W2023-41 JAIRO Cloudを対象としたアイテムデポジット機能の開発

.gitignore

@@ -1,160 +1,47 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
-*$py.class
-
-# C extensions
-*.so
+*.pyc
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
 downloads/
 eggs/
 .eggs/
-lib/
-lib64/
+# lib/
+# lib64/
 parts/
 sdist/
 var/
-wheels/
-share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
 *.spec
 
+app/tmp/*
+
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
+.pytest_cache/
 .tox/
-.nox/
 .coverage
 .coverage.*
 .cache
 nosetests.xml
 coverage.xml
 *.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-cover/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-.pybuilder/
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-#   For a library or package, you might want to ignore these files since the code is
-#   intended to run in multiple environments; otherwise, check them in:
-# .python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# poetry
-#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
-#   This is especially recommended for binary packages to ensure reproducibility, and is more
-#   commonly ignored for libraries.
-#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-
-# pdm
-#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
-#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
-#   in version control.
-#   https://pdm.fming.dev/#use-with-ide
-.pdm.toml
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
+*.db
 venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# pytype static type analyzer
-.pytype/
-
-# Cython debug symbols
-cython_debug/
-
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/

Dockerfile

@@ -0,0 +1,36 @@
+FROM python:3.12-slim-bookworm
+WORKDIR /code
+ENV FLASK_APP=app
+ENV FLASK_DEBUG=1
+RUN adduser --uid 1000 --disabled-password --gecos '' depositor
+
+COPY /app/requirements.txt ./
+# COPY /app/requirements-depositor-modules.txt ./
+
+ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/code/app
+
+ENV PYTHONPATH=$PYTHONPATH:/code/app/modules/depositor_admin_setting
+ENV PYTHONPATH=$PYTHONPATH:/code/app/modules/depositor_item_register
+ENV PYTHONPATH=$PYTHONPATH:/code/app/modules/depositor_login
+ENV PYTHONPATH=$PYTHONPATH:/code/app/modules/depositor_models
+ENV PYTHONPATH=$PYTHONPATH:/code/src/grobid_client
+
+ENV DEPOSITOR_WEB_HOST=127.0.0.1
+ENV DEPOSITOR_POSTGRESQL_HOST=postgresql
+ENV DEPOSITOR_POSTGRESQL_DBNAME=depositor
+ENV DEPOSITOR_POSTGRESQL_DBUSER=depositor
+ENV DEPOSITOR_POSTGRESQL_DBPASS=dbpass123
+
+# shibbolethログインがモックの為、パスワードは固定値
+ENV MOCK_PASSWORD=testpass
+# 一時ファイルを置くフォルダのパス、コンテナ内のフォルダを参照しているため絶対パスで指定するとコンテナ内でのみ一時フォルダが生成される。
+# マウントされている位置のパスを指定するとローカルにも保存される。
+ENV TMPORARY_FILE_PATH=./tmp/
+
+RUN apt-get update
+RUN apt-get -y install libpq-dev
+RUN apt-get install gcc -y
+
+RUN pip install --upgrade pip
+
+RUN pip install -r requirements.txt

app/app.py

@@ -0,0 +1,37 @@
+
+import logging
+import sys
+import os
+from flask import Flask
+from flask_login import LoginManager
+from depositor_login.ext import LoginApp
+from depositor_admin_setting.ext import AdminSettingApp
+from depositor_item_register.ext import ItemRegisterApp
+from depositor_models.db_setting import init_db, DATABASE_URI
+from depositor_models.user import User_manager
+
+app = Flask(__name__)
+app.config['SECRET_KEY'] = "secret"
+app.config['SQLALCHEMY_TRACK_MODIFICATIONS']=False
+
+# 接続先DBの設定
+app.config['SQLALCHEMY_DATABASE_URI'] = DATABASE_URI
+app.logger.setLevel(logging.INFO)
+app.logger.addHandler(logging.StreamHandler(sys.stdout))
+app.logger.setLevel(logging.DEBUG)
+
+init_db(app)
+login_manager = LoginManager()
+login_manager.init_app(app)
+
+loginapp = LoginApp()
+loginapp.init_app(app)
+adminapp = AdminSettingApp()
+adminapp.init_app(app)
+itemregister = ItemRegisterApp()
+itemregister.init_app(app)
+
+@login_manager.user_loader
+def load_user(user_id):
+    user=User_manager.get_user_by_id(user_id)
+    return user

