Provided by: python3-gavo_2.6+dfsg-1_all 
NAME
dachs - data publishing infrastructure for the Virtual Observatory (VO)
SYNOPSIS
dachs [global-options] <subcommand> [options] function-argument ...
DESCRIPTION
dachs provides support for data ingestion and publishing, for metadata handling, and for
a variety of VO protocols and standards, e.g. the Table Access Protocol (TAP) or the
Simple Cone Search (SCS).
There are numerous sub-commands covering the various tasks (importing, controlling the
server, running tests, etc).
Subcommand names can be abbreviated to the shortest unique prefix.
A centeral concept of DaCHS is the Resource Descriptor (RD), and XML description of a data
collection including metadata, ingestion rules, service definitions, and regression tests.
They are usually referenced through their RD ids, which are the relative paths from DaCHS'
inputs directory to the file containing the RD, with the conventional extension .rd
stripped. For instance, in a default install, the file /var/gavo/inputs/myrsc/q.rd would
have myrsc/q as RD id.
Most commands dealing with RD ids will also pick up RDs if referenced by path; in the
example above, if you are in /var/gavo/inputs/myrsc, you could also reference the RD as
either q or q.rd.
Several commands take references to RD elements (table definitions, exec items, direct
grammar, etc). These consist of an RD id as just discussed, a hash mark, and the XML id
of the target element. Tables have an id automatically, for other elements you may have
to add an artificial id.
GLOBAL OPTIONS
Global options are given before the subcommand name.
--debug
produce debug info as appropriate
--enable-pdb
run pdb on all errors
-h, --help
show this help message and exit
--hints
if there are hints on an error, display them
--profile-to=PROFILEPATH
enable profiling and write a profile to PROFILEPATH
--suppress-log
suppress logging of exceptions to the dachs-specific log files
--version
shows the versions of the software, of the database schema expected by the software
and of the database schema actually on disk (if the latter two disagree, run dachs
upgrade).
THE ADMIN SUBCOMMAND
Synopsis:
dachs admin [-h] subsubfunction [subfunction-arguments ...]
This is a somewhat random collection of commands related to administering a data center.
In particular, this is where you create and edit accounts.
subsubcommands can be abbreviated as long as the abbreviation is unique. For instance
dachs adm xsd will do an XSD validation.
For more information on the subsubfunctions, pass a -h flag.
Subsubcommands
• addtogroup user group -- adds a user to a group
• adduser user password [remarks] -- add a user/password pair to the DaCHS user table.
Note that as of DaCHS 1.0 the password is stored in clear text and also transmitted in
clear text since DaCHS only supports HTTP basic authentication. Do not use valuable
passwords here
• changeuser user password [remarks] -- change remarks and/or password for a DC user. See
adduser for details.
• cleantap -- remove expired Universal Worker Service (UWS) jobs
• delfromgroup user group -- remove a user from a group
• deluser user -- remove a DaCHS user from the user table.
• dumpDF path -- Dumps the source of a file included with the DaCHS distribution. The
argument is a package resource path (like /inputs/__system__/scs.rd); for system RDs,
the special //rd-id syntax is supported.
• execute exec-id -- Execute the contents of an RD execute element. You must give that
element an explicit id in order to make this work; then exec-id is rd-id#exec-id
• hashPassword pw -- hash a password. adduser and friends already hash themselves, so
this is likely only useful for the [web]adminPasswd setting.
• indexStatements tableRef -- show the statements to create the indices on a table. The
tableRef has the format RD-id#table-id; it is not a database table reference.
• listusers -- dump the user table
• makedelrec ivoid -- create a registry record of ivoid saying the resource is removed.
This is only necessary when recovering from disasters that made you lose records from
DaCHS' internal tables.
• suggestucds tableId -- Make suggestions for UCDs of the columns of the referenced table
(rd-id#table-id format) not having one. This is based on their descriptions and uses a
GAVO web service.
