Add columns for photometric errors in the fluxstd table

alembic/pfsa-db01-gb/alembic/README.md

@@ -0,0 +1,25 @@
+# Generic single-database configuration.
+
+## Basic workflow
+
+Reference: https://alembic.sqlalchemy.org/en/latest/tutorial.html
+
+### Modify code of targetdb
+
+
+### Run alembic
+
+Create a new revision file.
+
+```bash
+alembic -c <config file> revision --autogenerate -m "Add columns"
+```
+
+Check the output file under the `versions` directory.
+
+Upgrade to the new revision.
+
+```bash
+alembic -c <config file> upgrade head
+```
+

alembic/pfsa-db01-gb/alembic/versions/20221020-172724_99f7f6b4c0d1_add_columns_for_photometric_errors_in_.py

@@ -0,0 +1,24 @@
+"""Add columns for photometric errors in the fluxstd table
+
+Revision ID: 99f7f6b4c0d1
+Revises: 9c71ca3a4254
+Create Date: 2022-10-20 17:27:24.541747
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '99f7f6b4c0d1'
+down_revision = '9c71ca3a4254'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass

alembic/pfsa-db01-gb/alembic/versions/20221020-173436_a63ff2b68f44_add_columns_for_photometric_errors_in_.py

@@ -0,0 +1,24 @@
+"""Add columns for photometric errors in the fluxstd table
+
+Revision ID: a63ff2b68f44
+Revises: 99f7f6b4c0d1
+Create Date: 2022-10-20 17:34:36.681006
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'a63ff2b68f44'
+down_revision = '99f7f6b4c0d1'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    pass
+
+
+def downgrade():
+    pass

alembic/pfsa-db01-gb/alembic/versions/20221020-174527_c4e16db3e7e1_add_columns_for_photometric_errors_in_.py

@@ -0,0 +1,50 @@
+"""Add columns for photometric errors in the fluxstd table
+
+Revision ID: c4e16db3e7e1
+Revises: a63ff2b68f44
+Create Date: 2022-10-20 17:45:27.991776
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'c4e16db3e7e1'
+down_revision = 'a63ff2b68f44'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('fluxstd', sa.Column('psf_mag_error_g', sa.Float(), nullable=True, comment='Error in g-band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_mag_error_r', sa.Float(), nullable=True, comment='Error in r-band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_mag_error_i', sa.Float(), nullable=True, comment='Error in i-band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_mag_error_z', sa.Float(), nullable=True, comment='Error in z-band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_mag_error_y', sa.Float(), nullable=True, comment='Error in y-band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_mag_error_j', sa.Float(), nullable=True, comment='Error in J band PSF magnitude (AB mag)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_g', sa.Float(), nullable=True, comment='Error in g-band PSF flux (nJy)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_r', sa.Float(), nullable=True, comment='Error in r-band PSF flux (nJy)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_i', sa.Float(), nullable=True, comment='Error in i-band PSF flux (nJy)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_z', sa.Float(), nullable=True, comment='Error in z-band PSF flux (nJy)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_y', sa.Float(), nullable=True, comment='Error in y-band PSF flux (nJy)'))
+    op.add_column('fluxstd', sa.Column('psf_flux_error_j', sa.Float(), nullable=True, comment='Error in J band PSF flux (nJy)'))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('fluxstd', 'psf_flux_error_j')
+    op.drop_column('fluxstd', 'psf_flux_error_y')
+    op.drop_column('fluxstd', 'psf_flux_error_z')
+    op.drop_column('fluxstd', 'psf_flux_error_i')
+    op.drop_column('fluxstd', 'psf_flux_error_r')
+    op.drop_column('fluxstd', 'psf_flux_error_g')
+    op.drop_column('fluxstd', 'psf_mag_error_j')
+    op.drop_column('fluxstd', 'psf_mag_error_y')
+    op.drop_column('fluxstd', 'psf_mag_error_z')
+    op.drop_column('fluxstd', 'psf_mag_error_i')
+    op.drop_column('fluxstd', 'psf_mag_error_r')
+    op.drop_column('fluxstd', 'psf_mag_error_g')
+    # ### end Alembic commands ###

