Merge bb8e1d5 into 65ebac7

microsetta_private_api/admin/admin_impl.py

@@ -1,11 +1,19 @@
+import uuid
+
 import flask
 from flask import jsonify
 import datetime
 
+from microsetta_private_api.admin.email_templates import EmailMessage
+from microsetta_private_api.config_manager import SERVER_CONFIG
+from microsetta_private_api.model.log_event import LogEvent
 from microsetta_private_api.exceptions import RepoException
 from microsetta_private_api.repo.account_repo import AccountRepo
+from microsetta_private_api.repo.event_log_repo import EventLogRepo
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.admin_repo import AdminRepo
+from microsetta_private_api.util.email import SendEmail
+from microsetta_private_api.util.redirects import build_login_redirect
 from werkzeug.exceptions import Unauthorized, BadRequest
 
 
@@ -164,3 +172,82 @@ def create_kits(body, token_info):
             t.commit()
 
     return jsonify(kits), 201
+
+
+def get_account_events(account_id, token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        events = EventLogRepo(t).get_events_by_account(account_id)
+        return jsonify([x.to_api() for x in events]), 200
+
+
+def send_email(body, token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        account_id = None
+        email = None
+        resolution_url = None
+        contact_name = None
+
+        # Depending on issue type, determine what email to send to and
+        # what account is involved, as well as what link to send user to
+        # address the problem if that is required by the email template
+        if body["issue_type"] == "sample":
+            # TODO:  Building resolution url is very tricky, and it's not clear
+            #  what component should be responsible for doing it.  It requires
+            #  knowing what endpoint the client minimal interface is hosted at,
+            #  as well as a sample barcode's associated
+            #       account_id,
+            #       source_id,
+            #       sample_id
+            #  which generally requires lookup in the db with admin privilege.
+
+            diag = AdminRepo(t).retrieve_diagnostics_by_barcode(
+                       body["template_args"]["sample_barcode"],
+                       grab_kit=False)
+            account_id = diag["account"].id
+            source_id = diag["source"].id
+            sample_id = diag["sample"].id
+            email = diag["account"].email
+            contact_name = diag["account"].first_name + " " + \
+                diag["account"].last_name
+            contact_name = contact_name.strip()
+            endpoint = SERVER_CONFIG["endpoint"]
+            resolution_url = build_login_redirect(
+                endpoint + "/accounts/%s/sources/%s/samples/%s" %
+                (account_id, source_id, sample_id)
+            )
+        else:
+            raise Exception("Update Admin Impl to support more issue types")
+
+        # Determine what template must be sent, and build the template args
+        # from whatever is in the body and the resolution url we determined
+        template = EmailMessage[body['template']]
+        template_args = dict(body['template_args'])
+        template_args['resolution_url'] = resolution_url
+        template_args['contact_name'] = contact_name
+
+        # Send the email
+        SendEmail.send(email, template, template_args)
+
+        # Add an event to the log that we sent this email successfully
+        event = LogEvent(
+            uuid.uuid4(),
+            template.event_type,
+            template.event_subtype,
+            None,
+            {
+                # account_id and email are necessary to allow searching the
+                # event log.
+                "account_id": account_id,
+                "email": email,
+                "template": body["template"],
+                "template_args": body["template_args"]
+            })
+        EventLogRepo(t).add_event(event)
+
+        t.commit()
+
+    return '', 204

microsetta_private_api/admin/email_templates.py

@@ -0,0 +1,43 @@
+from enum import Enum
+from flask import render_template
+from werkzeug.exceptions import BadRequest
+from microsetta_private_api.model.log_event import EventType, EventSubtype
+
+
+class EmailTemplate:
+    def __init__(self, filepath, required):
+        self.filepath = filepath
+        self.required = required
+
+    def render(self, template_args):
+        for key in self.required:
+            if key not in template_args:
+                raise BadRequest("Missing Required Argument: " + str(key))
+        return render_template(self.filepath, **template_args)
+
+
+class EmailMessage(Enum):
+    incorrect_sample_type = (
+        "Incorrect Sample Type",
+        "email/incorrect_sample_type.jinja2",
+        "email/incorrect_sample_type.plain",
+        ("contact_name", "sample_barcode", "recorded_type", "received_type",
+         "resolution_url"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_INCORRECT_SAMPLE_TYPE
+    )
+    missing_sample_info = (
+        "Missing Sample Info",
+        "email/missing_sample_info.jinja2",
+        "email/missing_sample_info.plain",
+        ("contact_name", "sample_barcode", "received_type", "resolution_url"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_MISSING_SAMPLE_INFO
+    )
+
+    def __init__(self, subject, html, plain, required, event_type, event_sub):
+        self.subject = subject
+        self.html = EmailTemplate(html, required)
+        self.plain = EmailTemplate(plain, required)
+        self.event_type = event_type
+        self.event_subtype = event_sub