• tapabort jobId helpMsg -- manually abort a TAP job and return helpMsg to the requesting
user as error message.
• updateTAPSchema -- Update the TAP_SCHEMA metadata for all RDs mentioned in TAP_SCHEMA.
• xsdValidate path -- Validate a file against built-in VO schemas and with built-in schema
validator.
THE CONFIG SUBCOMMAND
Synopsis:
dachs config [section-name] config-key
This outputs values of DaCHS' configuration to stdout. section-name defaults to general.
This is most commonly used to make external components aware of DaCHS' file locations,
e.g., through inputs_dir=$(dachs config inputsDir).
See the operator's guide for a documentation on DaCHS' configuration options.
THE DATAPACK SUBCOMMAND
Synposis:
dachs datapack [-h] {create,load} ...
Management of full DaCHS resources in the frictionless data package format. Note that
while DaCHS-created data packages should work as normal data packages, DaCHS can only
(automatically) load data packages generated by DaCHS itself -- there simply is not enough
metadata in generic data packages to produce usable resources.
Subsubcommands
datapack create
Synopsis:
dachs datapack create [-h] id dest
Positional arguments:
id Absolute RD id to produce a datapack for
dest Name of a zip file to dump to
The command creates a data package containing the RD, a README in the resource directory
if it exists, auxiliary files (like a booster grammar or a custom core) the RD may have,
and all data files that the sources in the RD yield; for collecting these files, sources
elements with ignoreSources children reading from the database are ignored, because that
would make behaviour a bit too unpredictable.
To include further files, you can use the datapack-extrafiles property on the RD. This
must contain a json sequence literal with resdir-relative shell patterns that should be
included as well. Non-existing paths and directories in this list are silently ignored.
You cannot include files outside of the resource directory in a data package.
datapack load
Synopsis:
dachs datapack load [-h] [-t] [--force] source
Positional argument:
source Name of a DaCHS-produced data package zip file.
Optional arguments:
-t, --no-test
Do not run tests after importing.
--force
If the resdir the package declares already exists, remove it before unpacking
(rather than bailing out.
This unpacks a DaCHS-produced data package, imports it, and runs tests on it (which you
will want to suppress if you do not have a DaCHS server running locally).
THE DROP SUBCOMMAND
Synopsis:
drop [-h] [-s] [--all] rd-id [dd-id ...]
This is the reverse of import: Tables created by a dachs imp with identical arguments are
being torn down by dachs drop. This will not work reliably if the RD has been modified
between the imp and the drop, in particular if the RD has been deleted. In such
situations, you can use the -f flag, which unconditionally tears down everything DaCHS has
recorded as coming from the referenced RD.
Arguments
rd-id RD path or ID to drop
dd-id optional data descriptor (DD) ID(s) if you do not want to drop the entire RD; note
that no service publications will be undone if you give DD IDs
Options
--all drop all DDs in the RD, not only the auto ones (overrides manual selection)
-s, --system
drop tables even if they are system tables
THE DUMP SUBCOMMAND
Synopsis:
dachs dump [-h] {load,create,ls} ...
This is an interface to dumping database tables and inspecting and restoring the generated
dumps.
This is mainly intended for small to medium tables that are just kept in the database,
e.g., DaCHS' administrative tables and the like. For normal user tables, built from
science data, doing re-imports is the recommended way to deal with data loss.
In particular, this command is not designed (at this point) for really large tables. For
technical reasons (that could be overcome), currently the individual dumps are kept in
memory during creation (but not during loading).
Before loading, the target tables are dropped if they are already present; note that this
will also drop any views they might be part of, as well as any rows that have foreign keys
on this table. After loading, indices and primary keys on the restored tables will be
recreated, but no scripts or similar are run. Hence, you will have to manually re-create
any dependent resources after a restore.
This also means that, for example, restoring a table with products without also restoring
//products#products will lose the products that previously were in the restored table from
the products table.
Subsubcommands
dump create
Synopsis:
dachs dump create [options] dumpFile ids [ids ...]
