine2/__init__.py

 import os as _os
 
-from .install_jre import get_jre_home
-from .install_mzmine2 import get_mzmine2_home
+from .installers import get_jre_home, get_mzmine2_home
 
 if get_mzmine2_home() is None or get_jre_home() is None:
 
     def init():
-        from .install_jre import install_jre
-        from .install_mzmine2 import install_mzmine2
+        from .installers import install_jre, install_mzmine2
 
         install_jre()
         install_mzmine2()
@@ -24,19 +22,23 @@ if get_mzmine2_home() is None or get_jre_home() is None:
 
 else:
 
+    # cleanup ns
+    del get_jre_home
+    del get_mzmine2_home
+
     def init():
         print("nothing to do")
 
-    HERE = _os.path.dirname(_os.path.abspath(__file__))
+    here = _os.path.dirname(_os.path.abspath(__file__))
 
     def _start_jvm_if_not_done_yet():
+        return
 
         import jpype
 
         if not jpype.isJVMStarted():
 
-            from .install_mzmine2 import get_mzmine2_home
-            from .install_jre import set_java_home
+            from .installers import get_mzmine2_home, set_java_home
 
             set_java_home()
 
@@ -44,7 +46,7 @@ else:
 
             java_dll = jpype.getDefaultJVMPath()
 
-            #cp = "/Users/uweschmitt/Projects/mzmine2/build/MZmine-2.52-macOS/lib/*"
+            cp = "/Users/uweschmitt/Projects/mzmine2/build/MZmine-2.52-macOS/lib/*"
 
             try:
                 # on win the jvm dll requires dlls from its parent folder
@@ -55,8 +57,8 @@ else:
                     jpype.getDefaultJVMPath(),
                     "-Djava.awt.headless=true",
                     classpath=[
-                        get_mzmine2_home() + "/lib/*",
-                        _os.path.join(HERE, "java", "extensions.jar"),
+                        _os.path.join(get_mzmine2_home(), "lib", "*"),
+                        _os.path.join(here, "java", "extensions.jar"),
                     ],
                     convertStrings=True,
                 )

emzed/ext/mzmine2/install_jre.py

-#! /usr/bin/env python
-# Copyright © 2019 Uwe Schitt <uwe.schmitt@id.ethz.ch>
-
-import os
-import sys
-
-from .utils import default_install_target, download, unpack
-
-ROOT = "http://emzed.ethz.ch/downloads/"
-
-URLS = {
-    "linux": ROOT + "latest-jre-linux2.tar.gz",
-    "darwin": ROOT + "latest-jre-darwin.tar.gz",
-    "win32": ROOT + "latest-jre-win32.zip",
-}
-
-SUPPORTED_PLATFORMS = list(URLS.keys())
-
-JVM_HOME_FILE = "jvm_home"
-
-"""
-original jres were downloaded from https://adoptopenjdk.net
-"""
-
-
-def _default_jre_folder():
-    return os.path.join(default_install_target(), "jre")
-
-
-def install_jre(platform=sys.platform, target_folder=_default_jre_folder()):
-    assert (
-        platform in SUPPORTED_PLATFORMS
-    ), f"platform must be one of {SUPPORTED_PLATFORMS}"
-
-    if not os.path.exists(target_folder):
-        os.makedirs(target_folder)
-
-    url = URLS[platform]
-    target_path = os.path.join(target_folder, os.path.basename(url))
-
-    if os.path.exists(target_path):
-        print("jre is already installed")
-        return
-
-    print("download", url)
-    download(url, target_path)
-
-    print("unpack", target_path)
-    unpacked_to = unpack(target_path)
-
-    with open(os.path.join(target_folder, JVM_HOME_FILE), "w") as fh:
-        fh.write(unpacked_to)
-
-
-def get_jre_home(folder=_default_jre_folder()):
-    jvm_home_path = os.path.join(folder, JVM_HOME_FILE)
-    print("HOME PATH", jvm_home_path)
-    if not os.path.exists(jvm_home_path):
-        return None
-
-    path = open(jvm_home_path).read().strip()
-    if not os.path.exists(path):
-        raise RuntimeError(f"file {jvm_home_path} contains invalid path {path}")
-
-    return path
-
-
-def set_java_home(folder=_default_jre_folder()):
-    import os
-    path = get_jre_home(folder)
-    if path is None:
-        raise RuntimeError(f"did not find jre, did you run download_jre()?")
-    #path = "/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home/"
-    #path = "/Users/uweschmitt/Downloads/jdk-11.0.2.jdk/Contents/Home/"
-    #path = "/Library/Java/JavaVirtualMachines/openjdk-12.0.2.jdk/Contents/Home/"
-    os.environ["JAVA_HOME"] = path

