scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.0__py3-none-any.whl

pyworkflow/utils/which.py

@@ -1,229 +0,0 @@
-
-# Copyright (c) 2002-2005 ActiveState Corp.
-# See LICENSE.txt for license details.
-# Author:
-#   Trent Mick (TrentM@ActiveState.com)
-# Home:
-#   http://trentm.com/projects/which/
-
-"""Find the full path to commands.
-
-which(command, path=None, verbose=0, exts=None)
-    Return the full path to the first match of the given command on the
-    path.
-
-whichall(command, path=None, verbose=0, exts=None)
-    Return a list of full paths to all matches of the given command on
-    the path.
-
-whichgen(command, path=None, verbose=0, exts=None)
-    Return a generator which will yield full paths to all matches of the
-    given command on the path.
-    
-"""
-
-import os
-import sys
-import stat
-# ---- exceptions
-
-
-class WhichError(Exception):
-    pass
-
-# ---- internal support stuff
-
-
-def _getRegisteredExecutable(exeName):
-    """Windows allow application paths to be registered in the registry."""
-    registered = None
-    if sys.platform.startswith('win'):
-        if os.path.splitext(exeName)[1].lower() != '.exe':
-            exeName += '.exe'
-        import winreg
-        try:
-            key = "SOFTWARE\\Microsoft\\Windows\\CurrentVersion\\App Paths\\" +\
-                  exeName
-            value = winreg.QueryValue(winreg.HKEY_LOCAL_MACHINE, key)
-            registered = (value, "from HKLM\\"+key)
-        except winreg.error:
-            pass
-        if registered and not os.path.exists(registered[0]):
-            registered = None
-    return registered
-
-
-def _samefile(fname1, fname2):
-    if sys.platform.startswith('win'):
-        return (os.path.normpath(os.path.normcase(fname1)) ==
-                os.path.normpath(os.path.normcase(fname2)))
-    else:
-        return os.path.samefile(fname1, fname2)
-
-
-def _cull(potential, matches, verbose=0):
-    """Cull inappropriate matches. Possible reasons:
-        - a duplicate of a previous match
-        - not a disk file
-        - not executable (non-Windows)
-    If 'potential' is approved it is returned and added to 'matches'.
-    Otherwise, None is returned.
-    """
-    for match in matches:  # don't yield duplicates
-        if _samefile(potential[0], match[0]):
-            if verbose:
-                sys.stderr.write("duplicate: %s (%s)\n" % potential)
-            return None
-    else:
-        if not stat.S_ISREG(os.stat(potential[0]).st_mode):
-            if verbose:
-                sys.stderr.write("not a regular file: %s (%s)\n" % potential)
-        elif not os.access(potential[0], os.X_OK):
-            if verbose:
-                sys.stderr.write("no executable access: %s (%s)\n"
-                                 % potential)
-        else:
-            matches.append(potential)
-            return potential
-
-        
-# ---- module API
-
-def whichgen(command, path=None, verbose=0, exts=None):
-    """Return a generator of full paths to the given command.
-    
-    :param command: is a the name of the executable to search for.
-    :param path: is an optional alternate path list to search. The default it
-        to use the PATH environment variable.
-    :param verbose: if true, will cause a 2-tuple to be returned for each
-        match. The second element is a textual description of where the
-        match was found.
-    :param exts: optionally allows one to specify a list of extensions to use
-        instead of the standard list for this system. This can
-        effectively be used as an optimization to, for example, avoid
-        stat's of "foo.vbs" when searching for "foo" and you know it is
-        not a VisualBasic script but ".vbs" is on PATHEXT. This option
-        is only supported on Windows.
-
-    :return: This method returns a generator which yields either full paths to
-        the given command or, if verbose, tuples of the form (<path to
-        command>, <where path found>).
-
-    """
-    matches = []
-    if path is None:
-        usingGivenPath = 0
-        path = os.environ.get("PATH", "").split(os.pathsep)
-        if sys.platform.startswith("win"):
-            path.insert(0, os.curdir)  # implied by Windows shell
-    else:
-        usingGivenPath = 1
-
-    # Windows has the concept of a list of extensions (PATHEXT env var).
-    if sys.platform.startswith("win"):
-        if exts is None:
-            exts = os.environ.get("PATHEXT", "").split(os.pathsep)