microsetta_private_api/api/microsetta_private_api.yaml

@@ -1185,6 +1185,47 @@ paths:
             application/json:
               schema:
                 type: object
+  '/admin/events/accounts/{account_id}':
+    get:
+      operationId: microsetta_private_api.admin.admin_impl.get_account_events
+      tags:
+        - Admin
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+      responses:
+        '200':
+          description: Event log associated with the account
+          content:
+            application/json:
+              schema:
+                type: array
+  '/admin/email':
+    post:
+      operationId: microsetta_private_api.admin.admin_impl.send_email
+      tags:
+        - Admin
+      summary: Send a templated email to an end user
+      description: Send a templated email to an end user
+      requestBody:
+        content:
+          application/json:
+            schema:
+              type: object
+              properties:
+                # issue type defines what resolution_url the user should go to
+                issue_type:
+                  type: string
+                  enum: ["sample"]
+                template:
+                  type: string
+                  enum: ["incorrect_sample_type",
+                         "missing_sample_info"]
+                  example: "incorrect_sample_type"
+                template_args:
+                  type: object
+      responses:
+        '204':
+          description: Email sent
 
 components:
   parameters:

microsetta_private_api/api/tests/test_admin_api.py

@@ -6,8 +6,9 @@
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.repo.account_repo import AccountRepo
 from microsetta_private_api.repo.admin_repo import AdminRepo
-from microsetta_private_api.api.tests.test_api import client, MOCK_HEADERS, \
-    ACCT_ID_1, ACCT_MOCK_ISS, ACCT_MOCK_SUB  # noqa
+from microsetta_private_api.api.tests.test_api import client  # noqa Screw you flake8, we use this by name.
+from microsetta_private_api.api.tests.test_api import MOCK_HEADERS, \
+    ACCT_ID_1, ACCT_MOCK_ISS, ACCT_MOCK_SUB
 
 DUMMY_PROJ_NAME = "test project"
 

microsetta_private_api/model/log_event.py

@@ -23,9 +23,10 @@ class EventSubtype(Enum):
     EMAIL_SAMPLE_RECEIVED_PLATED = "sample_received_plated"
     # indicate a previously banked sample is now being plated
     EMAIL_BANKED_SAMPLE_NOW_PLATED = "banked_sample_plated"
-    # indicate if there is a problem with a sample
-    # (messaging should be tailored to the problem)
-    EMAIL_SAMPLE_RECEIVED_WITH_PROBLEMS = "sample_received_with_problems"
+    # Indicate a sample was received but doesn't match the information provided
+    EMAIL_INCORRECT_SAMPLE_TYPE = "incorrect_sample_type"
+    # Indicate a sample was received but necessary information was not provided
+    EMAIL_MISSING_SAMPLE_INFO = "missing_sample_info"
 
 
 class LogEvent(ModelBase):

