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====== Frequently Asked Questions ====== | ====== Frequently Asked Questions ====== | ||
- | ===== How should metadata in the database be mapped to a DIF XML? ===== | + | ===== Features ===== |
+ | |||
+ | ==== What is the purpose of METAMOD? ==== | ||
+ | |||
+ | METAMOD was initially developed to support scientific projects with data management. Development has focused on a cost effective system where several projects or operational services can share the same backend while maintaining a custom built user interface specific for each project. One METAMOD implementation may support many METAMOD instances. The first instance always own the database and some maintenance and configuration aspects are only available through this instance. | ||
+ | |||
+ | ==== What are the main features of METAMOD? ==== | ||
+ | |||
+ | METAMOD was developed to support data management focusing on: | ||
+ | - Metadata handling | ||
+ | - Human and machine interfaces | ||
+ | - Import/ | ||
+ | - Support for dataset uploading | ||
+ | - Interactive and automated | ||
+ | - Through web interface, FTP, scp etc | ||
+ | - Ad hoc and regular data streams | ||
+ | - Configurable conformance check of NetCDF/CF files uploaded | ||
+ | - Automatic extraction of metadata from datasets uploaded | ||
+ | - When uploaded as NetCDF/CF following the convention of METAMOD | ||
+ | - Connection to online datasets | ||
+ | - METAMOD is usually linked to a THREDDS Data Server actually serving the data sets | ||
+ | |||
+ | ===== Configuration ===== | ||
+ | |||
+ | ==== How do I change the runtime environment? | ||
+ | |||
+ | The runtime environment is generated during installation of the software (see the README file coming with the software for details). Basically the following procedure is used to set up a METAMOD instance: | ||
+ | - Edit '' | ||
+ | - Run '' | ||
+ | - This creates a runtime source code tree located as defined within '' | ||
+ | - If a first time set up, run '' | ||
+ | - Run '' | ||
+ | - Start the system by running '' | ||
+ | |||
+ | If changes are made to '' | ||
+ | |||
+ | ==== How do I change the appearance of the web interface? ==== | ||
+ | |||
+ | The visual appearance of METAMOD is determined by style sheets and contents of the '' | ||
+ | - '' | ||
+ | - '' | ||
+ | - '' | ||
+ | - '' | ||
+ | |||
+ | ==== How do I change the menus of the METAMOD web interface? ==== | ||
+ | |||
+ | METAMOD has two main menu containers. One top left (available within all modules) and one left (mainly in the search module and the upload). The top left menu is set up using the '' | ||
+ | |||
+ | The search module menu is configured using the '' | ||
+ | - Activity type | ||
+ | - Area | ||
+ | - Variables (hidden) | ||
+ | - Topics and variables | ||
+ | - TBW | ||
+ | - TBW | ||
+ | - Institutions | ||
+ | - Datacollection period | ||
+ | - Map search | ||
+ | - Operational status | ||
+ | |||
+ | In addition the keyword '' | ||
+ | |||
+ | In order to add new search categories the following sequence is required: | ||
+ | - Edit the file '' | ||
+ | - Reinitialise the static part of the database by running the script '' | ||
+ | If several METAMOD instances are using the same database, this has to be done in the METAMOD instance that actually own the database. If the database has been running for a while, reinitialisation may take some time during which the METAMOD instances using the database will be unavailable. | ||
+ | |||
+ | ==== How do I configure the conformance check for NetCDF/CF files? ==== | ||
+ | |||
+ | FIXME | ||
+ | |||
+ | ===== Operation and maintenance ===== | ||
+ | |||
+ | ==== Which metadata standards are supported ==== | ||
+ | |||
+ | The [[: | ||
+ | * 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 " | ||
+ | |||
+ | 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" | ||
+ | |||
+ | Sometimes, the solution above is insufficient. Under such conditions, direct modification of metadata and import of these from the webrun directory using '' | ||
+ | |||
+ | ==== 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. | ||
+ | |||
+ | < | ||
+ | <wmsInfo xmlns: | ||
+ | < | ||
+ | < | ||
+ | <w:layer name=" | ||
+ | <w:layer name=" | ||
+ | <w:layer name=" | ||
+ | <w:layer name=" | ||
+ | </ | ||
+ | </ | ||
+ | </ | ||
+ | |||
+ | This section describes the initial view to present and the layers that are available. If the number of layers should be truncated, add '' | ||
+ | |||
+ | To enable transformation of a gridded dataset, add '' | ||
+ | |||
+ | If the dataset is not a gridded dataset, but e.g. a timeseries, addition of a MM2 field named '' | ||
+ | |||
+ | < | ||
+ | < | ||
+ | </ | ||
+ | |||
+ | 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 / | ||
+ | - sudo / | ||
+ | - sudo -u <web server owner> < | ||
+ | - sudo / | ||
+ | - sudo / | ||
+ | |||
+ | ==== 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 '' | ||
+ | ===== Metadata exchange ===== | ||
+ | |||
+ | ==== Which metadata exchange protocols do METAMOD support? ==== | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | ==== Which metadata standards do METAMOD support? ==== | ||
+ | |||
+ | METAMOD use an internal metadata standard that is mapped to [[http:// | ||
