Cherrypy to flask

.gitignore

@@ -1,3 +1,6 @@
+# Virtual environment for testing
+venv/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

LmCommon/common/api_query.py

@@ -2,6 +2,7 @@
 """
 from copy import copy
 import csv
+from http import HTTPStatus
 import json
 import os
 import urllib
@@ -12,8 +13,7 @@
 
 from LmCommon.common.lm_xml import fromstring, deserialize
 from LmCommon.common.lmconstants import (
-    BISON, BisonQuery, DwcNames, GBIF, HTTPStatus, Idigbio, IdigbioQuery,
-    Itis, URL_ESCAPES, ENCODING)
+    BISON, BisonQuery, DwcNames, GBIF, Idigbio, IdigbioQuery, Itis, URL_ESCAPES, ENCODING)
 from LmCommon.common.occ_parse import OccDataParser
 from LmCommon.common.ready_file import ready_filename
 

LmWebServer/common/lmconstants.py

@@ -1,12 +1,15 @@
 """This module contains constants used by the Lifemapper web services
 """
 import os
+import secrets
 
 from LmServer.base.utilities import get_mjd_time_from_iso_8601
 from LmServer.common.lmconstants import SESSION_DIR
 from LmServer.common.localconstants import SCRATCH_PATH, APP_PATH
 from LmWebServer.common.localconstants import PACKAGING_DIR
 
+FALLBACK_SECRET_KEY = secrets.token_hex()
+
 # CherryPy constants
 SESSION_PATH = os.path.join(SCRATCH_PATH, SESSION_DIR)
 SESSION_KEY = '_cp_username'
@@ -51,9 +54,9 @@ def boolify_parameter(param, default=True):
         try:
             # Try processing a string
             str_val = param.lower().strip()
-            if str_val == 'false' or str_val == 'no':
+            if str_val in('false', 'f', 'no','n'):
                 return False
-            if str_val == 'true' or str_val == 'yes':
+            if str_val in ('true', 't', 'yes', 'y'):
                 return True
         except Exception:
             pass
@@ -93,7 +96,7 @@ def boolify_parameter(param, default=True):
     },
     'atom': {
         QP_NAME_KEY: 'atom',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)  # Boolify, default is true
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)
     },
     'beforestatus': {
         QP_NAME_KEY: 'before_status',
@@ -143,18 +146,18 @@ def boolify_parameter(param, default=True):
     },
     'detail': {
         QP_NAME_KEY: 'detail',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'displayname': {
         QP_NAME_KEY: 'display_name'
     },
     'docalc': {
         QP_NAME_KEY: 'do_calc',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'domcpa': {
         QP_NAME_KEY: 'do_mcpa',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'envcode': {
         QP_NAME_KEY: 'env_code'
@@ -175,7 +178,7 @@ def boolify_parameter(param, default=True):
     },
     'fillpoints': {
         QP_NAME_KEY: 'fill_points',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'format': {
         # TODO: Forward to respFormat since format is reserved
@@ -190,7 +193,7 @@ def boolify_parameter(param, default=True):
     },
     'hasbranchlengths': {
         QP_NAME_KEY: 'has_branch_lengths',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)  # Boolify, default is true
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)
     },
     'height': {
         QP_NAME_KEY: 'height',
@@ -204,19 +207,19 @@ def boolify_parameter(param, default=True):
     },
     'includecsvs': {
         QP_NAME_KEY: 'include_csvs',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'includesdms': {
         QP_NAME_KEY: 'include_sdms',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)  # Boolify, default is false
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=False)
     },
     'isbinary': {
         QP_NAME_KEY: 'is_binary',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)  # Boolify, default is true
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)
     },
     'isultrametric': {
         QP_NAME_KEY: 'is_ultrametric',
-        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)  # Boolify, default is true
+        QP_PROCESS_KEY: lambda x: boolify_parameter(x, default=True)
     },
     'keyword': {
         QP_NAME_KEY: 'keyword',
@@ -235,7 +238,7 @@ def boolify_parameter(param, default=True):
     },
     'limit': {
         QP_NAME_KEY: 'limit',
-        QP_PROCESS_KEY: lambda x: max(1, int(x))  # Integer, minimum is one
+        QP_PROCESS_KEY: lambda x: max(1, int(x))  # min = 1
     },
     'map': {
         QP_NAME_KEY: 'map_name'
@@ -258,7 +261,7 @@ def boolify_parameter(param, default=True):
     },
     'minimumnumberofpoints': {
         QP_NAME_KEY: 'minimum_number_of_points',
-        QP_PROCESS_KEY: lambda x: max(1, int(x))  # Integer, minimum is one
+        QP_PROCESS_KEY: lambda x: max(1, int(x))  # min = 1
     },
     'numpermutations': {
         QP_NAME_KEY: 'num_permutations',
@@ -273,7 +276,7 @@ def boolify_parameter(param, default=True):
     },
     'offset': {
         QP_NAME_KEY: 'offset',
-        QP_PROCESS_KEY: lambda x: max(0, int(x))  # Integer, minimum is zero
+        QP_PROCESS_KEY: lambda x: max(0, int(x))  # min = 0
     },
     'pathbiogeoid': {
         QP_NAME_KEY: 'path_biogeo_id'

