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SeisHub - a seismological XML/SQL database hybrid

Python 75.92% CSS 22.00% JavaScript 0.04% XSLT 1.99% HTML 0.04% Eagle 0.03%

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bmorg krischer megies personlin calum-chamberlain cjhopp ilmosal ggzitha tugbayk

seishub.core's Issues

Problems starting and initializing a seishub instance

Hi,

I encounter a problem when starting my seishub instance. It started after installing the single package obspy version. I cloned seishub.core and seishub.plugins.seismology and updated sqlalchemy, but the error in the startup process remains:

2012-11-16 15:47:49,167 INFO sqlalchemy.engine.base.Engine {}
2012-11-16 15:47:49,173 INFO sqlalchemy.engine.base.Engine COMMIT
DEBUG: Updating IndexView /seismology/station ...
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/local/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/daemon.py", line 64, in <module>
    run()
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/daemon.py", line 60, in run
    SeisHubApplicationRunner(config, log_file).run()
  File "/usr/local/lib/python2.7/site-packages/Twisted-12.1.0-py2.7-linux-x86_64.egg/twisted/application/app.py", line 386, in run
    self.application = self.createOrGetApplication()
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/daemon.py", line 42, in createOrGetApplication
    return createApplication(self.config.get('rundir'), self.log_file)
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/daemon.py", line 23, in createApplication
    create=create)
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/env.py", line 102, in __init__
    self.update()
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/env.py", line 187, in update
    self.catalog.updateAllIndexViews()
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/xmlcatalog.py", line 343, in updateAllIndexViews
    self.index_catalog.updateIndexView(rt)
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/xmlindexcatalog.py", line 38, in updateIndexView
    query, joins = self._createIndexView(xmlindex_list[::-1])
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/xmlindexcatalog.py", line 89, in _createIndexView
    query, joins = self._joinIndexes(xmlindex_list, query)
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/xmlindexcatalog.py", line 225, in _joinIndexes
    idx_tab = idx._getElementCls().db_table.alias(keyval_label)
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/index.py", line 145, in _getElementCls
    return type_classes[self._getProcessorIndex().type]
  File "/data/userdata/richter/software/seishub_git/seishub.core/seishub/core/xmldb/index.py", line 155, in _getProcessorIndex
    mod = sys.modules[mod_name]
KeyError: u'seishub.plugins.seismology.package'

Well, I don't know if its an installation problem or a bug. I tried to initiate a new instance, too:

/home/richter% seishub-admin initenv ~/software/seihub_test/
Traceback (most recent call last):
  File "/usr/local/bin/seishub-admin", line 5, in <module>
    from pkg_resources import load_entry_point
  File "/home/richter/.local/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 2709, in <module>
    working_set.require(__requires__)
  File "/home/richter/.local/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 686, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/richter/.local/lib/python2.7/site-packages/distribute-0.6.21-py2.7.egg/pkg_resources.py", line 584, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: obspy.core>0.7.0

links to resources in web interface should be relative

Currently in the web interface panel Catalog>Resources links to single xml resources include a hard coded server name. This is annoying when tunneling ports and thus having some localhost address instead of the original server name. These links should be relative.

Quick Start or Tutorial for learning basic usage?

Is there any documentation for using seishub once it has been set up? It seems http://seishub.org/ is no longer there. Is seishub still supported?

specify latest working version of dependencies

I just installed seishub and its still working like a charm.

I had to downgrade some dependencies:
twisted<16 and zope.interface<4.1.

multiple schemas for one resource type

@barsch, @krischer currently, only one schema file can be stored per resource type. QuakeML bases on two separate schema files however.
I've tried to fix this here: https://github.com/barsch/seishub.core/blob/master/seishub/core/packages/installer.py#L58

                if env.registry.schemas.get(package_id, resourcetype_id, type):
                    msg = "Skipping Schema /%s/%s - %s"
                    msg = msg % (package_id, resourcetype_id, filename)
                    env.log.debug(msg)
                    continue

by checking against file name of the registered resources:

                to_skip = env.registry.schemas.get(package_id, resourcetype_id,
                                                   type)
                if any([str(x.getResource()).endswith(name) for x in to_skip]):

but then I get an error

WARN: ('Error storing an object.', IntegrityError('(IntegrityError) columns package_id, resourcetype_id, type are not unique',))

so I guess this case is not supported by the current setup. Where to fix this?

Activating seedfilemonitor

Hi all,

I've recently installed seishub.core as well as seishub.plugins.seismology (via 'setup.py install' as the PyPI method no longer functions) and started a test instance locally (using a postgre back-end).

I have a small directory of day-long miniseed files which I would like to index but I cannot seem to activate the seedfilemonitor service. I've added the following to my seishub.ini file:

[seedfilemonitor]
autostart = True
paths = /home/chet/data/test_mseed

But Seedfilemonitor doesn't appear in the 'Services' tab of the web interface as shown in @barsch 's dissertation (p. 25)

I'm obviously missing something. Any insight would be much appreciated.

Chet

numeric values of 0.0 in db

When indexing an xml resource, numeric values (e.g. magnitude) of 0.0 get stored as null/None/empty string in db.

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