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metamod:faq [2010-09-27 08:22:10]
steingod
metamod:faq [2013-10-14 14:53:50] (current)
steingod [Operation and maintenance]
Line 72: Line 72:
 FIXME FIXME
  
 +===== Operation and maintenance =====
 +
 +==== Which metadata standards are supported ====
 +
 +The [[:​metamod:​xml-format|XMD-files used within METAMOD]] has a tag that identifies the metadata standard used. Currently the following standards are supported:
 +  * GCMD DIF
 +  * ISO19115
 +  * MM2
 +The native format of METAMOD is MM2 and this is connected to the datamodel used in the database. As of version 2.13 work is ongoing to support a new format named MMD which makes translation to DIF and ISO easier. For a new format to be supported, modifications of the software is required.
 +
 +==== How do I remove datasets? ====
 +
 +The best solution is to use the administration interface (require login and appropriate user rights) and the "​Dataset manager"​. Within this interface datasets can be deactivated. they will still be in the database, but will be invisible. Sometimes conflicts between datasets may arise (due to naming conventions) which may require a full reinitialisation of the database. If a dataset is to be permanently removed, remove the XML and XMD files from the webrun directory and follow the steps under [[#How do I reinitialise the database?​]]. This require access to the webrun directory at the server running METAMOD.
 +
 +Unused or obsolete metadata files may be removed from the XML directory. Any warnings caused by this will be removed after full reinitialisation of the database.
 +
 +==== How do I edit metadata? ====
 +
 +FIXME - A new editor has been developed, but not fully integrated yet. 
 +
 +The preferred solution is to use the metadata editor included in the software. This is launched using the "File upload"​ menu and the option "​Dataset administration"​. Login and appropriate privileges are required.
 +
 +Sometimes, the solution above is insufficient. Under such conditions, direct modification of metadata and import of these from the webrun directory using ''​import_datasets''​ may be an option. This option should be used with care! 
 +
 +==== How do I control visualisation and transformation of datasets ====
 +
 +Visualisation and transformation of datasets are configured through metadata. ​
 +
 +For OGC WMS to be activated for a dataset a section similar to the one below is required.
 +
 +<​code>​
 +  <wmsInfo xmlns:​w="​http://​www.met.no/​schema/​metamod/​ncWmsSetup">​
 +    <​w:​ncWmsSetup url="​%THREDDS_DATAREF%"​ aggregate_url="​http://​thredds.nersc.no/​thredds/​wms/​normap/​arctic25km_seaice_aggr"​ xsi:​schemaLocation="​http://​www.met.no/​schema/​metamod/​ncWmsSetup ncWmsSetup.xsd ">
 +      <​w:​displayArea crs="​EPSG:​32661"​ left="​-1000000"​ right="​5000000"​ bottom="​-1000000"​ top="​5000000"/>​
 +      <w:layer name="​NORSEX"​ style="​BOXFILL/​rainbow"/>​
 +      <w:layer name="​NASA_Team"​ style="​BOXFILL/​rainbow"/>​
 +      <w:layer name="​Bristol"​ style="​BOXFILL/​rainbow"/>​
 +      <w:layer name="​Bootstrap"​ style="​BOXFILL/​rainbow"/>​
 +    </​w:​ncWmsSetup>​
 +  </​wmsInfo>​
 +</​code> ​
 +  ​
 +This section describes the initial view to present and the layers that are available. If the number of layers should be truncated, add ''​maxlayers="​0"''​ to ''​ncWmsSetup'''​. In the displayArea field, coordinate need to be provided in the coordinates of the map projection defined (using EPSG codes).
 +
 +To enable transformation of a gridded dataset, add ''​dataref_OPENDAP''​ to MM2 metadata or edit e.g. dif2MM2.xslt to reflect this variable.
 +
 +If the dataset is not a gridded dataset, but e.g. a timeseries, addition of a MM2 field named ''​timeseries''​ will remove the transform button and add Timeseries and ASCII buttons which are used to visualise a timeseries or download it as ASCII formatted data. The format of the timeseries field is of the form
 +
 +<​code>​
 +<​metadata name="​timeseries">​time,​sea_ice_extent</​metadata>​
 +</​code>​
 +
 +Where the first variable is used as the X axis. The others (up to two) will be plotted on the Y axis.
 +
 +==== How do I reinitialise the database? ====
 +
 +Use the following recipe (information in <> to be substituted as appropriate):​
 +
 +  - sudo /​etc/​init.d/​metamodServices-<​implementation>​ stop
 +  - sudo /​etc/​init.d/​catalyst-<​implementation>​ stop
 +  - sudo -u <web server owner> <​implementation directory>/​base/​init/​create_and_load_all.sh <​configuration directory>​
 +  - sudo /​etc/​init.d/​metamodServices-<​implementation>​ start
 +  - sudo /​etc/​init.d/​catalyst-<​implementation>​ start
 +
 +==== Manual modification of metadata ====
 +
 +This is possible provided the user has the correct priveliges. XML-files in the XML-directory may be edited manually and inserted in the database utilising the script ''​import_dataset.pl''​. This can also be used to include metadata harvested from an external system. ​
 ===== Metadata exchange ===== ===== Metadata exchange =====
  