LmWebServer/flask_app/base.py

@@ -0,0 +1,148 @@
+"""The module provides a base Lifemapper service class
+"""
+from flask import session
+from flask_login._compat import text_type
+import os
+
+from LmCommon.common.lmconstants import DEFAULT_POST_USER
+from LmServer.common.lmconstants import ARCHIVE_PATH 
+from LmServer.common.localconstants import PUBLIC_USER
+from LmServer.common.log import WebLogger
+from LmServer.common.lmuser import LMUser
+from LmServer.db.borg_scribe import BorgScribe
+
+# app = Flask(__name__)
+
+class WebUser(LMUser):
+    """Extends lmuser objects for flask-login"""
+
+    # ................................
+    def __init__(
+        self, user_id, email, password, is_encrypted=False, first_name=None, last_name=None, 
+        institution=None, addr_1=None, addr_2=None, addr_3=None, phone=None, mod_time=None):
+        """Constructor
+
+        Args:
+            user_id: user chosen unique id
+            email:  EMail address of user
+            password: user chosen password
+            first_name: The first name of this user
+            last_name: The last name of this user
+            institution: institution of user (optional)
+            addr_1: Address, line 1, of user (optional)
+            addr_2: Address, line 2, of user (optional)
+            addr_3: Address, line 3, of user (optional)
+            phone: Phone number of user (optional)
+            mod_time: Last modification time of this object (optional)
+        """
+        LMUser.__init__(
+            self, user_id, email, password, is_encrypted=is_encrypted, first_name=first_name, 
+            last_name=last_name, institution=institution, addr_1=addr_1, addr_2=addr_2, addr_3=addr_3, 
+            phone=phone, mod_time=mod_time)
+        self._authenticated = False
+        self._active = False
+
+    # ..........................
+    def is_authenticated(self):
+        return self._authenticated
+
+    # ..........................
+    def is_active(self):
+        if self.user_id in (PUBLIC_USER, DEFAULT_POST_USER):
+            return False
+        return True
+
+    # ..........................
+    def is_anonymous(self):
+        if self.user_id in (PUBLIC_USER, DEFAULT_POST_USER):
+            return True
+        return False
+
+    # ..........................
+    def get_id(self):
+        if self.user_id not in (PUBLIC_USER, DEFAULT_POST_USER):
+            try:
+                return text_type(self.user_id)
+            except AttributeError:
+                raise NotImplementedError('No `user_id` attribute - override `get_id`')
+        return
+
+
+
+# .............................................................................
+class LmService:
+    """This is the base Lifemapper service object
+
+    This is the base Lifemapper service object that the services can inherit
+    from.  It is responsible for getting a database connection and logger that
+    can be used for the service.
+    """
+
+    # ..........................
+    def __init__(self):
+        """Constructor
+
+        The constructor is only responsible for getting a logger, user and a
+        scribe instance for the service.  
+        """
+        log = WebLogger()
+        self.scribe = BorgScribe(log)
+        self.scribe.open_connections()
+        self.log = log
+
+    # ..........................
+    def get_user(self, user_id=None):
+        """Gets the user id for the service call.
+
+        Gets the user id for the service call.  If user_id is provided, try
+        that first.  Then try the session and finally fall back to the
+        PUBLIC_USER
+
+        TODO: Save the username in the session
+        """
+        if user_id is None:
+            self.get_user_id()
+        usr = self.scribe.find_user(user_id)
+        return usr
+
+    # ..........................
+    @classmethod
+    def get_user_id(cls, user_id=None):
+        """Gets the lmuser for the service call.
+
+        Gets the user id for the service call.  If urlUser is provided, try
+        that first.  Then try the session and finally fall back to the
+        PUBLIC_USER
+
+        TODO: Save the username in the session
+        """
+        # Check to see if we should use url user
+        if user_id is not None:
+            if user_id.lower() == 'public':
+                return PUBLIC_USER
+            if user_id.lower() == DEFAULT_POST_USER:
+                return DEFAULT_POST_USER
+        # Try to get the user from the session
+        try:
+            return session['username']
+        except Exception:
+            # Fall back to PUBLIC_USER
+            return PUBLIC_USER
+
+    # ................................
+    @classmethod
+    def get_user_dir(cls, user_id):
+        """Get the user's workspace directory
+
+        Todo:
+            Change this to use something at a lower level.  This is using the
+                same path construction as the getBoomPackage script
+        """
+        return os.path.join(ARCHIVE_PATH, user_id, 'uploads', 'biogeo')
+
+    # ..........................
+    @staticmethod
+    def OPTIONS():
+        """Common options request for all services (needed for CORS)
+        """
+        return