setup.py

@@ -161,7 +161,7 @@
     #
     # For an analysis of "install_requires" vs pip's requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
-    install_requires=["sqlalchemy", "pandas", "tabulate"],  # Optional
+    install_requires=["sqlalchemy", "pandas", "tabulate", "toml"],  # Optional
     #
     #
     # List additional groups of dependencies here (e.g. development
@@ -204,6 +204,7 @@
             "pfs_targetdb_drop_database=targetdb.cli.pfs_targetdb_database_helpers:main_drop_database",
             "pfs_targetdb_create_schema=targetdb.cli.pfs_targetdb_create_schema:main",
             "pfs_targetdb_generate_mdtable=targetdb.cli.pfs_targetdb_generate_mdtable:main",
+            "pfs_targetdb_draw_diagram=targetdb.cli.pfs_targetdb_draw_diagram:main",
         ],
     },
     #

src/targetdb/__init__.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
 
 from .manage import create_schema
+from .utils import draw_diagram
 from .utils import generate_schema_markdown

src/targetdb/cli/pfs_targetdb_draw_diagram.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python3
+
+import argparse
+
+import logzero
+from logzero import logger
+
+from .. import draw_diagram
+
+
+def get_arguments():
+    parser = argparse.ArgumentParser(
+        description="Create the ER diagram of the database in PDF"
+    )
+
+    parser.add_argument(
+        "conf",
+        type=str,
+        default="config.toml",
+        help="Config file for the script to run. Must be a .toml file (default: config.toml)",
+    )
+
+    parser.add_argument(
+        "--sc_info_level",
+        type=str,
+        default="maximum",
+        help="SchemaCrawler's info level (default: maximum)",
+    )
+    parser.add_argument(
+        "--sc_log_level",
+        type=str,
+        default="SEVERE",
+        help="SchemaCrawler's log level (default: SEVERE)",
+    )
+    parser.add_argument(
+        "--sc_outdir",
+        type=str,
+        default=".",
+        help="Output directory (default: .)",
+    )
+    parser.add_argument(
+        "--sc_outprefix",
+        type=str,
+        default="erdiagram_targetdb",
+        help="Prefix for the output file (default: erdiagram_targetdb)",
+    )
+    parser.add_argument(
+        "--sc_title",
+        type=str,
+        default="PFS Target Database",
+        help="Title of the output ER diagram (default: PFS Target Database)",
+    )
+    parser.add_argument("--debug", action="store_true", help=argparse.SUPPRESS)
+
+    args = parser.parse_args()
+
+    return args
+
+
+def main():
+
+    args = get_arguments()
+
+    if args.debug:
+        logzero.loglevel(logzero.DEBUG)
+    else:
+        logzero.loglevel(logzero.INFO)
+
+    logger.info(args)
+
+    draw_diagram(
+        args.conf,
+        sc_info_level=args.sc_info_level,
+        sc_log_level=args.sc_log_level,
+        sc_outdir=args.sc_outdir,
+        sc_outprefix=args.sc_outprefix,
+        sc_title=args.sc_title,
+        logger=logger,
+    )
+
+
+if __name__ == "__main__":
+    main()

src/targetdb/models/fluxstd.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 from sqlalchemy import BigInteger
 from sqlalchemy import Boolean
@@ -13,9 +13,9 @@
 from sqlalchemy.orm import backref
 from sqlalchemy.orm import relation
 
+# from . import proposal
 from . import Base
 from . import input_catalog
-from . import proposal
 from . import target_type
 
 
@@ -74,13 +74,27 @@ class fluxstd(Base):
     psf_mag_y = Column(Float, comment="y-band PSF magnitude (AB mag)")
     psf_mag_j = Column(Float, comment="J band PSF magnitude (AB mag)")
 
