webmo 1.4.2__tar.gz → 1.6.0__tar.gz

webmo-1.6.0/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: webmo
+Version: 1.6.0
+Summary: A Python-based interface to WebMO
+Home-page: https://github.com/jrschmidt2/webmo-python
+Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.6.0.tar.gz
+Author: J.R. Schmidt
+Author-email: schmidt@webmo.net
+License: MIT
+Keywords: WEBMO,REST,API
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: websockets
+Provides-Extra: spectrum
+Requires-Dist: numpy; extra == "spectrum"
+Provides-Extra: util
+Requires-Dist: PubChemPy; extra == "util"
+Provides-Extra: gui
+Requires-Dist: questionary; extra == "gui"
+Requires-Dist: ipywidgets; extra == "gui"
+Provides-Extra: all
+Requires-Dist: numpy; extra == "all"
+Requires-Dist: PubChemPy; extra == "all"
+Requires-Dist: questionary; extra == "all"
+Requires-Dist: ipywidgets; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

{webmo-1.4.2 → webmo-1.6.0}/setup.py

@@ -1,4 +1,4 @@
-from distutils.core import setup
+from setuptools import setup
 import codecs
 import os.path
 

{webmo-1.4.2 → webmo-1.6.0}/webmo/__init__.py

@@ -1,2 +1,2 @@
 from .webmo_rest import WebMOREST
-__version__ = "1.4.2"
+__version__ = "1.6.0"

{webmo-1.4.2 → webmo-1.6.0}/webmo/util.py

@@ -1,10 +1,11 @@
 import numpy as np
 
-def xyz_from_name(name):
+def xyz_from_name(name, include_atomic_number=False):
     """Obtains an XYZ-formatted geometry for the molecule name via PubChem lookup.
 
     Arguments:
         name(str): The name of the molecule.
+        include_atomic_number(bool): Whether to include the atomic number as well in the XYZ output (e.g. for GAMESS formatted Cartesian coordinates)
 
     Returns:
         A string containing the molecule's XYZ-formatted geometry.
@@ -19,10 +20,14 @@ def xyz_from_name(name):
     geom = ""
     for atom in record.atoms:
         element = atom.element
+        number = int(atom.number)
         x = float(atom.x)
         y = float(atom.y)
         z = float(atom.z)
-        geom += f"{element}\t{x:f}\t{y:f}\t{z:f}\n"
+        if include_atomic_number:
+            geom += f"{element}\t{number:d}\t{x:f}\t{y:f}\t{z:f}\n"
+        else:
+            geom += f"{element}\t{x:f}\t{y:f}\t{z:f}\n"
         
     return geom
 
@@ -33,8 +38,8 @@ def get_energy(results, include_units=False):
     Requires WebMO 25 or higher.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
-        bool(include_units): Whether to include the units with the returned energy (e.g. 1.5 vs. "1.5 Hartree")
+        results(dict): A dictionary of job results, obtained from get_job_results.
+        include_units(bool): Whether to include the units with the returned energy (e.g. 1.5 vs. "1.5 Hartree")
 
     Returns:
         The molecular energy.
@@ -65,8 +70,8 @@ def get_energies(results, include_units=False):
     """Returns a dictionary of available energies from the job results.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
-        bool(include_units): Whether to include the units with the returned energy (e.g. 1.5 vs. "1.5 Hartree")
+        results(dict): A dictionary of job results, obtained from get_job_results.
+        include_units(bool): Whether to include the units with the returned energy (e.g. 1.5 vs. "1.5 Hartree")
 
     Returns:
         A dictionary of available energies.
@@ -92,7 +97,7 @@ def get_geometry(results):
     """Returns the XYZ-formatted final geometry from the job results.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
+        results(dict): A dictionary of job results, obtained from get_job_results.
 
     Returns:
         The XYZ-formatted final geometry as a string.
@@ -116,7 +121,7 @@ def get_stoichiometry(results):
     """Returns the stoichiometry from the job results.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
+        results(dict): A dictionary of job results, obtained from get_job_results.
 
     Returns:
         The stoichiometry as a string.
@@ -129,7 +134,7 @@ def get_dipole_moment(results):
     """Returns the dipole moment from the job results.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
+        results(dict): A dictionary of job results, obtained from get_job_results.
 
     Returns:
         The magnitude of the dipole moment.
@@ -147,8 +152,8 @@ def get_property(results, property_name):
     """Returns an arbitrary calculated property from the job results.
 