Line 183: Line 250:
  
 ===== File formats ===== ===== File formats =====
 +
 +==== File formats relevance for METAMOD ====
 +
 +METAMOD is essentially agnostic concerning file formats. However, [[#​NetCDF/​CF|as mentioned below]], METAMOD has extended support for data uploaded as NetCDF/CF following the requirements of METAMOD.
 +
 +Basically METAMOD can relate to any file as long as the metadata are created manually and uploaded, but metadata can be extracted automatically from NetCDF/CF files. ​
  
 ==== NetCDF/CF ==== ==== NetCDF/CF ====
  
-TBW+METAMOD has extended support for NetCDF/CF files where conformance checks and automatic extraction of metadata are supported. Some relevant information concerning NetCDF/CF can be found here: 
 +  * [[http://​www.unidata.ucar.edu/​software/​netcdf/​|NetCDF]] 
 +  * [[http://​www.unidata.ucar.edu/​software/​netcdf/​docs/​BestPractices.html|NetCDF - best practises]] 
 +  * [[http://​www.cfconventions.org/​|CF metadata standard]] 
 +    * [[http://​cf-pcmdi.llnl.gov/​documents/​other/​cf_overview_viewgraphs.pdf|CF Overview (Talk)]] 
 +    * [[http://​cf-pcmdi.llnl.gov/​documents/​other/​cf_overview_article.pdf|CF Overview (Paper)]] 
 +  * [[http://​nco.sourceforge.net/​|NetCDF Operator]] provides useful software e.g. to concatenate files 
 + 
 +==== CDL ==== 
 + 
 +Common Data Language provides an ASCII representation of NetCDF files. METAMOD do support direct upload of CDL files and will perform the same conformance checks in CDL as on NetCDF/CF files, as well as conversion to NetCDF/CF.
  
