Merge pull request #542 from biocore/csymons_reactivate_japanese

Reactivate Japanese Locale

Author: cassidysymons

microsetta_private_api/LEGACY/locale_data/japanese_gut.py

@@ -6,24 +6,24 @@
 _NEW_PARTICIPANT = {
     'ADD_HUMAN_TITLE': '新しいプロフィール情報を追加する',
     'SEL_AGE_RANGE': '参加者の年齢層を選択する:',
-    'AGE_0_6': '',
-    'AGE_7_12': '',
-    'AGE_13_17': '',
+    'AGE_0_6': '3ヶ月 -  6才',
+    'AGE_7_12': '7〜12才',
+    'AGE_13_17': '13〜17年',
     'AGE_18': '18歳以上',
 
     'PARTICIPATION_AGREEMENT': '''''',
 
     'EXHIBIT_A': '''''',
     'BILL_OF_RIGHTS': '''研究被験者の権利章典''',
     'TEXT_I_HAVE_READ_1': '私は同意書を読みました (又は代読してもらいました)。研究試験への参加を求められていることを理解し、この試験への参加に自由意志で同意します。私の個人データが処理される方法、関連した私の権利を理解しており、この同意書に記載されているように私のデータが処理されることに同意します。',
-    'TEXT_I_HAVE_READ_SIMPLIFIED': '',
-    'PERSON_ATTAINING_ASSENT': '',
-    'TEXT_ASSENT_WITNESS': '',
-    'OBTAINER_NAME': '',
-    'TEXT_I_HAVE_READ_PARENT': '',
+    'TEXT_I_HAVE_READ_SIMPLIFIED': 'はい、あなたはこの調査研究に参加します。',
+    'PERSON_ATTAINING_ASSENT': '同意を得る人の署名',
+    'TEXT_ASSENT_WITNESS': '私の判断において、参加者は自発的かつ自主的に同意し、研究に参加する意思を示す法的能力を持っています。',
+    'OBTAINER_NAME': '同意を得る人の名前',
+    'TEXT_I_HAVE_READ_PARENT': '私はこのフォームを読みました（または誰かが代読した）。私は、我が子の調査研究への参加に、同意を求められていることを理解しました。私は自発的に我が子がこの研究に参加することに同意します。我が子の個人データの処理方法、これに関連する権利、そして提供す',
     'PARTICIPANT_NAME': '参加者名',
     'PARTICIPANT_EMAIL': 'Eメール',
-    'PARTICIPANT_PARENT_1': '',
+    'PARTICIPANT_PARENT_1': '親/保護者の名前',
     'PARTICIPANT_PARENT_2': '',
     'PARTICIPANT_DECEASED_PARENTS': '',
     'DATE_SIGNED': 'DATE_SIGNED',

microsetta_private_api/api/__init__.py

@@ -18,7 +18,8 @@
 from ._source import (
     create_source, read_source, update_source, read_sources,
     create_human_source_from_consent, check_duplicate_source_name,
-    scrub_source, check_source_ffq_prereqs, check_prompt_survey_update
+    scrub_source, check_source_ffq_prereqs, check_prompt_survey_update,
+    get_external_reports, get_external_report, get_external_report_bytes
 )
 from ._survey import (
     read_survey_template, read_survey_templates, read_answered_survey,
@@ -84,6 +85,9 @@
     'read_source',
     'check_source_ffq_prereqs',
     'check_prompt_survey_update',
+    'get_external_reports',
+    'get_external_report',
+    'get_external_report_bytes',
     'update_source',
     'scrub_source',
     'read_sources',

microsetta_private_api/api/_source.py

@@ -1,6 +1,6 @@
 import uuid
 from datetime import date
-from flask import jsonify
+from flask import jsonify, make_response
 