LmWebServer/flask_app/biotaphy_names.py

@@ -0,0 +1,43 @@
+"""This module provides a wrapper around GBIF's names service for use in the Biotaphy web application"""
+import werkzeug.exceptions as WEXC
+
+from LmCommon.common.api_query import GbifAPI
+from LmWebServer.flask_app.base import LmService
+from LmWebServer.flask_tools.lm_format import lm_formatter
+
+
+# .............................................................................
+class GBIFTaxonService(LmService):
+    """Class to get and filter results from GBIF name-matching service."""
+
+    # ................................
+    @lm_formatter
+    def get_gbif_results(self, names_obj):
+        """Queries GBIF for accepted names matching the provided list of names
+
+        Args:
+            names_obj(dict): a JSON list of name strings to match
+        """
+        if not isinstance(names_obj, list):
+            return WEXC.BadRequest('Name data must be a JSON list')
+
+        retval = []
+        for name in names_obj:
+            try:
+                gbif_resp = GbifAPI.get_accepted_names(name)[0]
+            except Exception as e:
+                self.log.error('Could not get accepted name from GBIF for name {}: {}'.format(name, e))
+                retval.append({
+                    GbifAPI.SEARCH_NAME_KEY: name,
+                    GbifAPI.ACCEPTED_NAME_KEY: None,
+                    GbifAPI.TAXON_ID_KEY: None
+                })
+            else:
+                retval.append({
+                    GbifAPI.SEARCH_NAME_KEY: name,
+                    GbifAPI.ACCEPTED_NAME_KEY: gbif_resp[
+                        GbifAPI.SPECIES_NAME_KEY],
+                    GbifAPI.TAXON_ID_KEY: gbif_resp[
+                        GbifAPI.SPECIES_KEY_KEY]
+                })
+        return retval