     Arguments:
-        dict(results): A dictionary of job results, obtained from get_job_results.
-        str(property_name): The name of the desired property
+        results(dict): A dictionary of job results, obtained from get_job_results.
+        property_name(str): The name of the desired property
 
     Returns:
         The value of the calculated property (scalar or dictionary).
@@ -266,6 +271,72 @@ def get_dihedral_angle(results, index1, index2, index3, index4):
 
     return np.arctan2(y, x)*180./np.pi
 
+def get_option_matching(template, variable, desired_value_aliases, ignore_missing_variables=False):
+    """Returns the best matching template variable option for the specified variable.
+
+    This can be useful when an engine uses non-standard names for options and you want to use a
+    more descriptive name (like that shown in the dropdown) rather than the corresponding value. It attempts
+    to match either the corresponding option value (if it exists) OR the description.
+
+    For example:
+        get_option_matching(template, 'basisSet', '6-31G(d)')
+    will return the value:
+        "N31 NGAUSS=6 NDFUNC=1"
+    since it matches the corresponding option description "Routine: 6-31G(d)" in the dropdown.
+
+    Arguments:
+        template(dict): The desired job template (from get_templates)
+        variable(str): The template variable
+        desired_value_aliases(list): A list of potentially matching values, or aliases thereof; a single string is also acceptable.
+        ignore_missing_variables(bool, opt): Whether to raise an exception if the template variable does not exist in the template
+
+    Returns:
+        The best matching corresponding variable value
+    """
+
+    def ends_with_whole_word(text, target_word):
+        # Check if it ends with the word
+        if not text.endswith(target_word):
+            return False
+        # Get the start index of the target word in the text
+        idx = len(text) - len(target_word)
+        # If it's at the very beginning of the string, it's a whole word
+        if idx == 0:
+            return True
+        # Check if the character just before our word is a space or a colon
+        return text[idx - 1].isspace() or text[idx - 1] == ':'
+
+    #immediately return if the desired value is blank (for some reason)
+    if isinstance(desired_value_aliases, str) and not desired_value_aliases.strip():
+        return ""
+
+    #normalize any scalar arguement ot a list
+    if not isinstance(desired_value_aliases, list):
+        desired_value_aliases = [desired_value_aliases]
+    #immediately return if this variable does not exist in this particular template
+    if not variable in template['variables']:
+        if ignore_missing_variables:
+            return ""
+        else:
+            raise ValueError(f"Could not locate variable {variable} in template")
+    #ensure that the template variable is a 'dropdown' type
+    if template['variables'][variable]['type'] != 'dropdown':
+        raise ValueError(f"Template variable {variable} is not of type dropdown")
+
+    options = template['variables'][variable]['options']
+    for desired_value in desired_value_aliases:
+        for key, value in options.items():
+            #check if the specified value exists as value in the options dictionary
+            if value.casefold() == desired_value.casefold():
+                return value
+            #otherwise check if it matches the end of any key in the dictionary
+            if ends_with_whole_word(key.casefold(), desired_value.casefold()):
+                return options[key]
+
+    #not found!
+    raise ValueError(f"Could not locate option {desired_value_aliases} for template variable {variable}")
+
+
 def _xyz_to_array(xyz):
     xyz = xyz.strip()
 
@@ -284,4 +355,4 @@ def _xyz_to_array(xyz):
     del geom[0::4]
 
     #convert to an array of floats and return
-    return np.array(geom,dtype=float)
+    return np.array(geom,dtype=float)

{webmo-1.4.2 → webmo-1.6.0}/webmo/webmo_rest.py

@@ -16,30 +16,43 @@ class WebMOREST:
     creation/destruction.
     """
     
-    def __init__(self, base_url, username, password="", expiration=24):
+    def __init__(self, base_url, username, password="", expiration=24, totp="", recovery_code=""):
         """Constructor for WebMOREST
-        
+
         This constructor generates a WebMOREST object and also generates and stores a newly
         session token.
-        
+
         Args:
             base_url(str): The base URL (ending in rest.cgi) of the WeBMO rest endpoint
             username(str): The WebMO username
             password(str, optional): The WebMO password; if omitted, this is supplied interactively
             expiration(int, optional): The expiration time (in hours) of the REST session token
-            
+            totp(str, optional): The current TOTP code from an authenticator app, for users with MFA enabled;
+                if omitted and MFA is required, a TOTP or recovery code is supplied interactively
+            recovery_code(str, optional): A single-use MFA recovery code, as an alternative to totp
+
         Returns:
             object: The newly constructed WebMO object
         """
         from getpass import getpass
-        
+
         #prompt for WebMO password if not specified
         if not password:
             password=getpass(prompt="Enter WebMO password for user %s:" % username)
         #obtain a REST token using the specified credentials
-        login={'username' : username, 'password' : password, 'expiration' : expiration}
+        login={'username' : username, 'password' : password, 'expiration' : expiration,
+            'totp' : totp, 'recoveryCode' : recovery_code}
         r = requests.post(base_url + '/sessions', data=login)
-        r.raise_for_status() #raise an exception if there is a problem with the request
+        #prompt for an MFA code if required but not specified; a request without a code
+        #does not count as a failed MFA attempt, and a lockout is reported as an error below
+        if not totp and not recovery_code and WebMOREST._is_mfa_required(r):
+            code = input("Enter WebMO MFA code (or recovery code) for user %s:" % username).strip()
+            if code.isdigit():
+                login['totp'] = code
+            else:
+                login['recoveryCode'] = code
+            r = requests.post(base_url + '/sessions', data=login)
+        WebMOREST._check_status(r) #raise an exception if there is a problem with the request
         