-            # If '.exe' is not in exts then obviously this is Win9x and
-            # or a bogus PATHEXT, then use a reasonable default.
-            for ext in exts:
-                if ext.lower() == ".exe":
-                    break
-            else:
-                exts = ['.COM', '.EXE', '.BAT']
-        elif not isinstance(exts, list):
-            raise TypeError("'exts' argument must be a list or None")
-    else:
-        if exts is not None:
-            raise WhichError("'exts' argument is not supported on "
-                             "platform '%s'" % sys.platform)
-        exts = []
-
-    # File name cannot have path separators because PATH lookup does not
-    # work that way.
-    if os.sep in command or os.altsep and os.altsep in command:
-        pass
-    else:
-        for i in range(len(path)):
-            dirName = path[i]
-            # On windows the dirName *could* be quoted, drop the quotes
-            if sys.platform.startswith("win") and len(dirName) >= 2\
-               and dirName[0] == '"' and dirName[-1] == '"':
-                dirName = dirName[1:-1]
-            for ext in ['']+exts:
-                absName = os.path.abspath(
-                    os.path.normpath(os.path.join(dirName, command+ext)))
-                if os.path.isfile(absName):
-                    if usingGivenPath:
-                        fromWhere = "from given path element %d" % i
-                    elif not sys.platform.startswith("win"):
-                        fromWhere = "from PATH element %d" % i
-                    elif i == 0:
-                        fromWhere = "from current directory"
-                    else:
-                        fromWhere = "from PATH element %d" % (i-1)
-                    match = _cull((absName, fromWhere), matches, verbose)
-                    if match:
-                        if verbose:
-                            yield match
-                        else:
-                            yield match[0]
-        match = _getRegisteredExecutable(command)
-        if match is not None:
-            match = _cull(match, matches, verbose)
-            if match:
-                if verbose:
-                    yield match
-                else:
-                    yield match[0]
-
-
-def which(command, path=None, verbose=0, exts=None):
-    """Return the full path to the first match of the given command on
-    the path.
-
-    :param command: is a the name of the executable to search for.
-    :param path: is an optional alternate path list to search.
-        The default is to use the PATH environment variable.
-    :param verbose: if true, will cause a 2-tuple to be returned.
-        The second element is a textual description of where the match was found.
-    :param exts: optionally allows one to specify a list of extensions to use
-        instead of the standard list for this system. This can
-        effectively be used as an optimization to, for example, avoid
-        stat's of "foo.vbs" when searching for "foo" and you know it is
-        not a VisualBasic script but ".vbs" is on PATHEXT. This option
-        is only supported on Windows.
-
-    :return If no match is found for the command, an empty string is returned.
-
-    """
-    try:
-        match = next(whichgen(command, path, verbose, exts))
-    except StopIteration:
-        return ''
-    return match
-
-
-def commandExists(command):
-    path = which(command)
-    return path != ''
-
-
-def whichall(command, path=None, verbose=0, exts=None):
-    """Return a list of full paths to all matches of the given command
-    on the path.  
-
-    :param command: is a the name of the executable to search for.
-    :param path: is an optional alternate path list to search. The default it
-        to use the PATH environment variable.
-    :param verbose: if true, will cause a 2-tuple to be returned for each
-        match. The second element is a textual description of where the
-        match was found.
-    :param exts: optionally allows one to specify a list of extensions to use
-        instead of the standard list for this system. This can
-        effectively be used as an optimization to, for example, avoid
-        stat's of "foo.vbs" when searching for "foo" and you know it is
-        not a VisualBasic script but ".vbs" is on PATHEXT. This option
-        is only supported on Windows.
-
-    """
-    return list(whichgen(command, path, verbose, exts))

