the docs dev commented they couldn't replicate. And blamed it on our
> yeah. that's weird. I remember seeing this in the past, but thought it
> had been fixed.
>
> It looks like the non-index pages are generating responding with a 301
> 'moved permanently' response and appending a / to the URL
>
>> > curl -v --head
>> "
https://intermine.readthedocs.io/en/latest/database/data-sources/library/so"
>>
>> * Trying 137.116.78.48...
>> <snip>
>> > HEAD /en/latest/database/data-sources/library/so HTTP/1.1
>> > Host: intermine.readthedocs.io
>> > User-Agent: curl/7.60.0
>> > Accept: */*
>> >
>> < HTTP/1.1 301 Moved Permanently
>> HTTP/1.1 301 Moved Permanently
>> < Content-Length: 194
>> Content-Length: 194
>> < Content-Type: text/html
>> Content-Type: text/html
>> < Location:
>>
http://intermine.readthedocs.io/en/latest/database/data-sources/library/so/
>>
>> Location:
>>
http://intermine.readthedocs.io/en/latest/database/data-sources/library/so/
>>
>> < Server: nginx/1.14.0 (Ubuntu)
>> Server: nginx/1.14.0 (Ubuntu)
>> < X-Subdomain-TryFiles: True
>> X-Subdomain-TryFiles: True
>> < X-Served: Nginx
>> X-Served: Nginx
>> < X-Deity: web03
>> X-Deity: web03
>> < Date: Thu, 15 Nov 2018 16:44:46 GMT
>> Date: Thu, 15 Nov 2018 16:44:46 GMT
>>
>> <
>> * Connection #0 to host intermine.readthedocs.io left intact
>
> But URLs that point to /index respond with a 404 without any redirect.
> Are you running nginx as a proxy server or is it delivering content? It
> looks like the rewrite rules for index URL's needs a little tweaking.
>
>
> Joe
>
>>> Thanks for the updates.
>>>
>>> Another thing I noticed is a problem with the docs which has reared
>>> its ugly head again.
>>>
>>> Type ‘merging’ into the search box. The first two links I get are
>>> ‘Model Merging’ and ‘Data Model Overview’. These links work properly.
>>> But the third link ‘Database’ goes to a ‘SORRY This page does not
>>> exist yet’ error page.
>>>
>>> The issue seems to be that links that go to /path/to/page/index do
>>> not work, but /path/to/page/anything_else are OK. And, if you take
>>> /path/to/page/index and append .html to the URL, all is good.
>>>
>>> Joe
>>>
>>>> On Nov 14, 2018, at 2:24 AM, Julie Sullivan <
[hidden email]>
>>>> wrote:
>>>>
>>>> Thanks Joe! Really valuable feedback.
>>>>
>>>> I've updated the docs to reflect your comments, the instructions are
>>>> clearer now.
>>>>
>>>> On 13/11/2018 17:12, Joe Carlson wrote:
>>>>> Hi Julie,
>>>>> I think I see what my issues were. I was a bit confused by the docs.
>>>>> One issue was that the
>>>>>
https://intermine.readthedocs.io/en/latest/database/data-sources/custom/#run-make-source-script
>>>>> say make_source is invoked as ./make_source. But this script
>>>>> requires the skeletons directory below it and as far as I can tell
>>>>> needs to be invokes as /path/to/intermine-scripts/make_source.
>>>>> The second issue was that
>>>>>
https://intermine.readthedocs.io/en/latest/database/data-sources/custom/#global-additions-file
>>>>> refers to bio/sources/build.gradle. I was interpreting this as a
>>>>> path and kept looking for the sources folder inside bio. Perhaps
>>>>> this should be labeled as bio-sources or MYMINE-bio-sources, or
>>>>> something.
>>>>> And the final thing is that it seems that bioSourceDBModelConfig
>>>>> specific needs to be within the subprojects section of
>>>>> build.gradle. It I put it at top level, I get the 'Could not find
>>>>> method bioSourceDBModelConfig() for arguments...' error.
>>>>> Thanks,
>>>>> Joe
>>>>> On 11/13/18 1:06 AM, Julie Sullivan wrote:
>>>>>> Hi Joe
>>>>>>
>>>>>> The top level of your phytomine's bio/sources directory is the
>>>>>> correct placement for that additions file, and that parameter!
>>>>>> However the docs were out of date, I renamed that parameter to be:
>>>>>>
>>>>>> globalAdditionsFile
>>>>>>
>>>>>> because I thought it would be less confusing! :( I've now updated
>>>>>> the docs, apologies.
