diff dynamic_utils.py @ 0:078d77023c34 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_utils.py	Tue Jun 26 08:59:19 2018 -0400
@@ -0,0 +1,281 @@
+#!/usr/bin/env python
+# --------------------------------------------------------------------------------
+# Class for the dynamic options in the GMQL tools
+# --------------------------------------------------------------------------------
+# Luana Brancato, [e-mail]
+# --------------------------------------------------------------------------------
+
+import sys, requests
+
+
+def validate(request_context, error_map, params, inputs):
+    """Generic validate function, it checks if the user is valid."""
+
+    user = params.get('authToken', '')
+
+    if user:
+        try:
+            validate_user(user.file_name)
+        except:
+            error_msg = 'User has expired'
+            error_map['authToken'] = error_msg
+
+
+def validate_upload(request_context, error_map, params, inputs):
+    """Validate function for uploading tool. It also checks the chosen ds name does not exists already."""
+
+    validate(request_context, error_map, params, inputs)
+
+    name = params.get('name')
+
+    user = params.get('authToken')
+
+    #This MUST be changed in the future to a parametric solution. Hopefully in the future Galaxy will allow
+    #validation without external scripts
+
+    url = 'http://genomic.elet.polimi.it/gmql-rest/datasets'
+
+    datasets = get(url, user=user.file_name)
+    list_datasets = [x['name'] for x in datasets['datasets']]
+
+    if name in list_datasets:
+        error_msg = 'Dataset already exists. Choose another name.'
+        error_map['name'] = error_msg
+
+
+def validate_variables(request_context, error_map, params, inputs):
+    """Validate function for gmql_compositor. It checks that all queries input variables
+    have been previously defined. """
+
+    validate(request_context, error_map, params, inputs)
+
+    output_vars = set([])
+
+    # TODO: Include in the check output variables eventually defined previously in another query
+
+    for op in params.get('operations'):
+        op_curr = op.get('operation')
+        if op_curr.get('input', ''):
+            input_var = op_curr.get('input').get('input_var', '')
+            if input_var:
+                if input_var not in output_vars:
+                    error_msg = '%s has not been defined yet\n' % (input_var)
+                    name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', 'input', 'input_var'])
+                    error_map[name] = error_msg
+        else:
+            for key in op_curr.keys():
+                if key.startswith('input_var'):
+                    input_var = op_curr.get(key)
+                    if input_var:
+                        if input_var not in output_vars:
+                            error_msg = '%s has not been defined yet\n' % (input_var)
+                            name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', key])
+                            error_map[name] = error_msg
+
+        # Update output_vars with the result of current operation
+        output_vars.add(op_curr.get('output_var'))
+
+
+def validate_user(user):
+    """Check if the user is a valid one"""
+
+    if user:
+        with open(user, 'r') as f:
+            valid = f.readline().rstrip('\n').split('\t')[2]
+            if valid == 'False':
+                raise Exception, "User has expired"
+
+
+def get_metadata_attr(user, ds, ds_list):
+    options = []
+
+    try:
+        validate_user(user)
+        if ds_list:
+
+            owner = ''
+
+            with open(ds_list, 'r') as f:
+                for d in f.readlines():
+                    if d.split('\t')[0] == ds:
+                        owner = d.split('\t')[1].rstrip('\n')
+            f.close()
+
+            attr_list = get_metadata(user, ds, str(owner))
+
+            for i, att in enumerate(attr_list['attributes']):
+                options.append((att.get('key', ' '), att.get('key', ' '), i == 0))
+
+            return options
+
+        else:
+            return options
+    except:
+        return options
+
+
+def get_metadata_values(user, ds, ds_list, att):
+    options = []
+
+    try:
+        validate_user(user)
+        if ds_list:
+
+            owner = ''
+
+            with open(ds_list, 'r') as f:
+                for d in f.readlines():
+                    if d.split('\t')[0] == ds:
+                        owner = d.split('\t')[1].rstrip('\n')
+            f.close()
+
+            attr_list = get_metadata(user, ds, str(owner), att)
+
+            # By default first option is '*' i.e. any value
+            options.append(('any value', '*', 0))
+
+            for i, att in enumerate(attr_list['values']):