+ | |||
+ | ==== What is the structure of the metamod metadata xml files? ==== | ||
+ | |||
+ | Information and schemata of the metadata-files used since Metamod 2.1 can be found under [[xml-format]]. | ||
+ | |||
+ | ==== Where do I get the metadata as dif/ | ||
+ | |||
+ | http:// | ||
+ | |||
+ | ==== How should metadata in the database be mapped to a DIF XML? ==== | ||
The metadata structure is configurable, | The metadata structure is configurable, | ||
- | The METAMODPMH module contain a translation from the database to DIF XML. For the time being, this translation is imlemented | + | The METAMODPMH module contain a translation from the database to DIF XML. For the time being, this translation is implemented |
< | < | ||
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... | ... | ||
< | < | ||
+ | ... | ||
< | < | ||
+ | ... | ||
</ | </ | ||
... | ... | ||
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</ | </ | ||
- | This is the general rule, but some special rules apply: | + | The sequence of triples in the array define the sequence of the elements in the DIF XML. If possible, one triple will use the same higher level XML elements as the previous triple. |
+ | |||
+ | These points constitute | ||
- If an ' | - If an ' | ||
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- If several consecutive triples have the same metadata type name, they will appear as consecutive elements in the DIF XML. When this is the case, different conversions of the metatdata value will take place (indicated by a number as explained above). | - If several consecutive triples have the same metadata type name, they will appear as consecutive elements in the DIF XML. When this is the case, different conversions of the metatdata value will take place (indicated by a number as explained above). | ||
- Several metadata values for the same metadata type and dataset, produce several DIF XML elements. | - Several metadata values for the same metadata type and dataset, produce several DIF XML elements. | ||
- | - An asterix (*) prepending an element name in the sequence of element names will force the start of a new DIF XML element at this level. Othervise, new elements will, if possible, add to an already started higher level element. | + | - An asterix (*) prepending an element name in the sequence of element names will force the start of a new DIF XML element at this level. |
+ | |||
+ | ===== File formats ===== | ||
+ | |||
+ | ==== File formats relevance for METAMOD ==== | ||
+ | |||
+ | METAMOD is essentially agnostic concerning file formats. However, [[# | ||
+ | |||
+ | 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 ==== | ||
+ | |||
+ | 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:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | |||
+ | ==== 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/ | ||
+ | |||
+ | ==== NetCDF/CF global attributes ==== | ||
+ | |||
+ | 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 " | ||
+ | |topiccategory|A blank separated list of topic keywords describing the dataset. < | ||
+ | climatologyMeteorologyAtmosphere | ||
+ | environment | ||
+ | geoscientificinformation | ||
+ | imageryBaseMapsEarthCover | ||
+ | inlandWaters | ||
+ | oceans | ||
+ | society</ | ||
+ | |keywords|A blank separated list of keywords describing the dataset. FIXME|Active, | ||
+ | |gcmd_keywords|Newline separated list of GCMD scientific keywords describing the various variables. This will be used to categorize the datasets according to the " | ||
+ | |activity_type|Comma separated list of activity types. Current vocabulary includes < | ||
+ | Cruise | ||
+ | Aircraft | ||
+ | Model run | ||
+ | Land station | ||
+ | Ice station | ||
+ | Submersible | ||
+ | Float | ||
+ | Space borne instrument | ||
+ | Other</ | ||
+ | |operational_status|Status of the dataset, being one of < | ||
+ | Pre operational | ||
+ | Operational | ||
+ | Scientific</ | ||
+ | |Conventions|The metadata convention used, should be '' | ||
+ | |product_name|A product name of the dataset.|Active|Controlled vocabulary| | ||
+ | |history|Modification history of the dataset. Should be of the form: < | ||
+ | 2007-06-10 revision</ | ||
+ | |area|Area name describing the geographical area being studied.If several area names are used, separate them using comma. < | ||
+ | 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</ | ||
+ | |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 '' | ||
+ | |stop_date|Stop date and time of the dataset in the form '' | ||
+ | |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 '' | ||
+ | |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. < | ||
+ | Restricted to < | ||
+ | No access until < | ||
+ | |use_statement|A use statement describing conditions for using the dataset.< | ||
+ | Cite properly | ||
+ | No commercial use, cite properly | ||
+ | PIC/CC0 | ||
+ | PIC/ | ||
+ | |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 '' | ||
+ | |||
+ | Another possible cause is that the XML-information is inconsistent/ | ||
+ | |||
+ | ==== 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 '' | ||
+ | |||
+ | See [[#Why is METAMOD not including the XML-information located in the webrun directory? |