pyworkflow/webservices/__init__.py

@@ -1,8 +0,0 @@
-
-# Export all configuration variables in case they will be needed outside this module
-# Nonetheless, the recommend way is to import the classes or functions provided
-# by the module
-from .config import *
-
-from .notifier import ProjectWorkflowNotifier
-from .repository import WorkflowRepository

pyworkflow/webservices/config.py

@@ -1,11 +0,0 @@
-# Variable related to the online services (workflow stats and repository) that Scipion reports to or communicate.
-# These variables may change between Scipion versions but do not depend on the user or system
-
-# Web that gathers protocol usage
-SCIPION_STATS_SERVER = 'https://scipion.i2pc.es'
-SCIPION_STATS_WORKFLOW_APP = SCIPION_STATS_SERVER + '/report_protocols/api/workflow/workflow/'
-
-# Web that handles workflows
-WORKFLOW_REPOSITORY_SERVER = 'https://workflows.scipion.i2pc.es/'
-WORKFLOW_PROG_STEP1 = 'workflowProgStep1_add/'
-WORKFLOW_PROG_STEP2 = 'workflowProgStep2_add/'

pyworkflow/webservices/notifier.py

@@ -1,162 +0,0 @@
-# **************************************************************************
-# *
-# * Authors:    Roberto Marabini       (roberto@cnb.csic.es)
-#               J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
-# *
-# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * This program is free software; you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation; either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program; if not, write to the Free Software
-# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
-# * 02111-1307  USA
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-
-
-import os
-import time
-import threading
-import uuid
-from datetime import timedelta, datetime
-from urllib.parse import urlencode
-from urllib.request import build_opener, HTTPHandler
-
-import pyworkflow
-import pyworkflow.utils as pwutils
-from . import config
-
-
-class ProjectWorkflowNotifier(object):
-    """ Implement different types of notifications about a given
-    project. Currently, the protocols in a workflow will be sent.
-    """
-
-    def __init__(self, project):
-        self.project = project
-
-    def _getUuidFileName(self):
-        return self.project.getLogPath("uuid.log")
-
-    def _getDataFileName(self, fileName="data.log"):
-        return self.project.getLogPath(fileName)
-
-    def _getUuid(self):
-        # Load (or create if not exits) a file
-        # in the project Logs folder to store an unique
-        # project identifier
-        uuidFn = self._getUuidFileName()
-        try:
-            with open(uuidFn) as f:
-                uuidValue = f.readline()
-        except IOError:
-            uuidValue = str(uuid.uuid4())
-            with open(uuidFn, 'w') as f:
-                f.write(uuidValue)
-
-        return uuidValue
-
-    def _modifiedBefore(self, seconds):
-        """ Return True if the uuid.log file has been modified within a given
-        number of seconds. """
-        uuidFn = self._getUuidFileName()
-        if not os.path.exists(uuidFn):
-            return False
-        mTime = datetime.fromtimestamp(os.path.getmtime(uuidFn))
-        delta = datetime.now() - mTime
-
-        return delta < timedelta(seconds=seconds)
-
-    def _sendData(self, url, dataDict=None):
-        try:
-            # then connect to webserver a send json
-            # set debuglevel=0 for no messages
-            opener = build_opener(HTTPHandler(debuglevel=0))
-            data = urlencode(dataDict).encode()
-            content = opener.open(url, data=data).read()
-            now = time.time()
-            os.utime(self._getUuidFileName(), (now, now))
-        except Exception as e:
-            pass
-            # print("Could not notify, maybe there is not internet connection.")
-
-    def _dataModified(self, projectWorfklow):
-        try:
-            with open(self._getDataFileName()) as f:
-                projectWorfklow2 = f.readline()
-                if projectWorfklow2 == projectWorfklow:
-                    return False
-        except IOError:
-            pass
-        return True
-
-    def notifyWorkflow(self):
-
-        try:
-            # check if environment exists otherwise abort
-            if not pyworkflow.Config.SCIPION_NOTIFY:
-                return
-
-            # if project specifies not to send stats
-            if self._isProjectMuted():
-                return
-            # Check the seconds range of the notify, by default one day
-            seconds = int(os.environ.get('SCIPION_NOTIFY_SECONDS', '86400'))
-
-            if self._modifiedBefore(seconds):  # notify not more than once a day
-                return
-
-            # INFO: now we are only sending the protocols names in the project.
-            # We could pass namesOnly=False to get the full workflow template
-            projectWorfklow = self.project.getProtocolsJson(namesOnly=True)
-
-            # if list with workflow has not been altered do not sent it
-            if not self._dataModified(projectWorfklow):
-                return
-            else:
-                # For compatibility with version 1.0 check
-                # if Log directory exists. If it does not
-                # create it
-                # TODO: REMOVE this check in scipion 1.3
-                dataFile = self._getDataFileName()
-                # create the folder of the file path if not exists
-                pwutils.makeFilePath(dataFile)
-                with open(dataFile, 'w') as f:
-                    f.write(projectWorfklow)
-            dataDict = {'project_uuid': self._getUuid(),
-                        'project_workflow': projectWorfklow}
-
-            urlName = os.environ.get('SCIPION_NOTIFY_URL',
-                                     config.SCIPION_STATS_WORKFLOW_APP).strip()
-            urlName += "addOrUpdateWorkflow/"
-            t = threading.Thread(name="notifier", target=lambda: self._sendData(urlName, dataDict))
-            t.start()  # will execute function in a separate thread
-        except Exception as e:
-            print("Can't report usage: ", e)
-
-    def _isProjectMuted(self):
-        """ Projects are muted if they come from tests, Since there is no flag for it
-        we will assume that if the project name starts with Test it will be considered
-        a test and therefore no statistics will be sent"""
-        return os.path.basename(self.project.name).startswith("Test")
-
-    def getEntryFromWebservice(self, uuid):
-        if not pyworkflow.Config.SCIPION_NOTIFY:
-            return
-        urlName = os.environ.get('SCIPION_NOTIFY_URL').strip()
-        # remove last directory
-        urlName = os.path.split(urlName)[0]
-        url = urlName + "/?project_uuid=" + uuid
-        resultDict = self._sendData(url)