emzed/ext/mzmine2/install_mzmine2.py

-#! /usr/bin/env python
-# Copyright © 2019 Uwe Schitt <uwe.schmitt@id.ethz.ch>
-
-import os
-
-from .utils import default_install_target, download, unpack
-
-URL = "https://github.com/mzmine/mzmine2/releases/download/v2.41.2/MZmine-2.41.2.zip"
-
-MZMINE2_HOME_FILE = "mzmine2_home"
-
-
-def _default_mzmine2_folder():
-    return os.path.join(default_install_target(), "mzmine2")
-
-
-def install_mzmine2(target_folder=_default_mzmine2_folder()):
-
-    if not os.path.exists(target_folder):
-        os.makedirs(target_folder)
-
-    target_path = os.path.join(target_folder, os.path.basename(URL))
-
-    if os.path.exists(target_path):
-        print("mzmine2 is already installed")
-        return
-
-    print("download", URL)
-    download(URL, target_path)
-
-    print("unpack", target_path)
-    result_folder = unpack(target_path)
-
-    with open(os.path.join(target_folder, MZMINE2_HOME_FILE), "w") as fh:
-        fh.write(result_folder)
-
-
-def get_mzmine2_home(target_folder=_default_mzmine2_folder()):
-    mzmine2_path = os.path.join(target_folder, MZMINE2_HOME_FILE)
-
-    if not os.path.exists(mzmine2_path):
-        return None
-
-    path = open(mzmine2_path).read().strip()
-    if not os.path.exists(path):
-        raise RuntimeError(f"file {mzmine2_path} contains invalid path {path}")
-
-    return path

emzed/ext/mzmine2/parameters.py

@@ -44,13 +44,6 @@ def create_combo_checker(choices):
     return combo_checker
 
 
-_checkers = {
-    "DoubleParameter": double_checker,
-    "StringParameter": string_checker,
-    "BooleanParameter": bool_checker,
-}
-
-
 def create_descriptor(python_field_name, entry):
     java_type = entry["type"]
     choices = entry["choices"]

emzed/ext/mzmine2/remove_shoulder_peaks.py

@@ -2,54 +2,68 @@
 # Copyright © 2019 Uwe Schitt <uwe.schmitt@id.ethz.ch>
 
 
-import emzed.lib
-
-from .converters import create_mass_lists, from_peakmap, to_peakmap
-from .exceptions import MzMine2Exception
-from .parameters import ParameterBase, from_python_obj
+import tempfile
+import subprocess
 
+import emzed.lib
 
-class RemoveShoulderPeaksParameters(ParameterBase):
+from .parameters import ParameterField, create_combo_checker
+from .installers import construct_java_call_cli_args
 
-    _java_class = "ShoulderPeaksFilterParameters"
-    _fields = ["resolution", "peakModel"]
 
+class RemoveShoulderPeaksParameters:
 
-def remove_shoulder_peaks(peakmap, parameters):
-    assert isinstance(peakmap, emzed.lib.PeakMap)
+    resolution = ParameterField(
+        "resolution",
+        (
+            lambda v: isinstance(v, float) and v >= 0,
+            "nonnegative floating point value required",
+        ),
+    )
 