Dump one or more tables to DaCHS' dump format. When you pass in RD ids, all onDisk-tables
defined in the RD will be dumped.
Positional arguments:
dumpFile
Name of a file to write the dump to; use - to dump to stderr.
ids ids of table definitions (as in myres/q#main) or RDs to dump.
Options:
--text write dumps in text format. You need that when objects in the tables have no
binary representation. At least in 2020, that is true for all pgsphere objects.
dump load
Synopsis:
dachs dump load [-h] source
Restore table(s) from a file created by the dump create subcommand before
Positional argument:
source File to restore from. Use - to restore from stdin.
dump ls
Synopsis:
dachs dump ls [-h] source
List tables and dump metadata from a DaCHS dump.
Positional arguments:
source source file to list
THE GENCOL SUBCOMMAND
Synopsis:
dachs gencol [-h] [-f {fits,vot,viz}] FILE
The gencol subcommand quickly generates a set of basic column elements for inclusion in
RDs. It is particularly convenient together with dachs start.
This currently understands FITS binary tables, VOTables and Vizier-Style byte-by-byte
descriptions (the latter somewhat haphazardly). It assumes there is only one table in
each file (and will ignore others in the FITS and VizieR case).
It will extract what metadata there is and emit formatted RD XML to stdout; this should
work just fine for cut-and-paste into <table> elements in RD. Note that usually,
important metadata will be missing (e.g., UCDs for FITS and VizieR), and usually data
providers are not terribly careful when writing metadata. Hence, you should definitely
thoroughly review the elements created before using them in a public service.
The program tries to guess the applicable parser from a file name (e.g., README or
anything ending in .txt will be treated as Vizier-like). Where this fails, use the -f
option.
For Vizier-like descriptions, the program also dumps colDefs material for use in
columnGrammar-s.
Argument
FILE Source file to generate the columns from. This can be a FITS, a VOTable, or Vizier
Column-by-column description, and DaCHS will guess based on the extension. Use the
format option if it guesses wrong.
Options
-h, --help
show this help message and exit
-f FMT, --format FMT
Format of the input table: FITS binary (fits), VOTable (vot), or Vizier
byte-by-byte (viz)
THE IMPORT SUBCOMMAND
Synopsis:
dachs import [options] rd-name [data-id]
This subcommand is used to ingest data described by an RD. For special applications,
ingestion can be restricted to specific data items within an RD.
Options
-h, --help
show this help message and exit
-n, --updateRows
Deprecated. Use updating data items instead.
-d, --dumpRows
Dump raw rows as they are emitted by the grammar.
-D, --dumpIngestees
Dump processed rows as emitted by the row makers.
-R, --redoIndex
Drop indices before updating a table and recreate them when done
-m, --meta-only
just update table meta (privileges, column descriptions,...). This will also
update the tables' obscore clauses, but you will have to dachs imp //obscore to
update the obscore view itself in this case.
-I, --meta-and-index
do not import, but update table meta (privileges, column descriptions,...) and
recreate the indices
-u, --update
update mode -- don't drop tables before writing.
-s, --system
(re-)create system tables, too
-v, --verbose
talk a lot while working
-r, --reckless
Do not validate rows before ingestion
-M MAX, --stop-after=MAX
Stop after having parsed MAX rows
-b N, --batch-size=N
deliver N rows at a time to the database.
-c, --continue-bad
do not bail out after an error, just skip the current source and continue with the
next one.
-L, --commit-after-meta
commit the importing transaction after updating the meta tables. Use this when
loading large (hence -L) data sets to avoid keeping a lock on the meta tables for
the duration of the input, i.e., potentially days. The price is that users will
see empty tables during the import.
--hide-adql
Interpret adql=True on tables as adql=hidden (this is for fallback mirrors)
THE INFO SUBCOMMAND
Synopsis:
dachs info [-h] table-id
This displays column statistics about the table referred to in the argument (which must be
a fully qualified table name resolvable by the database system).