+                options.append(('%s (%d)' % (att.get('text', ' '), att.get('count', 0)), att.get('text', ' '), i == 0))
+
+            return options
+
+        else:
+            return options
+    except:
+        return options
+
+
+def get_metadata(user, ds, owner='', att_name=''):
+    """Return the metadata attributes names for the given dataset"""
+
+    url = 'http://genomic.elet.polimi.it/gmql-rest/metadata/{datasetName}/filter'
+
+    # Format url
+    if (owner == 'public'):
+        url = url.format(datasetName='public.' + ds)
+    else:
+        url = url.format(datasetName=ds)
+
+    if att_name:
+        url = '{url}/{att}'.format(url=url, att=att_name)
+
+    content = dict()
+    content.update(attributes=[])
+
+    metadata = post(url, content, user=user)
+
+    return metadata
+
+
+def read_token(input):
+    """It takes the tabular file with the information over the user
+     name   authToken   valid_flag
+     It checks if the user is still valid and extract the authToken for the REST calls"""
+
+    with open(input, 'r') as f_in:
+        user = f_in.readline().rstrip('\n').split('\t')
+
+    if user[2]:
+        token = user[1]
+    else:
+        stop_err("This session is no longer valid")
+
+    return token
+
+
+def get(url, user=None, response_type='json'):
+    """GET Request
+    :param url: url where to fetch the requested resource
+    :param user: for authenticated requests; if not provided make an unauthenticated request (es. for login)
+    :param response_type: type of the fetched response.
+        JSON ( Default )
+        TEXT
+        ZIP
+        FILE
+    """
+
+    # Set request headers
+    headers = dict()
+
+    if user:
+        headers.update({'X-AUTH-TOKEN': read_token(user)})
+
+    if response_type == 'text':
+        headers.update({'Accept': 'text/plain'})
+    elif response_type == 'zip':
+        pass
+    elif response_type == 'file':
+        headers.update({'Accept': 'file'})
+    else:
+        headers.update({'Accept': 'application/json'})
+
+    # Make the request
+    response = requests.get(url, headers=headers)
+
+    # Check returned server status
+    status_code = response.status_code
+
+    # Read result. If Server OK, read according to response_type. Raise an error otherwise.
+    if status_code == requests.codes.ok:
+        if response_type == 'json':
+            return response.json()
+        elif response_type == 'text':
+            return response.text
+        else:
+            return response
+    elif status_code == requests.codes.unauthorized:
+        #expire_user(user)
+        stop_err("You are not authorized to do this. \nPlease login first.")
+    elif status_code == requests.codes.not_found:
+        stop_err("Resource not found for this user.")
+    else:
+        stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
+                                                            reason=response.reason,
+                                                            message=response.content))
+
+def post(url, payload, user=None, params=None, content_type='json', response_type='json') :
+    """ POST Request
+    :param url: url where to post data
+    :param payload: payload for the post request. Type is specified by content_type.
+    :param user:  for authenticated requests; if not provided make an unauthenticated request (es. for registration)
+    :param params: optional query parameters
+    :param content_type
+    :param response_type: Default is json
+    """
+
+
+    # Set request headers
+    headers = dict()
+
+    if user:
+        headers.update({'X-AUTH-TOKEN': read_token(user)})
+
+    headers.update({'Accept': 'application/json'})
+
+    if content_type == 'text' :
+        headers.update({'Content-Type' : 'text/plain'})
+        response = requests.post(url, params=params, headers=headers, data=payload)
+    elif content_type == 'multiform' :
+        response = requests.post(url, params=params, headers=headers, files=payload)
+    else :
+        headers.update({'Content-Type': 'application/json'})
+        response = requests.post(url, params=params, headers=headers, json=payload)
+
+    # Check returned server status
+    status_code = response.status_code
+
+
+    if status_code == requests.codes.ok :
+       return response.json()
+    elif status_code == requests.codes.unauthorized :
+       #expire_user(user)
+       stop_err("You are not authorized to do this. \nPlease login first.")
+    else :
+        stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
+                                                 reason=response.reason,
+                                                 message=response.content))
+
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
\ No newline at end of file