Merge pull request #11 from sdss/archive

adds access to archive database to sdssdb

.travis.yml

@@ -10,12 +10,16 @@ python:
 - '2.7'
 - '3.5'
 - '3.6'
+- '3.7'
 
 os:
 - linux
 
 matrix:
   fast_finish: true
+  allow_failures:
+    - python: '2.7'
+    - python: '3.5'
 
 notifications:
   email: false
@@ -27,7 +31,6 @@ branches:
 install:
 - pip install -U pip wheel --quiet
 - pip install --upgrade setuptools --quiet
-- pip install -r requirements.txt --quiet
 - pip install pytest
 - pip install pytest-coverage
 - pip install coveralls

CHANGELOG.rst

@@ -3,6 +3,10 @@
 Changelog
 =========
 
+This document records the main changes to the ``sdssdb`` code.
+
+* Added ``archive`` database with ``sas`` schema.
+
 * :release:`0.3.0 <2019-09-23>`
 * Removed ``TIC v6``.
 * Added ``TIC v8``.

README.rst

@@ -1,7 +1,7 @@
 sdssdb
 ======
 
-|python| |docs|
+|python| |docs| |travis| 
 
 `SDSS <https://sdss.org>`__ product for database management.
 
@@ -30,3 +30,6 @@ How to use
     :alt: Documentation Status
     :scale: 100%
     :target: https://sdssdb.readthedocs.io/en/latest/?badge=latest
+
+.. |travis| image:: https://travis-ci.org/sdss/sdssdb.svg?branch=master
+    :target: https://travis-ci.org/sdss/sdssdb

docs/sphinx/intro.rst

@@ -39,6 +39,8 @@ Currently, we support the following databases and schemas:
 * **sdss5db**: the SDSS-V development database.
     * *catalogdb*: schema for source catalogues used for target selection.
     * *targetdb*: schema with the results of the target selection and positioner information.
+* **archive**: the SDSS science archive database.
+    * *sas*: schema for SAS.
 
 Note that the level of readiness is not necessarily identical in both Peewee and SQLAlchemy. This table summarises what schemas are available for each library. Green indicates fully supported, yellow partial support, and red means that there are currently not model classes available for that schema. You can download the graph visualisation of the schema, showing the tables, columns, and relations between tables.
 
@@ -119,6 +121,13 @@ Note that the level of readiness is not necessarily identical in both Peewee and
             <td class="warning"></td>
             <td align="center"><a class="glyphicon glyphicon-download-alt" href="_static/schema_graphs/auto/sdss5db.targetdb.pdf"></a></td>
         </tr>
+        <tr>
+            <td class="active">archive</td>
+            <td class="active">sas</td>
+            <td class="danger"></td>
+            <td class="success"></td>
+            <td align="center"><a class="glyphicon glyphicon-download-alt" href="../../../../schema/archive/archive_sas.pdf"></a></td>
+        </tr>
         </tbody>
     </table>
 

python/sdssdb/etc/sdssdb.yml

@@ -14,8 +14,6 @@ lco:
     domain: lco.cl
 
 local:
-    host: localhost
-    port: 5432
     domain: null
 
 lore:

python/sdssdb/sqlalchemy/archive/__init__.py

@@ -0,0 +1,26 @@
+# !usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Licensed under a 3-clause BSD license.
+#
+# @Author: Brian Cherinka
+# @Date:   2018-09-23 16:06:18
+# @Last modified by: José Sánchez-Gallego ([email protected])
+# @Last Modified time: 2018-10-10 11:25:13
+
+from __future__ import print_function, division, absolute_import
+
+from sdssdb.connection import SQLADatabaseConnection
+from sqlalchemy.ext.declarative import declarative_base, DeferredReflection
+from sdssdb.sqlalchemy import BaseModel
+
+# we need a shared common Base when joining across multiple schema
+ArchiveBase = declarative_base(cls=(DeferredReflection, BaseModel,))
+
+
+class ArchiveDatabaseConnection(SQLADatabaseConnection):
+    dbname = 'archive_20190507'
+    base = ArchiveBase
+
+
+database = ArchiveDatabaseConnection(autoconnect=True)