Argument
table-id
table ID (of the form rdId#tableId)
THE INIT SUBCOMMAND
Synopsis:
dachs init [-h] [-d DSN] [--nodb]
This initialises DaCHS' file system and database environment. Calling dachs init on an
existing site should not damage anything. It might, however, fix things if, for instance,
permissions on some directories went funny.
Options
-d <DSN>, --dsn <DSN>
data source name (DSN) to use to connect to the future DaCHS database; the DSN
must let DaCHS connect to the database as an administrator; dbname, host, and
port get copied to the profile, if given; this is not required if the calling
user has superuser privileges on a database running on localhost. Otherwise, the
DSN has to look like "host=example.org dbname=mydb user=superuser password=secret".
--nodb inhibit initialization of the database (you may want to use this when refreshing
the file system hierarchy)
THE LIMITS SUBCOMMAND
Synopsis:
dachs limits [-h] item-id {item-id}
This creates or updates DaCHS' estimates of various metadata of RDs or tables, in
particular the STC coverage, the size of the tables and, unless -t is given, the column
statistics. This may take a long time for large tables, in which case you may use the
--sample-percent option, which makes DaCHS only look at a subset of the full data.
When running dachs limits on an RD, it will skip views under the assumption that in the
typical case, column metadata for the interesting columns will already have been obtained
for the source tables. For views for which this is assumption is wrong, set the
forceStats property to True.
You should in general run dachs limits before publishing a resource.
Arguments
item-id
either an RD id or a table reference in the from rd-id#table-id. A single ALL will
expand to all RDs that already have limits-obtained metadata.
Options
-t, --tables-only
Only acquire table/resource-level metadata (rather than column metadata, which
usually takes a lot longer).
-s P, --sample-percent P
Only look at P percent of the table to determine min/max/mean.
-d, --dump
Do not obtain statistics but rather dump the results of the last run
THE MKBOOST SUBCOMMAND
Synopsis:
dachs mkboost [option] <id-of-directGrammar>
This writes a C source skeleton for using the direct grammar referenced to fill a database
table. See the Guide to Write Booster Grammars in the DaCHS documentation for how to use
this command.
Options
-b, --binary
generate a skeleton for a binary parser
-s <SPLITTER>, --splitter=<SPLITTER>
generate a split skeleton with split string <SPLITTER>
THE MKRD SUBCOMMAND
Synopsis:
dachs mkrd [option] sample
Rudimentary support for generating RDs from data. This was probably a bad idea. Better
use dachs start.
Options
-f <SRCFORM>, --format=<SRCFORM>
source format: FITS or VOT; default: detected from file name
-t <TABLENAME>, --table-name=<TABLENAME>
name of the generated table
THE PUBLISH SUBCOMMAND
Synopsis:
dachs pub [-h] [-a] [-m] [-k] [-u] rd [rd ...]
This marks data and/or services contained in an RD as published; this will make them
displayed in DaCHS' portal page or pushed to the VO registry through DaCHS' OAI-PMH
endpoint. See the Operator's Guide for details.
Arguments
rd RDs to publish; you can give ids or file paths. Use the magic value ALL to check
all published RDs, ALL_RECURSE to look for RDs in the file system (check twice for
detritus before doing that later thing).
Options
-k, --keep-timestamps
Preserve the time stamp of the last record modification. This may sometimes be
desirable with minor updates to an RD that don't justify a re- publication to the
VO.
-u, --unpublish
Unpublish all resources coming from this RD Note that this will in general create
"deleted records", i.e., essentially empty resource records only stating that the
resource referenced by an identifier is no longer available. This is important for
reliable operation in the presence of incremental harvesting.
THE PURGE SUBCOMMAND
Synopsis:
dachs purge [-h] tablename [tablename...]
This will delete tables in the database and also remove their metadata from DaCHS'
internal tables (e.g., TAP_SCHEMA, table of published records). Use this if dachs drop
fails for to remove some table for one reason or another.