app/config.json

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+{
+    "grobid_server": "http://grobid:8070",
+    "batch_size": 100,
+    "sleep_time": 5,
+    "timeout": 60,
+    "coordinates": [ "persName", "figure", "ref", "biblStruct", "formula", "s", "note", "title" ]
+}

app/modules/depositor_admin_setting/depositor_admin_setting/__init__.py

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+
+from .ext import AdminSettingApp
+__all__ = ('AdminSettingApp')

app/modules/depositor_admin_setting/depositor_admin_setting/ext.py

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+from .views import blueprint
+
+class AdminSettingApp(object):
+    def __init__(self, app=None):
+        if app:
+            self.init_app(app)
+
+    def init_app(self, app):
+        app.register_blueprint(blueprint)
+        app.extensions['adminsetting'] = self

app/modules/depositor_admin_setting/depositor_admin_setting/static/js/add_affili.js

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+function closeError() {
+    document.getElementById("errors").innerHTML = "";
+}
+
+function showMsg(msg , success=false) {
+    text = '<div class="alert ' + (success? "alert-success":"alert-danger") + ' alert-dismissable" id="alert">' +
+    '<button type="button" class="close" data-dismiss="alert" aria-hidden="true" onclick=closeError()>' +
+    '&times; </button>' + msg + '</div>';
+    document.getElementById("errors").insertAdjacentHTML('afterbegin',text);
+
+}
+
+async function componentDidMount() {
+/** set errorMessage Area */
+    const header = document.getElementsByClassName("content-header")[0];
+    if (header) {
+        const errorElement = document.createElement('div');
+        errorElement.setAttribute('id', 'errors');
+        header.insertBefore(errorElement, header.firstChild);
+    }
+}
+
+function isEmpty(value){
+  if (!value){
+    return true;
+  }else{
+    return false;
+  }
+}
+
+function handleAddSubmit(){
+  closeError();
+  const affiliation_name = document.getElementById("affiliation_name");
+  const affiliation_idp_url = document.getElementById("affiliation_idp_url");
+  //Validate 
+  // required check
+  NGList = [];
+  if(isEmpty(affiliation_name.value)){
+    NGList.push('機関名');
+  }
+  if(isEmpty(affiliation_idp_url.value)){
+    NGList.push('認証機関先URL');
+  }
+  if(NGList.length){
+    return showMsg("The following items is required. Please recheck and input." + NGList , false);
+  }
+
+  const form ={
+      'affiliation_name': document.getElementById("affiliation_name").value,
+      'affiliation_idp_url': document.getElementById("affiliation_idp_url").value,
+  }
+    let pattern = /^(https?|ftp)(:\/\/[\w\/:%#\$&\?\(\)~\.=\+\-]+)/
+    if(pattern.test(form.affiliation_idp_url)){
+      fetch("/admin_setting/add" ,{method:'POST' ,headers:{'Content-Type':'application/json'} ,credentials:"include", body: JSON.stringify(form)})
+      .then(res => {
+        if(!res.ok){
+          console.log(etext);
+      }
+        console.log("ok");
+        showMsg("Successfully Registered Settings." , true);
+      })
+      .catch(error => {
+        console.log(error);
+        showMsg("Failed To Register Settings" , false);
+      });
+    }else{
+      showMsg("Idp URL: Please input in URL format." , false);
+    }
+}
+componentDidMount();