-    from . import _start_jvm_if_not_done_yet
+    peak_model = ParameterField(
+        "peak_model", create_combo_checker(["GAUSS", "LORENTZ", "LORENTZEXTENDED"])
+    )
 
-    _start_jvm_if_not_done_yet()
 
-    from .classes import ShoulderPeaksFilterTask, PeakModelType
+"""
+TODO
 
-    try:
-        mzmine2_parameters = from_python_obj(parameters)
-    except AssertionError as e:
-        raise ValueError(f"the parameters you passed are not valid: {e}")
+1. rt format issu: pm_back in tests has truncated rt values
+2. extract sepctra from masslists
+3. cleanup code
+"""
 
-    # fix combo parameters
-    mzmine2_parameters.peakModel.setValue(
-        {
-            "GAUSS": PeakModelType.GAUSS,
-            "LORENTZ": PeakModelType.LORENTZ,
-            "LORENTZEXTENDED": PeakModelType.LORENTZEXTENDED,
-        }[mzmine2_parameters.peakModel.getValue()]
-    )
 
-    # set reasonbale default for emzed:
-    mzmine2_parameters.autoRemove.setValue(True)
-    mzmine2_parameters.massList.setValue("_mass_list")
-    mzmine2_parameters.suffix.setValue("")
+def remove_shoulder_peaks(peakmap, parameters):
+    assert isinstance(peakmap, emzed.lib.PeakMap)
 
-    writer = from_peakmap(peakmap)
-    create_mass_lists(writer, "_mass_list")
+    temp_file_in = tempfile.mktemp(".mzXML")
+    temp_file_out = tempfile.mktemp(".mzML")
+    peakmap.store(temp_file_in)
 
-    task = ShoulderPeaksFilterTask(writer, mzmine2_parameters)
-    task.run()
-    msg = task.getErrorMessage()
-    if msg is not None:
-        raise MzMine2Exception(msg)
+    cli = construct_java_call_cli_args() + [
+        "ch.ethz.emzed.RemoveShoulderPeaks",
+        temp_file_in,
+        str(parameters.resolution),
+        parameters.peak_model,
+        temp_file_out,
+    ]
 
-    return to_peakmap(writer, "_mass_list ")
+    p = subprocess.Popen(
+        " ".join(cli), shell=True, stderr=subprocess.STDOUT, stdout=subprocess.PIPE
+    )
+    for line in iter(p.stdout.readline, b""):
+        line = str(line, "utf-8").rstrip()
+        if line.startswith("!!!ERROR"):
+            raise RuntimeError("calling java failed")
+        if line.startswith("!!!DONE"):
+            break
+        print(line)
+
+    peakmap_back = emzed.lib.PeakMap.load(temp_file_out)
+
+    # the mzXML parser of mzedmin2 rounds rt values, we fix this here:
+    for s, s_back in zip(peakmap.spectra, peakmap_back.spectra):
+        s_back.rt = s.rt
+    return peakmap_back

tests/conftest.py

@@ -6,10 +6,7 @@ from functools import partial
 
 import pytest
 
-from emzed.ext.mzmine2.install_jre import set_java_home
-from emzed.ext.mzmine2 import _start_jvm_if_not_done_yet
-
-_start_jvm_if_not_done_yet()
+from emzed.ext.mzmine2.installers import set_java_home
 
 
 def pytest_addoption(parser):

tests/test_remove_shoulder_peaks.py

@@ -23,6 +23,8 @@ def test_remove_shoulder_peaks(data_path):
     assert pm_back.spectra[0].mzs.shape == (241,)
     assert pm_back.spectra[1].mzs.shape == (259,)
 
+    assert pm_back.spectra[0].rt == pm.spectra[0].rt
+
 
 def execute(what):
     f, *args = dill.loads(what)