+    psf_mag_error_g = Column(Float, comment="Error in g-band PSF magnitude (AB mag)")
+    psf_mag_error_r = Column(Float, comment="Error in r-band PSF magnitude (AB mag)")
+    psf_mag_error_i = Column(Float, comment="Error in i-band PSF magnitude (AB mag)")
+    psf_mag_error_z = Column(Float, comment="Error in z-band PSF magnitude (AB mag)")
+    psf_mag_error_y = Column(Float, comment="Error in y-band PSF magnitude (AB mag)")
+    psf_mag_error_j = Column(Float, comment="Error in J band PSF magnitude (AB mag)")
+
     psf_flux_g = Column(Float, comment="g-band PSF flux (nJy)")
     psf_flux_r = Column(Float, comment="r-band PSF flux (nJy)")
     psf_flux_i = Column(Float, comment="i-band PSF flux (nJy)")
     psf_flux_z = Column(Float, comment="z-band PSF flux (nJy)")
     psf_flux_y = Column(Float, comment="y-band PSF flux (nJy)")
     psf_flux_j = Column(Float, comment="J band PSF flux (nJy)")
 
+    psf_flux_error_g = Column(Float, comment="Error in g-band PSF flux (nJy)")
+    psf_flux_error_r = Column(Float, comment="Error in r-band PSF flux (nJy)")
+    psf_flux_error_i = Column(Float, comment="Error in i-band PSF flux (nJy)")
+    psf_flux_error_z = Column(Float, comment="Error in z-band PSF flux (nJy)")
+    psf_flux_error_y = Column(Float, comment="Error in y-band PSF flux (nJy)")
+    psf_flux_error_j = Column(Float, comment="Error in J band PSF flux (nJy)")
+
     filter_g = Column(String, comment="g-band filter (g_hsc, g_ps1, g_sdss, etc.)")
     filter_r = Column(String, comment="r-band filter (r_hsc, r_ps1, r_sdss, etc.)")
     filter_i = Column(String, comment="i-band filter (i_hsc, i_ps1, i_sdss, etc.)")
@@ -131,12 +145,24 @@ def __init__(
         psf_mag_z,
         psf_mag_y,
         psf_mag_j,
+        psf_mag_error_g,
+        psf_mag_error_r,
+        psf_mag_error_i,
+        psf_mag_error_z,
+        psf_mag_error_y,
+        psf_mag_error_j,
         psf_flux_g,
         psf_flux_r,
         psf_flux_i,
         psf_flux_z,
         psf_flux_y,
         psf_flux_j,
+        psf_flux_error_g,
+        psf_flux_error_r,
+        psf_flux_error_i,
+        psf_flux_error_z,
+        psf_flux_error_y,
+        psf_flux_error_j,
         filter_g,
         filter_r,
         filter_i,
@@ -170,12 +196,24 @@ def __init__(
         self.psf_mag_z = psf_mag_z
         self.psf_mag_y = psf_mag_y
         self.psf_mag_j = psf_mag_j
+        self.psf_mag_error_g = psf_mag_error_g
+        self.psf_mag_error_r = psf_mag_error_r
+        self.psf_mag_error_i = psf_mag_error_i
+        self.psf_mag_error_z = psf_mag_error_z
+        self.psf_mag_error_y = psf_mag_error_y
+        self.psf_mag_error_j = psf_mag_error_j
         self.psf_flux_g = psf_flux_g
         self.psf_flux_r = psf_flux_r
         self.psf_flux_i = psf_flux_i
         self.psf_flux_z = psf_flux_z
         self.psf_flux_y = psf_flux_y
         self.psf_flux_j = psf_flux_j
+        self.psf_flux_error_g = psf_flux_error_g
+        self.psf_flux_error_r = psf_flux_error_r
+        self.psf_flux_error_i = psf_flux_error_i
+        self.psf_flux_error_z = psf_flux_error_z
+        self.psf_flux_error_y = psf_flux_error_y
+        self.psf_flux_error_j = psf_flux_error_j
         self.filter_g = filter_g
         self.filter_r = filter_r
         self.filter_i = filter_i