 ==== NetCDF/CF global attributes ==== ==== NetCDF/CF global attributes ====
  
-TBW+The following global attributes are required in NetCDF/CF files uploaded through METAMOD for proper stewardship. Please note that this is a minimum requirement and is subject to change (some proposed changes are indicated below). 
 + 
 +^Name^Purpose^Status^Comment^ 
 +|title|A short description of the data set|Active| | 
 +|abstract|A short summary of the data collection activity and data set. This element may alternatively be provided as the global attribute "​comment"​ in a NetCDF file.|Active| | 
 +|topiccategory|A blank separated list of topic keywords describing the dataset. <​code>​biota 
 +climatologyMeteorologyAtmosphere 
 +environment 
 +geoscientificinformation 
 +imageryBaseMapsEarthCover 
 +inlandWaters 
 +oceans 
 +society</​code>​|Active| | 
 +|keywords|A blank separated list of keywords describing the dataset. FIXME|Active,​ TBR|Controlled vocabulary| 
 +|gcmd_keywords|Newline separated list of GCMD scientific keywords describing the various variables. This will be used to categorize the datasets according to the "​Topics and variables"​ menu selection in the metadata search facility. If proper standard names have been used for the variables, data will be mapped for search under Topics and variables even without the gcmd_keywords attribute. FIXME|Active|Controlled vocabulary| 
 +|activity_type|Comma separated list of activity types. Current vocabulary includes <​code>​Moored instrument 
 +Cruise 
 +Aircraft 
 +Model run 
 +Land station 
 +Ice station 
 +Submersible 
 +Float 
 +Space borne instrument 
 +Other</​code>​|Active|Controlled vocabulary, should be harmonised with other existing vocabularies and simplified| 
 +|operational_status|Status of the dataset, being one of <​code>​Experimental 
 +Pre operational 
 +Operational 
 +Scientific</​code>​|Active|Controlled vocabulary| 
 +|Conventions|The metadata convention used, should be ''​CF-1.x''​ where x=1, 2, or 3.|Active|Controlled vocabulary| 
 +|product_name|A product name of the dataset.|Active|Controlled vocabulary| 
 +|history|Modification history of the dataset. Should be of the form: <​code>​2007-05-12 creation 
 +2007-06-10 revision</​code>​ and separated by newlines.|Active| | 
 +|area|Area name describing the geographical area being studied.If several area names are used, separate them using comma. <​code>​Arctic Ocean 
 +Barents Sea 
 +Beufort Sea 
 +Chukchi Sea 
 +Denmark Strait Sea 
 +East Siberian Sea 
 +Fram Strait 
 +Greenland Sea 
 +Iceland Sea 
 +Kara Sea 
 +Laptev Sea 
 +Nordic Seas 
 +Northern Hemisphere 
 +White Sea</​code>​|Active|Controlled vocabulary, should be harmonised with other existing vocabularies. These keywords are mapped to GCMD geographical keywords currently.| 
 +|southernmost_latitude|Elements to describe a geographicalbounding box for the data. Should be a floating point value (decimal degrees).|Active| | 
 +|northernmost_latitude|Elements to describe a geographicalbounding box for the data. Should be a floating point value (decimal degrees).|Active| | 
 +|westernmost_longitude|Elements to describe a geographicalbounding box for the data. Should be a floating point value (decimal degrees) with positive values towards the East.|Active| | 
 +|easternmost_longitude|Elements to describe a geographicalbounding box for the data. Should be a floating point value (decimal degrees) with positive values towards the East.|Active| | 
 +|start_date|Start date and time of the dataset in the form ''​2007-06-12 12:30:00 UTC''​|Active| | 
 +|stop_date|Stop date and time of the dataset in the form ''​2007-06-12 12:30:00 UTC''​|Active| | 
 +|institution|Name of the institution responsible for the dataset. FIXME|Active|Controlled vocabulary| 
 +|PI_name|Name of the person responsible for the data set.|Active| | 
 +|PI_address|Address to the person responsible for the dataset.|Proposed|FIXME| 
 +|contact|email address to responsible user support or principal investigator. If the email address of the principal investigator is used, the variable ''​PI_name''​ should be set accordingly.|Active| | 
 +|citation|Information on how to cite the information properly.|Proposed|FIXME| 
 +|distribution_statement|A distribution statement describing the conditions for distributing and access to the dataset. <​code>​Free 
 +Restricted to <​project>​ until <​YYYY-MM-DD>​ 
 +No access until <​YYYY-MM-DD></​code>​|Active|Controlled vocabulary| 
 +|use_statement|A use statement describing conditions for using the dataset.<​code>​Free 
 +Cite properly 
 +No commercial use, cite properly 
 +PIC/CC0 
 +PIC/​CCby</​code>​|Proposed|Controlled vocabulary, or link to CC license or similar. FIXME| 
 +|project_name|Name of the project within which the data were collected. Several project dependencies can be indicated using comma separated project names.|Active|Controlled vocabulary| 
 + 
 +===== Common pitfalls ===== 
 + 
 +==== Why is METAMOD not including the XML-information located in the webrun directory? ==== 
 + 
 +One possible cause can be that there is a conflict between users. Please remember that all scripts and processes has to be run under the user that owns the web server (e.g. www-user or www-data). If this is not the case, try removing the ''​webrun''​ directory and reinstall everything using ''​sudo -u <​user>​ ...''​. 
 + 
 +Another possible cause is that the XML-information is inconsistent/​incomplete. If metadata files has been added manually, check that they are consistent (e.g. using [[http://​xmlsoft.org/​xmllint.html|xmllint]] or similar tools) prior to import. Furthermore,​ in the current version each XML-file has to be accompanied by a XMD-file providing additional information on data sources and metadata organisation. If this is absent, metadata are not processed for import. Check the log in the webrun directory for details. 
 + 
 +==== Why is METAMOD not showing the data I uploaded? ==== 
 + 
 +One possible cause can be that the dataset tag is not correct. Check the contents of the ''​master_config.txt''​ and especially elements ''​DATASET_TAGS'',​ ''​UPLOAD_OWNERTAG'',​ ''​QUEST_OWNERTAG'',​ and ''​PMH_EXPORT_TAGS''​ for consistency. 
 + 
 +See [[#Why is METAMOD not including the XML-information located in the webrun directory?​]] as well.
metamod/faq.1285575730.txt.gz · Last modified: 2010-09-27 08:22:10 by steingod