pyworkflow/webservices/repository.py

@@ -1,59 +0,0 @@
-import webbrowser
-import json
-import requests
-
-from pyworkflow import CORE_VERSION
-from . import config
-
-
-class WorkflowRepository(object):
-    """ Manager to communicate with the workflow repository services.
-    It will provide functions to:
-    - Search workflows (open the url in a browser).
-    - Upload a given workflow json file.
-    """
-    def __init__(self,
-                 repositoryUrl=config.WORKFLOW_REPOSITORY_SERVER,
-                 uploadFileSuffix=config.WORKFLOW_PROG_STEP1,
-                 uploadMdSuffix=config.WORKFLOW_PROG_STEP2):
-        self._url = repositoryUrl
-        self._uploadFileUrl = repositoryUrl + uploadFileSuffix
-        self._uploadMdUrl = repositoryUrl + uploadMdSuffix
-
-    def search(self):
-        """ Open the repository URL in a web browser. """
-        webbrowser.open(self._url)
-
-    def upload(self, jsonFileName):
-        """ Upload a given workflow providing the path ot the json file.
-
-        First the file is uploaded, then the metadata is uploaded.
-        The script uploads the file and then opens a browser for the metadata
-        Note that the two steps are needed since no initial value can be passed
-        to a file field. poster3 module is needed. Poster3 is pure python
-        so it may be added to the directory rather than installed if needed.
-
-        The server is django a uses filefield and csrf_exempt.
-        csrf_exempt disable csrf checking. filefield
-        """
-
-        # we are going to upload a file so this is a multipart
-        # connection
-        with open(jsonFileName, "rb") as workflowFile:
-            file_dict = {"json": workflowFile}
-            response = requests.post(self._uploadFileUrl, files=file_dict)
-
-        # server returns  a json stored as text at response.text
-        _dict = json.loads(response.text)
-
-        version = CORE_VERSION
-        # version hack end
-
-        fnUrl = "?jsonFileName=%s&versionInit=%s" % (_dict['jsonFileName'],
-                                                     version)  # use GET
-        # open browser to fill metadata, fileName will be saved as session
-        # variable. Note that I cannot save the file never in the
-        # session in the first connection because the browser changes
-        # from urlib2 to an actual browser
-        # so sessions are different
-        webbrowser.open(self._uploadMdUrl + fnUrl)

pyworkflow/webservices/workflowhub.py

@@ -1,74 +0,0 @@
-import json
-from urllib.request import Request, urlopen
-from pyworkflow.template import Template
-
-
-class WHTemplate(Template):
-
-    def __init__(self, source, name, description, url):
-        super().__init__(source, name, description)
-        self.url = url
-
-    def loadContent(self):
-        """ Download the file pointer by url and read the content"""
-
-        return make_request(self.url, asJson=False)
-
-
-def make_request(url, asJson=True):
-    """ Makes a request to the url and returns the json as a dictionary"""
-
-    req = Request(url)
-    req.add_header("accept", "application/json")
-
-    with urlopen(req, timeout=1) as response:
-        if asJson:
-            data = json.load(response)
-        else:
-            html_response = response.read()
-            encoding = response.headers.get_content_charset('utf-8')
-            data = html_response.decode(encoding)
-        return data
-
-
-def get_workflow_file_url(workflow_id, version):
-    root_url = "https://workflowhub.eu/workflows/%s/git/%s/" % (workflow_id, version)
-    url = root_url + 'tree'
-
-    result = make_request(url)
-
-    for file in result["tree"]:
-        path = (file["path"])
-        if path.endswith(".json.template"):
-            return root_url + 'raw/' + path
-
-
-def get_wh_templates(template_id=None, organization="Scipion%20CNB"):
-    """ Returns a list of scipion templates available in workflow hub"""
-
-    url = "https://workflowhub.eu/ga4gh/trs/v2/tools?organization=%s" % organization
-
-    response = make_request(url)
-
-    template_list = []
-
-    for workflow in response:
-        workflow_id = workflow["id"]
-        name = workflow["name"]
-        description = workflow['description']
-        version = workflow["versions"][-1]
-        version_id = version["id"]
-        template_url = get_workflow_file_url(workflow_id, version_id)
-
-        new_template = WHTemplate("Workflow hub", name, description, template_url)
-        if template_id is None or new_template.getObjId() == template_id:
-            template_list.append(new_template)
-
-    return template_list
-
-
-if __name__ == "__main__":
-
-    templates = get_wh_templates()
-    for template in templates:
-        print(template)