python/sdssdb/sqlalchemy/archive/sas.py

@@ -0,0 +1,143 @@
+# !usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Licensed under a 3-clause BSD license.
+#
+# @Author: Joel Brownstein
+# @Date:   2019-08-01 06:54:15
+# @Last modified by: N Benjamin Murphy ([email protected])
+# @Date:   2019-09-04 16:31:00
+
+from __future__ import absolute_import, division, print_function
+
+from sdssdb.sqlalchemy.archive import database, ArchiveBase
+from sqlalchemy.ext.declarative import AbstractConcreteBase, declared_attr
+from sqlalchemy.orm import relationship
+
+SCHEMA = 'sas'
+
+
+class Base(AbstractConcreteBase, ArchiveBase):
+    __abstract__ = True
+    _schema = SCHEMA
+    _relations = 'define_relations'
+
+    @declared_attr
+    def __table_args__(cls):
+        return {'schema': cls._schema}
+
+
+class Root(Base):
+    __tablename__ = 'root'
+    print_fields = ['identifier']
+
+
+class Tree(Base):
+    __tablename__ = 'tree'
+    print_fields = ['version']
+
+
+class Env(Base):
+    __tablename__ = 'env'
+
+
+class Directory(Base):
+    __tablename__ = 'directory'
+    print_fields = ['location']
+
+
+class File(Base):
+    __tablename__ = 'file'
+    print_fields = ['name']
+
+    @property
+    def name(self):
+        return self.location.rsplit('/', 1)[-1]
+
+
+class SymlinkFile(Base):
+    __tablename__ = 'symlink_file'
+    print_fields = ['location']
+
+
+class SymlinkDirectory(Base):
+    __tablename__ = 'symlink_directory'
+    print_fields = ['location']
+
+
+class ChecksumFile(Base):
+    __tablename__ = 'checksumfile'
+    print_fields = ['filename']
+
+
+class Checksum(Base):
+    __tablename__ = 'checksum'
+
+
+def define_relations():
+    """Setup relationships after preparation."""
+
+    # model relationships
+    Root.directories = relationship(Directory, backref='root')
+    Tree.envs = relationship(Env, backref='tree')
+
+    # class Checksum
+    Checksum.tree = relationship(Tree, backref='checksums')
+    Checksum.checksumfile = relationship(ChecksumFile, backref='checksums')
+    Checksum.file = relationship(File, backref='checksums')
+    Checksum.directory = relationship(Directory, backref='checksums')
+
+    # class Checksumfile
+    ChecksumFile.tree = relationship(Tree, backref='checksumfiles')
+    ChecksumFile.env = relationship(Env, backref='checksumfile')
+    ChecksumFile.directory = relationship(Directory, backref='checksumfile')
+    ChecksumFile.file = relationship(File, backref='checksumfile')
+
+    # class Directory
+    Directory.tree = relationship(Tree, backref='directories')
+    Directory.env = relationship(Env, backref='directories')
+
+    # class Env
+    # need to specify remote_side when foreign key points to itself
+    Env.real_env = relationship(Env, remote_side='Env.id', backref='env')
+
+    # class File
+    File.root = relationship(Root, backref='files')
+    File.tree = relationship(Tree, backref='files')
+    File.env = relationship(Env, backref='files')
+    File.directory = relationship(Directory, backref='files')
+
+    # class Symlink_directory
+    SymlinkDirectory.env = relationship(Env, backref='symlink_directories')
+    SymlinkDirectory.root = relationship(Root, backref='symlink_directories')
+    # need to specify foreign_keys when multiple columns points to same key
+    # need to specify primaryjoin when there are multiple ways to join the tables
+    SymlinkDirectory.directory = relationship(
+        Directory, backref='symlink_directories', foreign_keys='SymlinkDirectory.directory_id')
+    SymlinkDirectory.real_directory = relationship(Directory, backref='linked_symlink_directories',
+                                                   primaryjoin=('and_(SymlinkDirectory.'
+                                                                'real_directory_id==Directory.id)'))
+
+    SymlinkDirectory.tree = relationship(Tree, backref='symlink_directories',
+                                         foreign_keys='SymlinkDirectory.tree_id',
+                                         primaryjoin='and_(SymlinkDirectory.tree_id==Tree.id)')
+    SymlinkDirectory.real_tree = relationship(
+        Tree, backref='linked_symlink_directories',
+        primaryjoin='and_(SymlinkDirectory.real_tree_id==Tree.id)')
+
+    # class Symlink_file
+    SymlinkFile.directory = relationship(Directory, backref='symlink_files')
+    SymlinkFile.env = relationship(Env, backref='symlink_files')
+    SymlinkFile.real_file = relationship(File, backref='symlink_files')
+    SymlinkFile.root = relationship(Root, backref='symlink_files',
+                                    foreign_keys='SymlinkFile.root_id')
+
+    SymlinkFile.tree = relationship(Tree, backref='symlink_files',
+                                    foreign_keys='SymlinkFile.tree_id',
+                                    primaryjoin='and_(SymlinkFile.tree_id==Tree.id)')
+    SymlinkFile.real_tree = relationship(
+        Tree, backref='linked_symlink_files', primaryjoin='and_(SymlinkFile.real_tree_id==Tree.id)')
+
+
+# prepare the base
+database.add_base(Base)

python/sdssdb/tests/test_peewee.py

@@ -9,6 +9,13 @@
 from __future__ import unicode_literals
 
 import sdssdb.peewee.sdss5db.targetdb as targetdb
+import pytest
+
+
+@pytest.fixture(scope='session', autouse=True)
+def skipdb():
+    if targetdb.database.connected is False:
+        pytest.skip('no targetdb found')
 
 
 class TestPeewee(object):