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The tissue package is now in Guix upstream and longer in the
guix-forge channel.
* genenetwork-development.scm: Import tissue from (gnu packages web).
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* genenetwork-development.scm (build-xapian-index-gexp): Provide MySQL
URI to the xapian indexing script.
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We ought to share the mysqld socket directory into the container, not
the socket itself. If we only shared the socket, when the mysql server
is restarted and a new socket is created, the bind mounting into the
container would break and the container would need to be restarted.
* genenetwork-development-deploy.sh: Share /var/run/mysqld, not
/var/run/mysqld/mysqld.sock.
* genenetwork-development.scm (genenetwork-shepherd-services): Share
/run/mysqld, not /run/mysqld/mysqld.sock.
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*
genenetwork-development.scm (<genenetwork-configuration>)[data-directory]:
New field.
(genenetwork3-cd-gexp): Set DATA_DIR in settings file.
(genenetwork-shepherd-services): Map data directory into container.
(operating-system)[services]: Set data-directory of genenetwork
service to /export/data/genenetwork.
* genenetwork-development-deploy.sh: Expose entire data directory
/export/data/genenetwork instead of the contained genotype files
directory.
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* genenetwork-development.scm (%xapian-directory): Move from
/export/data/genenetwork/xapian to /export/data/genenetwork-xapian.
* genenetwork-development-deploy.sh (container_script): Share
/export/data/genenetwork-xapian instead of
/export/data/genenetwork/xapian.
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* genenetwork-development.scm (build-xapian-index-gexp): Clean up
xapian build directory if previous build failed to.
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This 502 error page is more informative than a generic "Bad Gateway"
error message. It tells the user that the CD is down but not the
entire container itself.
* genenetwork-development.scm: Import guile-lib from (gnu packages
guile-xyz).
(%ci-domain): New variable.
(cd-error-pages-gexp): New function.
(development-server-reverse-proxy-server-block):
Use (cd-error-pages-gexp) to construct error pages.
(laminar-reverse-proxy-server-block): Use %ci-domain.
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* genenetwork-development.scm: Import (gnu services mcron).
(%xapian-directory): New variable.
(build-xapian-index-gexp): New function.
(genenetwork-projects): Add genenetwork3-build-xapian-index CI job to
genenetwork3 project.
(operating-system)[sudoers-file]: Allow laminar user to start and stop
genenetwork3.
[services]: Add mcron service to trigger nightly xapian build. Use
%xapian-directory instead of its literal value. chown
%xapian-directory to the laminar user.
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* genenetwork-development.scm (genenetwork-projects): Separate out
"/run/setuid-programs/sudo" into ...
(sudo): ... new variable.
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* genenetwork-development.scm: use pytest rather than unittest to run
the tests.
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*
genenetwork-development.scm (<genenetwork-configuration>)[sparql-endpoint]:
New field.
(genenetwork3-cd-gexp): Set SPARQL_ENDPOINT in gn3.conf.
(%virtuoso-sparql-port): New variable.
(operating-system)[services]: Configure sparql-endpoint of genenetwork
service.
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In the interest of good organization, we keep all CD ports at
90*. Production and other services can use ports outside this range.
* genenetwork-development.scm (operating-system)[services]: Move
virtuoso ports from 8891, 8892 to 9081, 9082.
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* genenetwork-development.scm (dump-genenetwork-database): Import
GeneRIF by calling the unified dump script.
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* genenetwork-development.scm (dump-genenetwork-database): Find
GeneRIF data in root of export directory.
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* genenetwork-development.scm (dump-genenetwork-database): Use
guile-zlib.
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* genenetwork-development.scm (genenetwork2-tests): Ungexp
gn2-repository and gn3-repository correctly.
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* genenetwork-development.scm (genenetwork-projects): Import (guix
build utils) in after scripts of CI jobs.
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* genenetwork-development.scm (dump-genenetwork-database): Import
GeneRIF into RDF.
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We unite the genenetwork2 and genenetwork3 development servers into
a single Guix service. This unifies many of the configuration
settings and simplifies the configuration. Changes to the genenetwork3
repository also immediately reflect in the genenetwork2 continuous
deployment without guix-bioinformatics having to be updated.
* genenetwork-development.scm (<development-server-configuration>):
Delete type.
(<genenetwork-configuration>): New type.