Argument
tablename
(SQL) name of the table to drop, including the schema name
THE SERVE SUBCOMMAND
Synopsis:
dachs serve [-h] {debug | reload | restart | start | stop}
This exposes various functionality for managing DaCHS' server component. While these
usually are being called through init scripts or systemd components, the debug subfunction
is very convenient during service development off the production environment.
serve start, stop, and restart manage a PID file, which DaCHS does not do when running
under systemd. Hence, do not use these subcommands when systemd manages your DaCHS.
expireRD is fine, though.
Subsubcommands
• debug -- run a server and remain in the foreground, dumping all kinds of stuff to the
terminal. If you have an SSL certificate, this will try bind an https interface to port
40443; that's exclusively for little experiments, do not use it for actual operations.
• reload -- reload server configuration (incomplete)
• restart -- restart the server
• start -- start the server and put it in the background
• stop -- stop a running server
• expireRD <rdId> -- forget the cached RD in the running server. While in general, DaCHS
reloads an RD if it finds it changed, sometimes it does not realise some dependency has
changed. In that case, this subsubcommand can expunge the RD so it will be re-parsed
when the next access occurs. Note that this requires [web]adminpasswd be set; the
command uses [web]serverURL to figure out where to connect the running server.
The start subcommand accepts a --foreground/-f option. If you pass it, the server will
not double-detach and not redirect stderr to a log file and instead stay in the
foreground; it will also not check for PID files or create them. In contrast to debug, it
will change users, etc., and not put the DaCHS into debug mode. This option is primarily
useful for systemd units.
THE START SUBCOMMAND
Synopsis:
dachs start [-h] (list|<data-type-tag>)
The start subcommand generates a template RD for a certain type of data that you can then
fill out. The data-type-tag can be something like scs (for catalogs), siap (for images),
or ssap (for spectra). Pass list to see what is available.
The template uses the name of current directory as resdir and schema name. That means
that if starting a data collection, you should create its resdir as a child of
GAVO_ROOT/inputs and execute dachs start in that dicrectory.
To fill out the template RD, load it into a text editor and, ina first go, search for the
pattern %.*%. You should see enough hints from what is between the percent signs and the
environment to get a reasonable shot at filling things out. Then reead the comments; very
typcially, you can get an extremely basic data publication without that, but a good
service will normally require some extra work beyond filling things out.
Argument
data-type-tag
A short identifier for a data type. Pass list here to see a list of known tags and
their meanings.
THE TEST SUBCOMMAND
Synopsis:
dachs test [-h] [-v] [-V] [-d] [-t TAG] [-R N] [-T SECONDS] [-D FILE]
[-w SECONDS] [-u SERVERURL] [-n NTHREADS]
[--seed RANDOMSEED] [-k KEYWORDS]
id
This runs regression tests embedded in the whatever is reference by id (can be an RD, a
regression suite, or a single regression test). For details, see the chapter on
regression testing in the DaCHS Reference Manual.
Argument
id RD id or cross-RD identifier for a testable thing. Write ALL here to have DaCHS
search and test all RDs in the inputs, ignoring those in or below directories with
a file named DACHS_PRUNE.
Options
-h, --help
show this help message and exit
-v, --verbose
Talk while working
-d, --dump-negative
Dump the content of failing tests to stdout
-t TAG, --tag TAG
Also run tests tagged with TAG.
-R N, --n-repeat N
Run each test N times
-T SECONDS, --timeout SECONDS
Abort and fail requests after inactivity of SECONDS
-D FILE, --dump-to FILE
Dump the content of last failing test to FILE
-w SECONDS, --wait SECONDS
Wait SECONDS before executing a request
-u SERVERURL, --serverURL SERVERURL
URL of the DaCHS root at the server to test
-n NTHREADS, --number-par NTHREADS
Number of requests to be run in parallel
-k KEYWORDS, --keywords KEYWORDS
Only run tests with descriptions containing all (whitespace-separated) keywords.