>>>>>>
>>>>>> You can look at flymine here:
>>>>>>
>>>>>>
https://github.com/intermine/flymine-bio-sources/blob/master/build.gradle#L70
>>>>>>
>>>>>>
>>>>>> globalAdditionsFile = "flymine-global_additions.xml"
>>>>>>
>>>>>> And that file (flymine-global_additions.xml) lives in the root
>>>>>> directory of flymine-bio-sources.
>>>>>>
>>>>>> Let me know if you have any more issues!
>>>>>> Julie
>>>>>>
>>>>>>
>>>>>> On 13/11/2018 01:49, Joe Carlson wrote:
>>>>>>> Hi Julie,
>>>>>>>
>>>>>>> I'm still migrating to gradle. I have a question about the global
>>>>>>> additions to the data model.
>>>>>>>
>>>>>>> You have this in the docs:
>>>>>>>
>>>>>>>
>>>>>>> Global Additions File
>>>>>>>
>>>>>>> Previously the data model was merged from all data sources’
>>>>>>> additions XML file (plus the SO terms, core and genomic
>>>>>>> additons). This is no longer true. Since each source is in its
>>>>>>> own JAR now, the data model is self-contained for each data
>>>>>>> source. Therefore if you reference a class in your data parser,
>>>>>>> it must be present in the additions file. Alternatively, you can
>>>>>>> specify a single data model file that will be merged into each
>>>>>>> source:
>>>>>>>
>>>>>>> //[in bio/sources/build.gradle]
>>>>>>> // uncomment to specify an extra additions filefor your bio-sources
>>>>>>> // this file will be merged with the additions filefor each
>>>>>>> datasource
>>>>>>> // and included in eachsource JAR.
>>>>>>> //bioSourceDBModelConfig{
>>>>>>> //extraAdditionsFile = "MY-MINE_additions.xml"
>>>>>>> //}
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> which build.gradle file are you referring to? I have a directory
>>>>>>> phytomine/ from the make_mine script; I assumed it was in this
>>>>>>> build.gradle file (there is not a bio/sources/ directory below
>>>>>>> this.), but trying to build the db was giving the message "Could
>>>>>>> not find method bioSourceDBModelConfig()". Also tried to put it
>>>>>>> in the top level of my phytomine-bio-sources. Same story.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Joe
>>>>>>>
>>>>>>> On 11/5/18 12:17 AM, Julie Sullivan wrote:
>>>>>>>> Hi Joe!
>>>>>>>>
>>>>>>>> 1. Yes, this is on purpose (for Travis) but you can have a local
>>>>>>>> biotestmine.properties that will be used instead of the default:
>>>>>>>>
>>>>>>>>
https://github.com/intermine/biotestmine/blob/master/setup.sh#L80>>>>>>>>
>>>>>>>> So the default properties file has localhost, but you can use
>>>>>>>> your own properties file if you need different settings. Is that
>>>>>>>> sufficient? Again, this script was written for travis but I can
>>>>>>>> update.
>>>>>>>>
>>>>>>>> 2. Whoops! Yes, sorry, reverted now. Just testing 3.0 and got
>>>>>>>> overzealous. You are right, 2.1.1 is the latest release.
>>>>>>>>
>>>>>>>> You are not doing anything wrong! :)
>>>>>>>> Julie
>>>>>>>>
>>>>>>>> On 02/11/2018 22:25, Joe Carlson wrote:
>>>>>>>>> Hi Julie,
>>>>>>>>>
>>>>>>>>> I'm back looking at the gradle build. A couple other things
>>>>>>>>> popped up:
>>>>>>>>>
>>>>>>>>> 1) setup.sh in biotestmine is also not coded for a
>>>>>>>>> non-localhost postgres server.
>>>>>>>>>
>>>>>>>>> 2) the more puzzling thing (for me, at least) is that
>>>>>>>>> gradle.properties specifies intermine plugin version 3.0+. From
>>>>>>>>> what I see, these have not been uploaded to jcenter (2.1.1
>>>>>>>>> seems to be the latest).
>>>>>>>>>
>>>>>>>>> Or am I doing something wrong here?
>>>>>>>>>
>>>>>>>>> Joe
>>>>>>>>>
>>>>>>>>> On 10/23/2018 02:26 AM, Julie Sullivan wrote:
>>>>>>>>>> 1. Whoops, yes, thanks for that. I'll fix. We only use
>>>>>>>>>> testmine for travis so I didn't catch that -- but that makes
>>>>>>>>>> sense to use testmine on not-localhost.