(development-server-redeploy, development-server-activation,
genenetwork2-project, genenetwork2-shepherd-service,
genenetwork3-project, genenetwork3-shepherd-service): Delete
functions.
(genenetwork2-tests): Accept <genenetwork-configuration> object
instead of <forge-project> object.
(%genotype-files, %xapian-db-path,
%default-genenetwork2-configuration, genenetwork2-service-type,
%default-genenetwork3-configuration, genenetwork3-service-type):
Delete variables.
(genenetwork-projects, genenetwork2-cd-gexp, genenetwork3-cd-gexp,
genenetwork-shepherd-services): New functions.
(operating-system)[services]: Replace genenetwork2 and genenetwork3
services with the unified genenetwork service.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp,
genenetwork3-runner-gexp): Delete functions.
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* genenetwork-development.scm (genenetwork2-shepherd-service): Do not
expose xapian index.
(genenetwork3-shepherd-service): Expose xapian index.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp): Do
not accept xapian index argument.
(genenetwork3-runner-gexp): Accept config file argument.
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*
genenetwork-development.scm (dump-genenetwork-database-project)[repository]:
Use GitHub URI.
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This was a typo.
* genenetwork-development.scm (genenetwork3-project)[ci-jobs]: Trigger
genenetwork2 using laminar, not shepherd.
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* genenetwork-development.scm: Import (forge socket).
(operating-system)[services]: Use <forge-ip-socket> object to specify
webhook port.
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* genenetwork-development.scm: Import (gnu build
linux-container), (gnu system file-systems) and (guix
least-authority).
(genenetwork2-shepherd-service, genenetwork3-shepherd-service):
Deprecate make-forkexec-constructor/container in favor of
least-authority-wrapper.
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Since genenetwork2 depends on genenetwork3, updates to genenetwork3
should trigger the genenetwork2 tests.
* genenetwork-development.scm (genenetwork3-project): Trigger
genenetwork2 tests after genenetwork3 tests.
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* genenetwork-development.scm (genenetwork2-project): Comment about
triggering of Mechanical Rob after genenetwork2 tests.
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* genenetwork-development.scm (genenetwork2-shepherd-service): Convert
port number to string on the host, not on the build side.
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So far, whenever genenetwork2 code needed the latest updates from
genenetwork3, the guix-bioinformatics channel had to be updated and
the development container had to be rebuilt. No more. From now on, the
latest genenetwork3 code will be pulled in at all times. The
development container need only be rebuilt when the dependencies of
genenetwork2 or genenetwork3 change. We may revisit this decision once
genenetwork2 and genenetwork3 are better decoupled and we have
semantically versioned releases.
* genenetwork-development.scm (genenetwork2-tests): Pull in latest
genenetwork3 when running genenetwork2 tests.
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* genenetwork-development.scm (%xapian-db-path): New variable.
(genenetwork2-shepherd-service)[start]: Share %xapian-db-path with the
container.
(%default-genenetwork2-configuration)[runner]: Pass %xapian-db-path to
CD runner.
* genenetwork/development-helper.scm (genenetwork2-runner-gexp):
Accept xapian-db-path argument and set XAPIAN_DB_PATH environment
variable.
* genenetwork-development-deploy.sh: Expose
/export/data/genenetwork/xapian in the container.
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* genenetwork-development.scm (genenetwork2-project)[ci-jobs]: Use
pytest instead of unittest.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
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The upstream laminar package now uses git-fetch instead of
url-fetch. Hence, we must adapt our laminar template G-expression.
* genenetwork-development.scm (laminar-template-gexp): Copy
/src/resources/index.html from git source instead of extracting it
from a tarball.
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* genenetwork-development.scm (laminar-template-gexp): Link to
continuous deployment from the navigation menu.
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* genenetwork-development.scm (%genenetwork2-port): New variable.
(genenetwork2-project): Use %genenetwork2-port.
(development-server-reverse-proxy-server-block): New function.
(operating-system)[services]: Use %genenetwork2-port. Add reverse
proxy block for cd.genenetwork.org.
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* genenetwork-development.scm (genenetwork2-tests): Use
%genenetwork3-port.
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* genenetwork-development.scm (%webhook-port): New variable.
(laminar-server-reverse-proxy-server-block): Expose webhook under
/hooks/.
(operating-system)[services]: Use %webhook-port.