Sequential tests will be run in full, nevertheless, if their head test matches.
THE VALIDATE SUBCOMMAND
Synopsis:
dachs validate [-h] [-x] [-v] rd [rd...]
This checks RDs for well-formedness and some aspects of VO-friendliness
Arguments
rd RD path or ID to validate. Write ALL here to have DaCHS search and validate all
RDs in your input and validate them, ignoring those in or below directories with a
file named DACHS_PRUNE.
Options
-h, --help
show this help message and exit
-p, --pre-publication
Validate as if all services were IVOA published even if they are not (this may
produce spurious errors if unpublished services are in the RD).
-v, --verbose
Talk while working
-t, --run-tests
Run regression tests embedded in the checked RDs
-T SECONDS, --timeout SECONDS
When running tests, abort and fail requests after inactivity of SECONDS
-c, --compare-db
Also make sure that tables that are on disk (somewhat) match the definition in the
RD.
-u, --accept-free-units
Do not warn against units not listed in VOUnits.
THE UPGRADE SUBCOMMAND
Synopsis:
dachs upgrade
Each DaCHS version has an associated database schema version, encoding the structure of
DaCHS' (and the implemented protocol versions') ideas of how system and user tables should
look like. dachs upgrade attempts to work out how to change the database to match the
expectations of the current version and executes the respective code. It will not touch
its data structures if it decrees that the installation is up to date.
Operating system packages will usually try to run dachs upgrade as part of their
management operation. In case dachs upgrade requires manual intervention, this may fail,
in which case operators may need to call dachs upgrade manually.
Operators keeping a manually installed DaCHS should run dachs upgrade after each svn
update or update from tar.
dachs upgrade cannot perform actions requiring superuser privileges, since none of its
roles have those. Currently, this is mainly updating postgres extensions DaCHS uses (if
you use extra ones, you can configure DaCHS' watch list in [db]managedExtensions). dachs
upgrade -e will attempt to figure out the instructions necessary to update extensions and
write them to stdout. Hence, operators should execute something like dachs upgrade -e |
psql gavo from a database superuser account after upgrading postgres extensions.
Options
--force-dbversion FORCEDBVERSION
assume this as the database's schema version. If you don't develop DaCHS, you
almost certainly should stay clear of this flag
-e, --get-extension-script
Dump a script to update DaCHS-managed extensions (will print nothing if no
extensions need updating). This will return 0 if material was written, 1
otherwise.
-t, --update-tap-schema
Update the TAP schema, i.e., re-read all the metadata from the TAP-published
tables. This isn't really related to upgrading, but it is generally a good idea
to sync on-disk representations with what you may have edited in the RDs.
THE ADQL SUBCOMMAND
Synopsis:
dachs adql query
This subcommand executes ADQL queries locally and writes the resulting VOTable to stdout.
We consider removing it.
INTERNAL OR DEPRECATED SUBCOMMANDS
The subcommands show, stc are deprecated and not documented here. They may disappear
without further notice.
the subcommands taprun, dlrun, uwsrun, gendoc, raise are used internally and should not be
directly used by DaCHS operators.
REPORTING BUGS
To report bugs and request support, please use our support mailing list
http://lists.g-vo.org/cgi-bin/mailman/listinfo/dachs-support.
SEE ALSO
Comprehensive, if always incomplete documentation on DaCHS is available in several
documents available at http://docs.g-vo.org/DaCHS/ (upstream site with PDF downloads and
the formatted reference documentation) and
http://dachs-doc.readthedocs.io/en/latest/index.html (with facilities for updating the
documents).
COPYRIGHT
Copyright © 2017 The GAVO project. License GPLv3+: GNU GPL version 3 or later <‐
http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and
redistribute it. There is NO WARRANTY, to the extent permitted by law.
AUTHOR
Markus Demleitner <gavo@ari.uni-heidelberg.de>