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Merged
monodera merged 3 commits into from
Jan 9, 2026
Merged

Add Web API support for target data transfer #128

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5fdd2d1
Add Web API support for target data transfer
monodera Jan 9, 2026
8778f63
Refactor transfer_data_from_uploader_via_webapi to reduce complexity
monodera Jan 9, 2026
3e21edb
Add .markdownlintrc to configure Markdown linting
monodera Jan 9, 2026
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17 changes: 17 additions & 0 deletions .markdownlintrc
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Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
# Markdownlint configuration for PFS Target Database documentation
default: true

# MD013: Line length - disable for auto-generated CLI docs and long URLs
MD013: false

# MD014: Dollar signs in shell commands - disable for CLI documentation
MD014: false

# MD033: Inline HTML - allow for documentation formatting (e.g., details/summary)
MD033: false

# MD034: Bare URLs - allow for reference links
MD034: false

# MD041: First line in file should be top-level heading - not always needed
MD041: false
32 changes: 32 additions & 0 deletions docs/reference/cli.md
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Expand Up @@ -28,9 +28,17 @@
host = "<hostname of uploader>"
user = "<user name of uploader>"
data_dir = "<path to the data directory on the uploader>"

# Optional section for Web API access
# The following parameters are used to download data via Web API instead of rsync.
[webapi]
url = "<base URL of the Web API endpoint>" # e.g., "https://example.com/get-upload/"
api_key = "<API key for authentication>" # Optional: leave empty ("") for no authentication
verify_ssl = true # Optional: set to false to disable SSL certificate verification
```

The `schemacrawler` section is required only if you want to draw an ER diagram of the database schema with SchemaCrawler.
The `webapi` section is used by the `transfer-targets-api` command to download data via Web API.

## `pfs-targetdb-cli`

Expand Down Expand Up @@ -60,6 +68,7 @@
- `update`: Update rows in a table in the PFS Target...
- `parse-alloc`: Parse an Excel file containing time...
- `transfer-targets`: Download target lists from the uploader to...
- `transfer-targets-api`: Download target lists from the uploader to...
- `insert-targets`: Insert targets using a list of input...
- `insert-pointings`: Insert user-defined pointings using a list...
- `update-catalog-active`: Update active flag in the input_catalog...
Expand Down Expand Up @@ -329,6 +338,29 @@

---

### `transfer-targets-api`

Download target lists from the uploader to the local machine via Web API.

**Usage**:

```console
$ pfs-targetdb-cli transfer-targets-api [OPTIONS] INPUT_FILE

Check notice on line 348 in docs/reference/cli.md

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Codacy Production / Codacy Static Code Analysis

docs/reference/cli.md#L348 

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```

**Arguments**:

- `INPUT_FILE`: Input catalog list file (csv). [required]

**Options**:

- `-c, --config TEXT`: Database configuration file in the TOML format. [required]
- `--local-dir PATH`: Path to the data directory in the local machine [default: .]
- `--force / --no-force`: Force download. [default: no-force]
- `--help`: Show this message and exit.

---

### `insert-targets`

Insert targets using a list of input catalogs and upload IDs.
Expand Down
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -25,6 +25,7 @@ dependencies = [
"pandas",
"psycopg2-binary",
"pyarrow",
"requests",
"sqlalchemy",
# "setuptools",
"sqlalchemy-utils",
Expand Down
81 changes: 65 additions & 16 deletions src/targetdb/cli/cli_main.py
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Expand Up @@ -25,6 +25,7 @@
parse_allocation_file,
prep_fluxstd_data,
transfer_data_from_uploader,
transfer_data_from_uploader_via_webapi,
update_input_catalog_active,
)