 from microsetta_private_api.api._account import _validate_account_access
 from microsetta_private_api.api.literals import SRC_NOT_FOUND_MSG,\
@@ -194,3 +194,56 @@ def check_prompt_survey_update(account_id, source_id, token_info):
         s_t_r = SurveyTemplateRepo(t)
         prompt_update = s_t_r.check_prompt_survey_update(source_id)
         return jsonify({"prompt": prompt_update}), 200
+
+
+def get_external_reports(account_id, source_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        source_repo = SourceRepo(t)
+        reports = source_repo.get_external_reports(source_id)
+        for r in reports:
+            r.file_contents = ""
+        return jsonify(reports), 200
+
+
+def get_external_report(
+        account_id, source_id, external_report_id, token_info
+):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        source_repo = SourceRepo(t)
+        reports = source_repo.get_external_reports(
+            source_id, external_report_id
+        )
+        if len(reports) != 1:
+            return jsonify(code=404, message="Report not found"), 404
+
+        report = reports[0]
+
+        # Trying to jsonify the actual contents gets ugly, so we return
+        # everything else here, and the contents in get_external_report_bytes
+        report.file_contents = ""
+        return jsonify(report.to_api()), 200
+
+
+def get_external_report_bytes(
+        account_id, source_id, external_report_id, token_info
+):
+    _validate_account_access(token_info, account_id)
+
+    with Transaction() as t:
+        source_repo = SourceRepo(t)
+        reports = source_repo.get_external_reports(
+            source_id, external_report_id
+        )
+
+        if len(reports) != 1:
+            return jsonify(code=404, message="Report not found"), 404
+
+        report = reports[0]
+        response = make_response(bytes(report.file_contents))
+        response.headers.set("Content-Type", report.file_type)
+
+        return response

microsetta_private_api/api/microsetta_private_api.yaml

@@ -679,6 +679,79 @@ paths:
           $ref: '#/components/responses/422UnprocessableEntity'
           # NB: This would be returned if source cannot be deleted bc has a sample assigned to it
 
+  '/accounts/{account_id}/sources/{source_id}/external_reports':
+    get:
+      operationId: microsetta_private_api.api.get_external_reports
+      tags:
+        - Sources
+      summary: Get external reports attached to the source
+      description: Get external reports attached to the source
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+        - $ref: '#/components/parameters/language_tag'
+      responses:
+        '200':
+          description: Successfully returned list of external reports
+          content:
+            application/json:
+              schema:
+                type: array
+                items:
+                  $ref: '#/components/schemas/external_report'
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+
+  '/accounts/{account_id}/sources/{source_id}/external_reports/{external_report_id}':
+    get:
+      operationId: microsetta_private_api.api.get_external_report
+      tags:
+        - Sources
+      summary: Get full contents of external report
+      description: Get full contents of external report
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+        - $ref: '#/components/parameters/external_report_id'
+        - $ref: '#/components/parameters/language_tag'
+      responses:
+        '200':
+          description: Successfully returned external report information
+          content:
+            application/json:
+              schema:
+                type: "object"
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+        '404':
+          $ref: '#/components/responses/404NotFound'
+
+  '/accounts/{account_id}/sources/{source_id}/external_reports/{external_report_id}/bytes':
+    get:
+      operationId: microsetta_private_api.api.get_external_report_bytes
+      tags:
+        - Sources
+      summary: Get full contents of external report
+      description: Get full contents of external report
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+        - $ref: '#/components/parameters/external_report_id'
+        - $ref: '#/components/parameters/language_tag'
+      responses:
+        '200':
+          description: Successfully returned contents of an external report
+        '401':
+          $ref: '#/components/responses/401Unauthorized'
+        '403':
+          $ref: '#/components/responses/403Forbidden'
+        '404':
+          $ref: '#/components/responses/404NotFound'
+
   '/accounts/{account_id}/sources/{source_id}/check_ffq_prereqs':
     get:
       operationId: microsetta_private_api.api.check_source_ffq_prereqs
@@ -3049,6 +3122,12 @@ components:
       description: Type of consent
       schema:
         $ref: '#/components/schemas/consent_type'
+    external_report_id:
+      name: external_report_id
+      in: path
+      description: Unique identifier of external report
+      schema:
+        $ref: '#/components/schemas/external_report_id'
 