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* genenetwork-development.scm (laminar-reverse-proxy-server-block):
Set host name of the laminar nginx server.
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The guix channel is a dependency of the gn-bioinformatics
channel. Therefore, it is always implicitly present.
* genenetwork-development.scm (operating-system)[services]: Do not
list guix channel in CI published channels.scm.
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The gn-gemtext-threads forge project does not need a website
directory. Its website is completely managed by the tissue service.
*
genenetwork-development.scm (gn-gemtext-threads-project)[website-directory]:
Remove.
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* genenetwork-development.scm (%genenetwork-accounts): New variable.
(genenetwork2-shepherd-service, genenetwork3-shepherd-service): Run as
genenetwork user and group.
(genenetwork2-service-type, genenetwork3-service-type): Create
genenetwork user and group.
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* genenetwork-development.scm: Add copyright line for Frederick
Muriuki Muriithi.
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* genenetwork-development.scm (genenetwork2-shepherd-service,
genenetwork3-shepherd-service): Move log files into /var/log/cd.
* genenetwork-development-deploy.sh: Share /var/log/cd with host.
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The urljoin function reduces a URL without a trailing slash to just
the base, e.g. "http://genenetwork.org/gn3-proxy" is reduced to
"http://genenetwork.org", which is not what we want.
* genenetwork-development.scm (genenetwork2-tests): Add trailing slash
to GN_PROXY_URL.
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* genenetwork-development.scm (genenetwork3-shepherd-service): Map
mysqld socket into the container.
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* genenetwork-development.scm (tissue-reverse-proxy-server-block):
Support URIs without the html extension.
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* genenetwork-development-deploy.sh: Share tissue state directory with
container.
* genenetwork-development.scm: Do not import tissue from (gn packages
gemini). Import (forge tissue).
(<tissue-configuration>, <tissue-host>): Delete types.
(%tissue-accounts, tissue-service-type): Delete variables.
(gn-gemtext-threads-website, gn-gemtext-threads-index,
tissue-conf-gexp, tissue-shepherd-service): Delete functions.
(gn-gemtext-threads-project)[ci-jobs]: Use tissue pull in
gn-gemtext-threads job.
(tissue-reverse-proxy-server-block): Use default tissue state
directory and unix socket paths. Do not accept them as arguments.
(operating-system)[services]: Use new tissue-service-type
parameters. Update invocation of tissue-reverse-proxy-server-block.
* genenetwork/development-helper.scm (tissue-website-gexp,
tissue-index-gexp): Delete functions.
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* genenetwork-development.scm (<tissue-configuration>)[address, port,
indexed-repository]: Delete fields.
[listen, hosts]: New fields.
* genenetwork-development.scm (<tissue-host>): New type.
(tissue-conf-gexp): New function.
(tissue-shepherd-service): Remove --address and --port
arguments. Compute and pass tissue.conf configuration file. Create
file system mappings for all hosts.
(operating-system)[services]: Use new tissue-configuration fields.
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* genenetwork-development.scm: Import shadow from (gnu packages
admin).
(gn-gemtext-threads-index): New function.
(gn-gemtext-threads-project)[ci-jobs]: Add gn-gemtext-threads-index.
(<tissue-configuration>): New type.
(tissue-shepherd-service, tissue-reverse-proxy-server-block): New
function.
(%tissue-accounts, tissue-service-type): New variables.
(operating-system)[services]: Add tissue tissue service and reverse
proxy it.
* genenetwork/development-helper.scm (tissue-index-gexp): New
function.
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tissue now uses libgit2 through guile-git and does not use the git CLI
tool.
* genenetwork-development.scm (gn-gemtext-threads-website): Remove
git-minimal from manifest.
* genenetwork/development-helper.scm (tissue-website-gexp): Remove
reassurance to git.
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This was missed out in 96fb9608242254a1fc53bbd71168db4245458c8f.
* genenetwork-development.scm (dump-genenetwork-database):
Import (srfi srfi-26).
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The --ignore-errors flag not only avoids printing triples, but also
actually ignores errors. What a surprise! ;-) As a result, rapper does
not stop invalid turtle files, and they end up erroring out when
uploaded to virtuoso.
* genenetwork-development.scm (dump-genenetwork-database): Send rapper
output to /dev/null instead of using --ignore-errors.
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