Yasmine-cli is a command-line script for merging/editing stationXML metadata files. Initial development has been supported by Résif. Development and addition of new features is shared and agreed upon between IRIS and Résif.
Yasmine-cli only provides a minimum level of validation against the stationXML .xsd schema.
For a proper validation, it should be used in conjunction with the dedicated IRIS stationXML validator.
Even if we have performed a lot of tests, yasmine-cli is currently released in beta version and some bugs and limitations might still be found.
obspy >= 1.2
pyyaml
These requirements should be automatically installed for you (see below).
Optionally, before installing the code, create a new python environment and activate it, e.g.,:
>conda create -n yasmine_test python=3.8
>conda activate yasmine_test
Note: In an empty python environment, installing yasmine-cli will trigger the installation of any dependent packages that are missing, including obspy, numpy, scipy and matplotlib. Because yasmine-cli contains code that uses matplotlib's backend to generate response plots, it is necessary to have a suitable backend plotting package, which matplotlib does not install by default. Trying to run yasmine-cli without a backend installed will likely end in failure.
More information, including a list of supported matplotlib backends can be found at:
https://matplotlib.org/stable/tutorials/introductory/usage.html#backends
The backend I like to use can be installed via:
>pip install pyqt5
There are a few different ways to obtain and install the code.
- The easiest way is to install the latest version from pypi.org
https://pypi.org/project/yasmine-cli
>pip install yasmine-cli
- You can clone the repository and install from there:
e.g.,
>git clone https://github.com/iris-edu/yasmine-stationxml-cli.git
>cd yasmine-stationxml-cli
>pip install .
Once you have installed it, you should be able to run it as a python module from any directory.
>yasmine-cli
usage: yasmine-cli [-h]
[--infiles // comma separated list of input xml files]
[--action [add/delete/update/select basenode] or
[default=update node attribute]]
...
Currently, the only thing configurable outside of the command line options pertains to logging:
>cat config.yml
LOG_DIR: some_path/to_my/log
LOG_LEVEL: WARNING
yasmine-cli will look for the config.yml first in your current dir (from where you are executing the cmd) and second in the yasmine-cli install dir. If it doesn't find a config.yml in either location, it will default to:
LOG_DIR: .
LOG_LEVEL: INFO
Regardless of whether or not it finds a config.yml file, you can override the LOG_LEVEL with the command line option:
>yasmine-cli ... --loglevel=ERROR ...
usage: yasmine-cli [-h | --help]
[--level_network II | --level_station II.* | --level_channel II.ANMO.00.*]
[--action [add/delete/update basenode]]
[--epoch_station int] [--epoch_channel int]
[--field FIELD] [--value VALUE | --from_yml fname.yml]
[--infiles] [-o] [-p] [--print_all] [--dont_validate]
[--schema_version ver] [--show_fields] [--plot_resp]
[--plot_dir path]
optional arguments:
-h, --help show this help message and exit
level options: [default=root is implied if no level set]:
--level_network II
--level_station II.*
--level_channel II.ANMO.00.*
action options: [default=update if no action set]:
--action [add/delete/update basenode]
epoch options: Use to filter down to epoch level:
--epoch_station int station epoch index to filter on, eg, --epoch_station=1
--epoch_channel int channel epoch index to filter on, eg, --epoch_channel=0
build options:
--field FIELD field, key or attribute to update. eg, --field=Latitude or --field=comments[1]
--value VALUE value of field, key or attribute to update. Ex. --value=34.97 or --value=yml:/path/comment.yml
--from_yml fname.yml Used to add new basenode object created from
fname.yml. eg, --from_yml=/some/path/network.yml
other optional arguments:
--infiles comma separated list of input xml files [default=stdin]
-o , --output Name of output xml file [default=stdout]. eg, --output=foo.xml
-p, --print Print out sorted Station/Channel epochs
--print_all Print out sorted Station/Channel epochs + operator/comment lists
--dont_validate Turn OFF StationXML validation on all inputs/outputs
--schema_version ver {1.0, 1.1}
--show_fields Print out allowable --field, + --value combinations
--plot_resp Plot all channel responses
--plot_dir path Path to dir to save plot responses
Examples:
>yasmine-cli --level_network=II --field=description --value='Network description' --infiles=...
>yasmine-cli --level_station=II.* --field=latitude --value=34.97 --infiles=...
>yasmine-cli --level_channel=II.ANMO.00.* --field=comments[0] --value=yml:/path/comment.yml --infiles=...
>yasmine-cli --level_network=* --action=add --from_yml=path/to/station.yml --infiles=...
An ObsPy Inventory object is essentially a container for a list of Networks and each of these is a container for a list of Stations, etc.
yasmine-cli reads the input StationXML files into an Inventory object which is then reorganized into a Python dictionary which is indexed by searchable fields (e.g., station_code, channel_code).
At the bottom of this dictionary are lists of Station(s) (=station epochs) which in turn contain Channel(s) (=channel epochs), and each of these is sorted alphabetically and chronologically.
More examples and details can be found in the EXAMPLES file.
In order to decide which element(s) the action (described below) should apply to, yasmine-cli looks at two flags:
- --level_{network, station, channel} [default=root]
- --station_epoch=int or --channel_epoch=int // used when finer grain control is desired
The level flags (--level_network, --level_station, --level_channel) are mutually exclusive. Which one you select depends on what level the action should operate on.