     # query parameters
     activation_code:
@@ -3470,6 +3549,18 @@ components:
       type: string
     assent_content:
       type: string
+    external_report_id:
+      type: string
+    file_name:
+      type: string
+    file_title:
+      type: string
+    file_type:
+      type: string
+    file_contents:
+      type: string
+    report_type:
+      enum: ["kit", "ffq"]
     nonhuman_source:
       type: object
       properties:
@@ -3517,6 +3608,27 @@ components:
                   type: string
               additionalProperties: false
       additionalProperties: false
+    external_report:
+      type: object
+      properties:
+        external_report_id:
+          $ref: '#/components/schemas/external_report_id'
+        source_id:
+          $ref: '#/components/schemas/source_id'
+        file_name:
+          $ref: '#/components/schemas/file_name'
+        file_title:
+          $ref: '#/components/schemas/file_title'
+        file_type:
+          $ref: '#/components/schemas/file_type'
+        file_contents:
+          $ref: '#/components/schemas/file_contents'
+        report_type:
+          $ref: '#/components/schemas/report_type'
+      required:
+        - external_report_id
+        - source_id
+        - report_type
 
     # survey template section
     survey_template_id:

microsetta_private_api/db/migration_support.py

@@ -742,6 +742,59 @@ def migrate_96(TRN):
                     (r[0], hsi))
         TRN.execute()
 
+    @staticmethod
+    def migrate_133(TRN):
+        ffq_key_path = SERVER_CONFIG["japanese_ffqs_path_key"]
+        ffq_file_path = SERVER_CONFIG["japanese_ffqs_path_reports"]
+
+        # The below string translates to "Food frequency questionnaire"
+        JFFQ_FILE_LABEL = "食物摂取頻度調査票"
+
+        if not os.path.exists(ffq_key_path):
+            print("Key not found:" + ffq_key_path)
+            return
+
+        with open(ffq_key_path) as csv_file:
+            csv_contents = csv.reader(csv_file)
+            header = True
+
+            for csv_row in csv_contents:
+                if header:
+                    header = False
+                    continue
+                ffq_id, barcode = csv_row
+
+                # Find the source associated with the barcode and make sure
+                # it wasn't scrubbed or removed
+                TRN.add(
+                    "SELECT akb.source_id "
+                    "FROM ag.ag_kit_barcodes akb "
+                    "INNER JOIN ag.source s "
+                    "ON akb.source_id = s.id "
+                    "WHERE akb.barcode = %s AND s.date_revoked IS NULL",
+                    (barcode, )
+                )
+                rows = TRN.execute()[-1]
+
+                if len(rows) == 1:
+                    row = rows[0]
+                    source_id = row[0]
+                    pdf_name = ffq_id + ".pdf"
+                    pdf_path = ffq_file_path + pdf_name
+                    pdf_contents = open(pdf_path, "rb").read()
+
+                    TRN.add(
+                        "INSERT INTO ag.external_reports ("
+                        "source_id, file_name, file_title, file_type, "
+                        "file_contents, report_type"
+                        ") VALUES (%s, %s, %s, %s, %s, %s)",
+                        (source_id, pdf_name, JFFQ_FILE_LABEL,
+                         "application/pdf", pdf_contents, "ffq")
+                    )
+                else:
+                    print("No mapping: " + ffq_id + " - " + barcode)
+        TRN.execute()
+
     MIGRATION_LOOKUP = {
         "0048.sql": migrate_48.__func__,
         "0050.sql": migrate_50.__func__,
@@ -753,6 +806,7 @@ def migrate_96(TRN):
         # "0082.sql": migrate_82.__func__
         # ...
         "0096.sql": migrate_96.__func__,
+        "0133.sql": migrate_133.__func__
     }
 
     @classmethod