>>>>>>>>>>
>>>>>>>>>> 2. Thanks for the fix! Not sure why you are seeing this error
>>>>>>>>>> and we aren't though.
>>>>>>>>>>
>>>>>>>>>> On 20/10/18 00:54, Joe Carlson wrote:
>>>>>>>>>>> Hello,
>>>>>>>>>>>
>>>>>>>>>>> I'm (finally) trying to build InterMine 2.0. But a couple of
>>>>>>>>>>> things have popped up when I tried your testmine demo:
>>>>>>>>>>>
>>>>>>>>>>> 1) The testmine demo does not appear to use anything other
>>>>>>>>>>> than localhost for the db server. There are a couple edits
>>>>>>>>>>> needed in setup.sh and testmodel.properties:
>>>>>>>>>>>
>>>>>>>>>>>> testmine> git diff dbmodel/resources/testmodel.properties
>>>>>>>>>>>> diff --git a/testmine/dbmodel/resources/testmodel.properties
>>>>>>>>>>>> b/testmine/dbmodel/resources/testmodel.properties
>>>>>>>>>>>> index e3ae168..488bcd2 100644
>>>>>>>>>>>> --- a/testmine/dbmodel/resources/testmodel.properties
>>>>>>>>>>>> +++ b/testmine/dbmodel/resources/testmodel.properties
>>>>>>>>>>>> @@ -1,9 +1,9 @@
>>>>>>>>>>>> -db.userprofile-test.datasource.serverName=localhost
>>>>>>>>>>>> +db.userprofile-test.datasource.serverName=SERVER
>>>>>>>>>>>> db.userprofile-test.datasource.databaseName=userprofile-demo
>>>>>>>>>>>> db.userprofile-test.datasource.user=PSQL_USER
>>>>>>>>>>>> db.userprofile-test.datasource.password=PSQL_PWD
>>>>>>>>>>>>
>>>>>>>>>>>> -db.unittest.datasource.serverName=localhost
>>>>>>>>>>>> +db.unittest.datasource.serverName=SERVER
>>>>>>>>>>>> db.unittest.datasource.databaseName=intermine-demo
>>>>>>>>>>>> db.unittest.datasource.user=PSQL_USER
>>>>>>>>>>>> db.unittest.datasource.password=PSQL_PWD
>>>>>>>>>>>> testmine> git diff setup.sh
>>>>>>>>>>>> diff --git a/testmine/setup.sh b/testmine/setup.sh
>>>>>>>>>>>> index 0d13f74..41bee60 100755
>>>>>>>>>>>> --- a/testmine/setup.sh
>>>>>>>>>>>> +++ b/testmine/setup.sh
>>>>>>>>>>>> @@ -74,11 +74,11 @@ fi
>>>>>>>>>>>>
>>>>>>>>>>>> echo "------> Checking databases..."
>>>>>>>>>>>> for db in $USERPROFILEDB $PRODDB; do
>>>>>>>>>>>> - if psql --list | egrep -q '\s'$db'\s'; then
>>>>>>>>>>>> + if psql -h $SERVER --list | egrep -q '\s'$db'\s'; then
>>>>>>>>>>>> echo $db exists.
>>>>>>>>>>>> else
>>>>>>>>>>>> echo Creating $db
>>>>>>>>>>>> - createdb $db
>>>>>>>>>>>> + createdb -h $SERVER -E UTF8 $db
>>>>>>>>>>>> fi
>>>>>>>>>>>> done
>>>>>>>>>>>
>>>>>>>>>>> (you want a pull request?)
>>>>>>>>>>>
>>>>>>>>>>> 2) The other thing is that the build tripping over UTF-8
>>>>>>>>>>> characters. There are a couple in the source comments (those
>>>>>>>>>>> are trivial), but the more important one was that I got an
>>>>>>>>>>> 'invalid byte sequence error' when inserting names; I assume
>>>>>>>>>>> it's Robert?? Setting the environment variable
>>>>>>>>>>> JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8 appears to have fixed
>>>>>>>>>>> that.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Joe
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> dev mailing list
>>>>>>>>>>>
[hidden email]
>>>>>>>>>>>
https://lists.intermine.org/mailman/listinfo/dev>>>>>>>>>
>>>
Locked