Each one takes a slightly different form, e.g.,
--level_network=IU (act on this network)
--level_network=* (act on all networks)
--level_station=IU.ANMO (act on this station)
--level_station=*.ANMO (act on this station in all networks)
--level_station=IU.* (act on all stations in this network)
--level_station=*.* (act on all stations in all networks)
--level_channel=IU.ANMO.00.BHZ (act on this channel)
--level_channel=IU.ANMO.00.* (act on all channels at this location_code)
--level_channel=IU.ANMO.*.* (act on all channels at all location_codes)
--level_channel=IU.*.*.* (act on all channels of all stns of this network)
--level_channel=*.*.*.* (act on all channels of all stns of all networks)
Internally, the flags are used to set the 'scnl_filter' (really NSLC since network.station.location.channel, but anyway ...)
By default, if no --level_.. flag is set, the level is assumed to be "root" so that any field you wish to modify must be part of the StationXML/Obspy_inventory root: --field={source, sender, module, module_uri}.
yasmine-cli allows 4 basic actions: update, select, add, delete.
If no --action is specified, the action will default to update (if --field and --value are specified) or to select (if not).
In conjunction with --from_yml=yml:/path/to/file.yml, this is used to insert a new basenode object (network, station or channel). Note that the path to the yml template file is relative to the installation dir of yasmine-cli.
For example, to add a new network to the StationXML from a yaml file in ./yml/network.yml:
>yasmine-cli --action=add --from_yml=yml:yml/network.yml --infiles=.. -o=..
Notice that it was not necessary to specify the --level_ in this case - A network can only go in the root level and this is the default level.
Similarly, to add a new station to only the II network within a StationXML file:
>yasmine-cli --action=add --level_network=II --from_yml=yml:yml/station.yml --infiles=.. -o=..
where now the level must be set (--level_network=* indicates all networks).
This is used to delete a basenode object(s) at the indicated level.
For example, to delete all the channels from station IU.ANMO:
>yasmine-cli --action=delete --level_station=IU.ANMO
This is used to select basenode object(s) that match the SCNL indicated by --level_.
To select (=filter all matching) stations where station.code == 'ANMO' and print to stdout:
>yasmine-cli --level_station=IU.ANMO --infiles=data/II.xml
This is used to update (or insert if missing) the value of a basenode field (attribute).
Every update takes two fields: --field and --value. The various --level and --epoch flags will help you select which basenode object you want to modify.
If the underlying type of the attribute is a simple type (e.g., double, int, string), then you can set the value on the command line, eg:
--field=code --value=STA1 --level_network=IU
--field=latitude --value=45. --level_station=IU.ANMO
--field=description --value='This is a station description' --level_station=*.*
If instead, the expected value is a complex type which is itself an ObsPy object, you can create it from yaml using the --value=yml: prefix:
--field=data_availability --value=yml:yml/dataavailability.yml --level_station=IU.ANMO
The yaml files should have structure that follows the method calls of the corresponding ObsPy objects.
For instance,
>cat yml/operator.yml
Operator:
agency: 'United States Geological Survey, USGS'
contacts:
- person:
names:
- 'Adam Ringler'
- 'Tyler Storm'
agencies:
- 'Albuquerque Seismic Lab'
emails:
- 'aringler@usgs.gov'
phones:
- (508)555-5555
website: http://google.com
Note: 'Operator' is capitalized (since this will be used to generate an ObsPy Operator(), and the fields must match those needed for successful initializing of the particular ObsPy object.
However, on the command line, all fields are lower-case, e.g: --field=operators or --field=comments. Note that fields that can have multiple occurrences within the StationXML file (e.g., multiple Operator or Comment elements), are indicated on the command line using plural strings (comments, operators, etc).
To see all allowable command-line fields for each level, do:
>yasmine-cli --show_fields
Here is another example of a BaseNodeType object to be added:
> cat yml/channel.yml
Channel:
code: 'HN1'
location_code: '30'
description: 'This is an added channel'
start_date: 2006-06-30T20:00:01.000000Z
end_date: 2399-12-31T23:59:59.000000Z
latitude: 34.945911
longitude: -106.457199
elevation: 1820.0
depth: 0.0
azimuth: 90.0
Note that the file contains all of the required fields (code, location_code, ..., depth) needed to initialize a Channel object, as well as one optional field (azimuth). The user can add as many optional fields as desired, provided the names and types correspond to those ObsPy is expecting for this object.
If the expected field/value is a list (e.g., ObsPy expects Station.comments = [Comments]), then there are several scenarios, depending on syntax.
- The field can be a list (e.g. field=operators) or a scalar (field=operators[2]) and this is the target.
- The value can be a list (value=[Operator1,Operator2,..] or value=[]) or a scalar (value=Operator or value=None), and this is the source.
Here are the allowable combinations (yasmine-cli will complain if you do something else):
-
List to List: Populate ANMO station epochs with Station.operators = list created from yaml
--field=operators --value=yml:yml/operators.yml --level_station=*.ANMO
-
List to empty list: Delete Station.operators:
--field=operators --value=[] --level_station=*.ANMO
-
List to scalar: Append a single operator (from yaml) to the end of the existing list:
--field=operators --value=yml:yml/operator.yml --level_station=*.ANMO
-
Scalar to scalar: Replace a single item at operators[2] with new operator (from yaml):
--field=operators[2] --value=yml:yml/operator.yml --level_station=*.ANMO
-
Scalar to None: Delete operators[2] from the operators list:
--field=operators[2] --value=None --level_station=*.ANMO
- Incorporated Research Institutions for Seismology (IRIS) Data Services - https://ds.iris.edu
- réseau sismologique et géodésique français (Résif) - https://www.resif.fr/
- FDSN StationXML Manual - https://stationxml-doc.readthedocs.io/en/release-1.1.0/
- FDSN StationXML Schema v1.1 - https://github.com/FDSN/StationXML/blob/v1.1/fdsn-station.xsd