pyworkflowtests/tests/test_canvas.py

@@ -1,72 +0,0 @@
-#!/usr/bin/env python
-# To run only the tests in this file, use:
-# python -m unittest test_canvas -v
-
-import pyworkflow.gui.canvas
-import tkinter
-import math
-from pyworkflow.tests import *
-
-
-class TestCanvas(BaseTest):
-    # IMPORTANT: Tk requires at least that DISPLAY is defined
-    # hence in some environments (like buildbot) the test may fail,
-    # check for the TclError exception
-
-    _labels = [PULL_REQUEST]
-
-    @classmethod
-    def setUpClass(cls):
-        setupTestOutput(cls)
-
-    def distance(self, c1, c2):
-        return round(math.hypot(c2[0] - c1[0], c2[1] - c1[1]), 2)
-
-    def allEqual(self, values):
-        return not values or values.count(values[0]) == len(values)
-
-    def allDifferent(self, values):
-        return not values or len(values) == len(set(values))
-
-    def test_connectorsCoords(self):
-        try:
-            root = tkinter.Tk()
-            canvas = pyworkflow.gui.canvas.Canvas(root, width=800, height=600)
-            tb1 = canvas.createTextbox("First", 100, 100, "blue")
-
-            connectorsCoords = tb1.getConnectorsCoordinates()
-            self.assertTrue(self.allDifferent(connectorsCoords))
-
-            print(connectorsCoords)
-
-            distances = {}
-            for i in range(len(connectorsCoords) - 1):
-                distances[i] = self.distance(connectorsCoords[i],
-                                             connectorsCoords[i + 1])
-
-                print(distances)
-                self.assertTrue(self.allEqual(list(distances.values())))
-                self.assertNotEqual(distances[0], 0)
-        except tkinter.TclError as ex:
-            print(ex)
-
-    def test_closestConnectors(self):
-        try:
-            root = tkinter.Tk()
-            canvas = pyworkflow.gui.canvas.Canvas(root, width=800, height=600)
-            tb1 = canvas.createTextbox("Textbox1", 100, 100, "blue")
-            tb2 = canvas.createTextbox("Textbox2", 300, 100, "blue")
-            tb3 = canvas.createTextbox("Textbox3", 100, 300, "blue")
-
-            tb1ConnectorsCoords = tb1.getConnectorsCoordinates()
-            tb2ConnectorsCoords = tb2.getConnectorsCoordinates()
-            tb3ConnectorsCoords = tb3.getConnectorsCoordinates()
-            c1, c2 = pyworkflow.gui.canvas.findStrictClosestConnectors(tb1, tb2)
-            c3, c4 = pyworkflow.gui.canvas.findStrictClosestConnectors(tb1, tb3)
-            # tb1 and tb2 are aligned vertically. tb1 and tb3, horizontally.
-            # So, their closest connectors must share one coordinate (y in case of c1&c2, x i n case of c3&c4)
-            self.assertEqual(c1[1], c2[1])
-            self.assertEqual(c3[0], c4[0])
-
-        except tkinter.TclError as ex:
-            print(ex)

pyworkflowtests/tests/test_domain.py

@@ -1,45 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
-# *
-# * [1] SciLifeLab, Stockholm University
-# *
-# * This program is free software: you can redistribute it and/or modify
-# * it under the terms of the GNU General Public License as published by
-# * the Free Software Foundation, either version 3 of the License, or
-# * (at your option) any later version.
-# *
-# * This program is distributed in the hope that it will be useful,
-# * but WITHOUT ANY WARRANTY; without even the implied warranty of
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * GNU General Public License for more details.
-# *
-# * You should have received a copy of the GNU General Public License
-# * along with this program.  If not, see <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-
-import pyworkflow.tests as pwtests
-import pyworkflowtests.objects as objectsMod
-from pyworkflowtests import Domain
-
-
-class TestDomain(pwtests.BaseTest):
-
-    def test_objects(self):
-        """ Test that all objects are properly discovered. """
-        objects = Domain.getObjects()
-        for k in dir(objectsMod):
-            v = getattr(objectsMod, k)
-            if isinstance(v, objectsMod.MockObject):
-                self.assertEqual(objects[k], v)
-
-    def test_viewers(self):
-        pass
-
-    def test_wizards(self):
-        pass