         self._base_url = base_url
         self._auth=r.json() #save an authorization token need to authenticate future REST requests
@@ -53,14 +66,15 @@ class WebMOREST:
         
         This destructor automatically deletes the session token using the REST interface
         """
-        #End the REST sessions; check in case requests has already been released
-        if requests.delete is not None:
+        #End the REST sessions; check in case requests has already been released,
+        #or the constructor failed before a session token was obtained
+        if requests.delete is not None and hasattr(self, '_auth'):
             r = requests.delete(self._base_url + '/sessions', params=self._auth)
         #do not raise an exception for a failed request in this case due to issues
         #with object management in Jupyter (i.e. on code re-run, a new token is made
         #prior to deletion!)
 
-        if self._callback_listener is not None:
+        if getattr(self, '_callback_listener', None) is not None:
             self._callback_listener.close()
     
     #
@@ -78,7 +92,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/users", params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["users"]
         
     def get_user_info(self, username):
@@ -95,7 +109,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/users/%s" % username, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()
 
     #
@@ -112,7 +126,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/groups", params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["groups"]
         
     def get_group_info(self, groupname):
@@ -129,7 +143,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/groups/%s" % groupname, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()
         
         
@@ -153,7 +167,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'user' : target_user})
         r = requests.get(self._base_url + "/folders", params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["folders"]
     
     #
@@ -179,7 +193,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'engine' : engine, 'status' : status, 'folderID' : folder_id, 'jobName' : job_name, 'user' : target_user})
         r = requests.get(self._base_url + '/jobs', params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["jobs"]
         
     def get_job_info(self, job_number):
@@ -195,7 +209,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/jobs/%d" % job_number, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()
 
     def _check_valid_job_list(self, job_numbers):
@@ -227,7 +241,7 @@ class WebMOREST:
             params.update({'jobNumber' : ",".join(str(job_number) for job_number in job_numbers)})
             r = requests.get(self._base_url + "/jobs/results", params=params)
 
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()
         
     def get_job_geometry(self, job_number):
@@ -243,7 +257,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/jobs/%d/geometry" % job_number, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["xyz"]
         
     def get_job_output(self, job_number):
@@ -259,7 +273,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/jobs/%d/raw_output" % job_number, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.text
         
     def get_job_archive(self, *job_numbers):
@@ -280,7 +294,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'jobNumber' : ",".join(str(job_number) for job_number in job_numbers)})
         r = requests.get(self._base_url + "/jobs/archive" % (), params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.text
         
     def get_job_spreadsheet(self, *job_numbers):
@@ -301,7 +315,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'jobNumber' : ",".join(str(job_number) for job_number in job_numbers)})
         r = requests.get(self._base_url + "/jobs/spreadsheet" % (), params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.text
         
     def delete_job(self, job_number):
@@ -314,7 +328,7 @@ class WebMOREST:
         """
         
         r = requests.delete(self._base_url + "/jobs/%d" % job_number, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         
     def import_job(self, job_name, output_filename, engine):
         """Imports an existing output file into WebMO
@@ -335,7 +349,7 @@ class WebMOREST:
         params.update({'jobName' : job_name, 'engine' : engine})
         output_file = {'outputFile' : ('output.log', open(output_filename, 'rb'), 'text/plain')}
         r = requests.post(self._base_url + '/jobs', data=params, files=output_file)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["jobNumber"]
         
     def submit_job(self, job_name, input_contents, engine, queue=None, nodes=1, ppn=1, **kwargs):
@@ -362,7 +376,7 @@ class WebMOREST:
         params.update({'jobName' : job_name, 'engine' : engine, 'inputFile': input_contents,
             'queue': queue, 'nodes': nodes, 'ppn': ppn, **kwargs})
         r = requests.post(self._base_url + '/jobs', data=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["jobNumber"]
         
     #
@@ -381,7 +395,7 @@ class WebMOREST:
         """
 
         r = requests.get(self._base_url + "/templates/%s" % engine, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["templates"]
 