microsetta_private_api/templates/email/incorrect_sample_type.jinja2

@@ -0,0 +1,43 @@
+<html>
+<head>
+    <meta content="text/html; charset=UTF-8" http-equiv="content-type">
+    <style type="text/css">ol{margin:0;padding:0}table td,table th{padding:0}.c2{background-color:#ffffff;margin-left:72pt;padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left;height:11pt}.c1{background-color:#ffffff;margin-left:36pt;padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left}.c3{color:#000000;font-weight:400;text-decoration:none;vertical-align:baseline;font-size:11pt;font-family:"Arial";font-style:normal}.c0{color:#000000;font-weight:400;text-decoration:none;vertical-align:baseline;font-size:12pt;font-family:"Arial";font-style:normal}.c6{color:#000000;font-weight:700;text-decoration:none;vertical-align:baseline;font-family:"Arial";font-style:normal}.c8{padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left}.c10{background-color:#ffffff;max-width:468pt;padding:72pt 72pt 72pt 72pt}.c9{background-color:#ffffff;margin-left:72pt}.c7{font-weight:700}.c5{height:11pt}.c11{margin-left:36pt}.c4{font-size:12pt}.title{padding-top:0pt;color:#000000;font-size:26pt;padding-bottom:3pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}.subtitle{padding-top:0pt;color:#666666;font-size:15pt;padding-bottom:16pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}li{color:#000000;font-size:11pt;font-family:"Arial"}p{margin:0;color:#000000;font-size:11pt;font-family:"Arial"}h1{padding-top:20pt;color:#000000;font-size:20pt;padding-bottom:6pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h2{padding-top:18pt;color:#000000;font-size:16pt;padding-bottom:6pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h3{padding-top:16pt;color:#434343;font-size:14pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h4{padding-top:14pt;color:#666666;font-size:12pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h5{padding-top:12pt;color:#666666;font-size:11pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h6{padding-top:12pt;color:#666666;font-size:11pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;font-style:italic;orphans:2;widows:2;text-align:left}</style>
+</head>
+<body class="c10">
+
+<p class="c1">
+    <span class="c0">Hello {{contact_name |e}},</span>
+</p>
+<p class="c1"><span class="c0">&nbsp;</span></p>
+<p class="c8 c9">
+    <span class="c0">We recently received the following sample from you and noticed that the sample type may have been incorrectly assigned. To update the sample type, please click on the link below.</span>
+</p>
+<p class="c2"><span class="c0"></span></p>
+<p class="c8 c9">
+    <ul class="c8 c9">
+        <li><span class="c0"> <a href={{resolution_url}} target="_blank">{{sample_barcode |e}}</a> - Marked {{recorded_type |e}} but appears to be {{received_type |e}}</span></li>
+    </ul>
+</p>
+<p class="c2">
+    <span class="c0"></span>
+</p>
+<p class="c8 c9">
+    <span class="c0">The sample type determines how the sample is handled in the lab, and ultimately how the sample results are assessed. We cannot process the sample until the sample type is verified.</span>
+</p>
+<p class="c8 c9"><span class="c0">&nbsp;</span></p>
+<p class="c8 c9">
+    <span class="c4">If you believe {{received |e}} is correct, then please confirm with us at <a href = "mailto: microsetta@ucsd.edu">microsetta@ucsd.edu</a> by replying to this email. We will then update your information so the sample can be appropriately associated.</span>
+</p>
+<p class="c1 c5"><span class="c0"></span></p>
+<p class="c1">
+    <span class="c0">If you have any questions, please reply to us at <a href = "mailto: microsetta@ucsd.edu">microsetta@ucsd.edu</a>. Thank you for supporting our project.</span>
+</p>
+<p class="c1"><span class="c0">&nbsp;</span></p>
+<p class="c1">
+    <span class="c0">Sincerely,</span>
+</p>
+<p class="c8 c11">
+    <span class="c4">The Microsetta Team</span>
+</p>
+</body>
+</html>

microsetta_private_api/templates/email/incorrect_sample_type.plain

@@ -0,0 +1,13 @@
+Hello {{contact_name |e}},
+    We recently received the following sample from you and noticed that the sample type may have been incorrectly assigned.
+
+        Barcode {{sample_barcode |e}} - Marked {{recorded_type |e}} but appears to be {{received_type |e}}
+
+    The sample type determines how the sample is handled in the lab, and ultimately how the sample results are assessed. We cannot process the sample until the sample type is verified. If you believe {{received |e}} is correct, then please confirm with us at microsetta@ucsd.edu by replying to this email. We will then update your information so the sample can be appropriately associated.
+
+    If you have any questions, please reply to us at microsetta@ucsd.edu.
+
+    Thank you for supporting our project.
+
+    Sincerely,
+    The Microsetta Team