Expand Down Expand Up @@ -196,7 +197,7 @@ def checkdups(
typer.Option("--skip-save-merged", help="Do not save the merged DataFrame."),
] = False,
additional_columns: Annotated[
List[str],
List[str] | None,
typer.Option(
"--additional-columns",
help="Additional columns to output for the merged file. (e.g., 'psf_mag_g' 'psf_mag_r'). "
Expand All @@ -217,7 +218,7 @@ def checkdups(
"--format",
help="File format of the merged data file.",
),
] = "parquet",
] = PyArrowFileFormat.parquet,
):
if additional_columns is None:
additional_columns = []
Expand Down Expand Up @@ -260,23 +261,23 @@ def prep_fluxstd(
),
],
input_catalog_id: Annotated[
int,
int | None,
typer.Option(
"--input_catalog_id",
show_default=False,
help="Input catalog ID for the flux standard star catalog.",
),
] = None,
input_catalog_name: Annotated[
str,
str | None,
typer.Option(
"--input_catalog_name",
show_default=False,
help="Input catalog name for the flux standard star catalog.",
),
] = None,
rename_cols: Annotated[
str,
str | None,
typer.Option(
"--rename-cols",
help='Dictionary to rename columns (e.g., \'{"fstar_gaia": "is_fstar_gaia"}\').',
Expand All @@ -288,7 +289,7 @@ def prep_fluxstd(
"--format",
help="File format of the output data file.",
),
] = "parquet",
] = PyArrowFileFormat.parquet,
):

if input_catalog_id is None and input_catalog_name is None:
Expand Down Expand Up @@ -419,15 +420,15 @@ def insert(
),
] = FluxType.total,
upload_id: Annotated[
str,
str | None,
typer.Option(
"--upload_id",
show_default=False,
help="Upload ID issued by the PFS Target Uploader. Only required for the `target` table.",
),
] = None,
proposal_id: Annotated[
str,
str | None,
typer.Option(
"--proposal_id",
show_default=False,
Expand Down Expand Up @@ -502,15 +503,15 @@ def update(
),
] = False,
upload_id: Annotated[
str,
str | None,
typer.Option(
"--upload_id",
show_default=False,
help="Upload ID issued by the PFS Target Uploader. Only required for the `target` table",
),
] = None,
proposal_id: Annotated[
str,
str | None,
typer.Option(
"--proposal_id",
show_default=False,
Expand Down Expand Up @@ -564,9 +565,9 @@ def parse_alloc(
writable=True,
help="Directory path to save output files.",
),
] = ".",
] = Path("."),
outfile_prefix: Annotated[
str,
str | None,
typer.Option(
show_default=False,
help="Prefix to the output files.",
Expand Down Expand Up @@ -603,12 +604,11 @@ def transfer_targets(
local_dir: Annotated[
Path,
typer.Option(
exists=True,
dir_okay=True,
writable=True,
help="Path to the data directory in the local machine",
),
] = ".",
] = Path("."),
force: Annotated[bool, typer.Option(help="Force download.")] = False,
):

Expand All @@ -627,6 +627,55 @@ def transfer_targets(
)


@app.command(
help="Download target lists from the uploader to the local machine via Web API."
)
def transfer_targets_api(
input_file: Annotated[
Path,
typer.Argument(
exists=True,
file_okay=True,
dir_okay=False,
readable=True,
show_default=False,
help="Input catalog list file (csv).",
),
],
config_file: Annotated[
str,
typer.Option(
"-c",
"--config",
show_default=False,
help=config_help_msg,
),
],
local_dir: Annotated[
Path,
typer.Option(
dir_okay=True,
writable=True,
help="Path to the data directory in the local machine",
),
] = Path("."),
force: Annotated[bool, typer.Option(help="Force download.")] = False,
):

logger.info(f"Loading config file: {config_file}")
config = load_config(config_file)

logger.info(f"Loading input data from {input_file} into a DataFrame")
df = load_input_data(input_file)

transfer_data_from_uploader_via_webapi(
df,
config,
local_dir=local_dir,
force=force,
)


@app.command(help="Insert targets using a list of input catalogs and upload IDs.")
def insert_targets(
input_catalogs: Annotated[
Expand Down Expand Up @@ -657,7 +706,7 @@ def insert_targets(
readable=True,
help="Path to the data directory.",
),
] = ".",
] = Path("."),
flux_type: Annotated[
FluxType,
typer.Option(
Expand Down Expand Up @@ -724,7 +773,7 @@ def insert_pointings(
readable=True,
help="Path to the data directory.",
),
] = ".",
] = Path("."),
commit: Annotated[
bool,
typer.Option("--commit", help="Commit changes to the database."),
Expand Down
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