 
@@ -399,6 +413,12 @@ class WebMOREST:
             A text-formatted input file
         """
         amend_variables = variables.copy()
+        #handle booleans, converting False to '' if the template variable is a checkbox
+        for var in amend_variables:
+            if isinstance(amend_variables[var], bool) and (var in template['variables']) and (template['variables'][var]['type'] == 'checkbox'):
+                if amend_variables[var] == False:
+                    amend_variables[var] = ''
+        #add in defaults, if appropriate
         if auto_defaults:
             #update and amend 'variables' with default values for missing template parameters
             for var in template['variables']:
@@ -409,7 +429,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'variables' : json.dumps(amend_variables)})
         r = requests.get(self._base_url + "/templates/%s" % template['id'], params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.text
 
     #
@@ -432,7 +452,7 @@ class WebMOREST:
         params = self._auth.copy()
         params.update({'user' : target_user})
         r = requests.get(self._base_url + "/engines", params=params)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()["engines"]
 
     #
@@ -479,7 +499,7 @@ class WebMOREST:
             await self._create_callback_listener()
 
         r = requests.get(self._base_url + "/jobs/%d/geometry" % job_number, params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         geometryJSON = json.dumps(r.json())
         geometryJSON = geometryJSON.replace("\\", "\\\\")
         
@@ -614,7 +634,7 @@ class WebMOREST:
         """
         
         r = requests.get(self._base_url + "/status", params=self._auth)
-        r.raise_for_status()
+        WebMOREST._check_status(r)
         return r.json()
         
         
@@ -651,7 +671,29 @@ class WebMOREST:
     #
     # Private helper methods
     #
-    
+    @staticmethod
+    def _check_status(response):
+        try:
+            response.raise_for_status()
+        except requests.exceptions.HTTPError as e:
+            # Grab the original message and append the body
+            new_message = f"{e.args[0]}\nResponse Body: {response.text[:500]}"
+            # Overwrite the exception arguments with your new message
+            e.args = (new_message,)
+            raise e
+
+    @staticmethod
+    def _is_mfa_required(response):
+        #MFA-enabled users without a valid code receive a 401 flagged with mfaRequired;
+        #an MFA lockout is flagged the same way, but prompting for a code would not help
+        if response.status_code != 401:
+            return False
+        try:
+            body = response.json()
+        except ValueError:
+            return False
+        return body.get('mfaRequired', False) and body.get('error') == 'MFA code required'
+
     def _inject_javascript(self):
         if self._init_javascript:
             config = self.get_status_info()

webmo-1.6.0/webmo.egg-info/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: webmo
+Version: 1.6.0
+Summary: A Python-based interface to WebMO
+Home-page: https://github.com/jrschmidt2/webmo-python
+Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.6.0.tar.gz
+Author: J.R. Schmidt
+Author-email: schmidt@webmo.net
+License: MIT
+Keywords: WEBMO,REST,API
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: websockets
+Provides-Extra: spectrum
+Requires-Dist: numpy; extra == "spectrum"
+Provides-Extra: util
+Requires-Dist: PubChemPy; extra == "util"
+Provides-Extra: gui
+Requires-Dist: questionary; extra == "gui"
+Requires-Dist: ipywidgets; extra == "gui"
+Provides-Extra: all
+Requires-Dist: numpy; extra == "all"
+Requires-Dist: PubChemPy; extra == "all"
+Requires-Dist: questionary; extra == "all"
+Requires-Dist: ipywidgets; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: download-url
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

webmo-1.4.2/PKG-INFO

@@ -1,15 +0,0 @@
-Metadata-Version: 2.1
-Name: webmo
-Version: 1.4.2
-Summary: A Python-based interface to WebMO
-Home-page: https://github.com/jrschmidt2/webmo-python
-Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.4.2.tar.gz
-Author: J.R. Schmidt
-Author-email: schmidt@webmo.net
-License: MIT
-Keywords: WEBMO,REST,API
-Provides-Extra: spectrum
-Provides-Extra: util
-Provides-Extra: gui
-Provides-Extra: all
-License-File: LICENSE

webmo-1.4.2/webmo.egg-info/PKG-INFO

@@ -1,15 +0,0 @@
-Metadata-Version: 2.1
-Name: webmo
-Version: 1.4.2
-Summary: A Python-based interface to WebMO
-Home-page: https://github.com/jrschmidt2/webmo-python
-Download-URL: https://github.com/jrschmidt2/webmo-python/archive/refs/tags/1.4.2.tar.gz
-Author: J.R. Schmidt
-Author-email: schmidt@webmo.net
-License: MIT
-Keywords: WEBMO,REST,API
-Provides-Extra: spectrum
-Provides-Extra: util
-Provides-Extra: gui
-Provides-Extra: all
-License-File: LICENSE