microsetta_private_api/templates/email/missing_sample_info.jinja2

@@ -0,0 +1,53 @@
+<html>
+<head>
+    <meta content="text/html; charset=UTF-8" http-equiv="content-type">
+    <style type="text/css">ol{margin:0;padding:0}table td,table th{padding:0}.c2{background-color:#ffffff;margin-left:72pt;padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left;height:11pt}.c1{background-color:#ffffff;margin-left:36pt;padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left}.c3{color:#000000;font-weight:400;text-decoration:none;vertical-align:baseline;font-size:11pt;font-family:"Arial";font-style:normal}.c0{color:#000000;font-weight:400;text-decoration:none;vertical-align:baseline;font-size:12pt;font-family:"Arial";font-style:normal}.c6{color:#000000;font-weight:700;text-decoration:none;vertical-align:baseline;font-family:"Arial";font-style:normal}.c8{padding-top:0pt;padding-bottom:0pt;line-height:1.15;orphans:2;widows:2;text-align:left}.c10{background-color:#ffffff;max-width:468pt;padding:72pt 72pt 72pt 72pt}.c9{background-color:#ffffff;margin-left:72pt}.c7{font-weight:700}.c5{height:11pt}.c11{margin-left:36pt}.c4{font-size:12pt}.title{padding-top:0pt;color:#000000;font-size:26pt;padding-bottom:3pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}.subtitle{padding-top:0pt;color:#666666;font-size:15pt;padding-bottom:16pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}li{color:#000000;font-size:11pt;font-family:"Arial"}p{margin:0;color:#000000;font-size:11pt;font-family:"Arial"}h1{padding-top:20pt;color:#000000;font-size:20pt;padding-bottom:6pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h2{padding-top:18pt;color:#000000;font-size:16pt;padding-bottom:6pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h3{padding-top:16pt;color:#434343;font-size:14pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h4{padding-top:14pt;color:#666666;font-size:12pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h5{padding-top:12pt;color:#666666;font-size:11pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;orphans:2;widows:2;text-align:left}h6{padding-top:12pt;color:#666666;font-size:11pt;padding-bottom:4pt;font-family:"Arial";line-height:1.15;page-break-after:avoid;font-style:italic;orphans:2;widows:2;text-align:left}</style>
+</head>
+<body class="c10">
+<p class="c1 c5"><span class="c0"></span></p>
+<p class="c1">
+    <span class="c0">Hello {{contact_name |e}},</span>
+</p>
+<p class="c1"><span class="c0">&nbsp;</span></p>
+<p class="c8 c9">
+    <span class="c4">Thank you for your interest and participation in The Microsetta Initiative. We are writing as we've encountered an issue processing your sample, and we would appreciate your assistance in helping to resolve this matter. Specifically, the following sample sent to the lab does not have </span>
+    <span class="c4">a recorded sample type, date or time. Please click on the URL below to update the sample information.</span>
+</p>
+<p class="c2"><span class="c0"></span></p>
+<p class="c8 c9">
+    <ul class="c8 c9">
+    <li><span class="c0"><a href={{resolution_url}} target="_blank">{{sample_barcode |e}}</a></span></li>
+    </ul>
+</p>
+<p class="c2">
+    <span class="c0"></span>
+</p>
+<p class="c8 c9">
+    <span class="c0">We require this information in order to process this sample in compliance with our human subjects research protocol. If you have a record of the associated sample type, date, and time for this sample, please provide us with this information. Based on what we can see, the sample type appears to be:</span>
+</p>
+<p class="c8 c9">
+    <span class="c0">&nbsp;</span>
+</p>
+<p class="c8 c9">
+    <ul class="c8 c9">
+    <li><span class="c0"><a href={{resolution_url}} target="_blank">{{sample_barcode |e}}</a> &ndash; {{received_type |e}}</span></li>
+    </ul>
+</p>
+<p class="c8 c9">
+    <span class="c0">&nbsp;</span>
+</p>
+<p class="c8 c9">
+    <span class="c0">If you believe {{received_type |e}} is correct, then please confirm with us at <a href = "mailto: microsetta@ucsd.edu">microsetta@ucsd.edu</a> by replying to this email. And if you have an approximate date and time of sample collection, we would greatly appreciate your sharing this information. We will then update your sample's information so it can be appropriately associated. Alternatively, if you would like to update the sample information directly, please click the link above to do so.</span>
+</p>
+<p class="c1 c5">
+    <span class="c0"></span>
+</p>
+<p class="c1">
+    <span class="c0">If you have any questions, please reply to us at <a href = "mailto: microsetta@ucsd.edu">microsetta@ucsd.edu</a></span>
+</p>
+<p class="c1"><span class="c0">&nbsp;</span></p>
+<p class="c1"><span class="c0">Thank you,</span></p>
+<p class="c8 c11"><span class="c0">The Microsetta Team</span></p>
+
+</body>
+</html>

microsetta_private_api/templates/email/missing_sample_info.plain

@@ -0,0 +1,17 @@
+Hello {{contact_name |e}},
+    Thank you for your interest and participation in The Microsetta Initiative. We are writing as we've encountered an issue processing your sample, and we would appreciate your assistance in helping to resolve this matter.
+
+    Specifically, the following sample sent to the lab does not have a recorded sample type, date or time:
+        Barcode {{sample_barcode |e}}
+
+    We require this information in order to process this sample in compliance with our human subjects research protocol. If you have a record of the associated sample type, date, and time for this sample, please provide us with this information.
+
+    Based on what we can see, the sample type appears to be:
+        Barcode {{sample_barcode |e}}: {{received_type |e}}
+
+    If you believe {{received_type |e}} is correct, then please confirm with us at microsetta@ucsd.edu by replying to this email. And if you have an approximate date and time of sample collection, we would greatly appreciate your sharing this information. We will then update your sample's information so it can be appropriately associated.
+
+    If you have any questions, please reply to us at microsetta@ucsd.edu
+
+    Thank you,
+    The Microsetta Team