JBrowse problem: Could not load reference sequence definitions

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JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang

Dear InterMiners,

The FAWmine has been successfully deployed (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108) with the following message:

It said that "Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404.".

I have committed the project to github for your checking https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources.

Thank you and best,

Pengcheng Yang



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Re: JBrowse problem: Could not load reference sequence definitions

sergio contrino-2
dear Pengcheng,
have you installed jbrowse (as illustrated here
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
?
if you did already, could you send us also your fawnmine.properties in
your .intermine directory?
thanks!
sergio


On 10/02/2020 04:15, Pengcheng Yang wrote:

> Dear InterMiners,
>
> The FAWmine has been successfully deployed
> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work
> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
> with the following message:
>
> It said that "Could not load reference sequence definitions.
> RequestError: Unable to load
> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
> status: 404.".
>
> I have committed the project to github for your checking
> https://github.com/pengchy/fawmine and
> https://github.com/pengchy/fawmine-bio-sources.
>
> Thank you and best,
>
> Pengcheng Yang
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang
Hi sergio,

Thank you for your reply. Below is the content of my fawmine.properties
and fawmine.properties.beta in the ~/.intermine directory.

best,

Pengcheng


====================== fawmine.properties =========================
# if true will log details about execution time of every query
os.production.verboseQueryLog=true

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawmine
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is
complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawmine
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx

================= fawmine.properties.beta================

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawminebeta
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is
complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawminebeta
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx


# userprofile database - used by the webapp to store logins, query history,
# saved bags, templates and tags.
db.userprofile-production.datasource.serverName=localhost
db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
db.userprofile-production.datasource.user=postgres
db.userprofile-production.datasource.password=xxxx

# files for ID resolvers
#resolver.file.rootpath=/DATA/idresolver

#####################
# webapp properties #
#####################

# Web application deployment properties

# location of tomcat server and path of webapp - e.g. access
http://localhost:8080/malariamine
webapp.deploy.url=http://insectmine.org:8080
webapp.path=fawmine

# tomcat username and password needed to deploy webapp
webapp.manager=manager
webapp.password=xxxx

# 'Home' link
webapp.baseurl=http://insectmine.org:8080

# account name for superuser (who can edit appearance and publish templates)
superuser.account=[hidden email]
superuser.initialPassword=xxxx

# run with no associated web site
project.standalone=true

# details for sending login e-mails
mail.host=localhost
mail.from=[hidden email]
mail.subject=Welcome to FAWMine
mail.text="Dear users\nYou have successfully created an account on
FAWMine. Please don't hesitate to feed back any of your suggestions for
the improvement of FAWMine.\nBest,\nPengcheng Yang\n"

# text that appears in the header and elsewhere
project.title=FAWMine
project.subTitle=An integrated Omics data warehouse for FAW,
<i>Spodoptera frugiperda </i>
project.releaseVersion=1.0

# various URLs use this as the prefix
project.sitePrefix=http://insectmine.org:8080/fawmine
project.helpLocation=http://www.flymine.org/help

# recipient of feedback form located on bottom of every page
feedback.destination = [hidden email]

inline.collections.in.tables = true



On 2020-2-10 20:04, sergio contrino wrote:

> dear Pengcheng,
> have you installed jbrowse (as illustrated here
> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
> ?
> if you did already, could you send us also your fawnmine.properties in
> your .intermine directory?
> thanks!
> sergio
>
>
> On 10/02/2020 04:15, Pengcheng Yang wrote:
>> Dear InterMiners,
>>
>> The FAWmine has been successfully deployed
>> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work
>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
>> with the following message:
>>
>> It said that "Could not load reference sequence definitions.
>> RequestError: Unable to load
>> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
>> status: 404.".
>>
>> I have committed the project to github for your checking
>> https://github.com/pengchy/fawmine and
>> https://github.com/pengchy/fawmine-bio-sources.
>>
>> Thank you and best,
>>
>> Pengcheng Yang
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>>
>

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Re: JBrowse problem: Could not load reference sequence definitions

sergio contrino-2
dear Pengcheng,
please add the link to your jbrowse installation in the properties file.

jbrowse.install.url = http://your.jbrowse/installation

(unless it is already in your mine web.properties)
please let me know
thanks
sergio


On 10/02/2020 14:10, Pengcheng Yang wrote:

> Hi sergio,
>
> Thank you for your reply. Below is the content of my fawmine.properties
> and fawmine.properties.beta in the ~/.intermine directory.
>
> best,
>
> Pengcheng
>
>
> ====================== fawmine.properties =========================
> # if true will log details about execution time of every query
> os.production.verboseQueryLog=true
>
> # Access to the postgres database to build into and access from the webapp
> db.production.datasource.serverName=localhost
> db.production.datasource.databaseName=fawmine
> db.production.datasource.user=postgres
> db.production.datasource.password=xxxx
>
> # Temporary database used during the build process, this is re-built
> # as sources are loaded and can be discarded once the warehouse build is
> complete
> # It uses the InterMine 'items' metadata format to describe objects.
>
> # common target items database
> db.common-tgt-items.datasource.serverName=localhost
> db.common-tgt-items.datasource.databaseName=items-fawmine
> db.common-tgt-items.datasource.user=postgres
> db.common-tgt-items.datasource.password=xxxx
>
> ================= fawmine.properties.beta================
>
> # Access to the postgres database to build into and access from the webapp
> db.production.datasource.serverName=localhost
> db.production.datasource.databaseName=fawminebeta
> db.production.datasource.user=postgres
> db.production.datasource.password=xxxx
>
> # Temporary database used during the build process, this is re-built
> # as sources are loaded and can be discarded once the warehouse build is
> complete
> # It uses the InterMine 'items' metadata format to describe objects.
>
> # common target items database
> db.common-tgt-items.datasource.serverName=localhost
> db.common-tgt-items.datasource.databaseName=items-fawminebeta
> db.common-tgt-items.datasource.user=postgres
> db.common-tgt-items.datasource.password=xxxx
>
>
> # userprofile database - used by the webapp to store logins, query history,
> # saved bags, templates and tags.
> db.userprofile-production.datasource.serverName=localhost
> db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
> db.userprofile-production.datasource.user=postgres
> db.userprofile-production.datasource.password=xxxx
>
> # files for ID resolvers
> #resolver.file.rootpath=/DATA/idresolver
>
> #####################
> # webapp properties #
> #####################
>
> # Web application deployment properties
>
> # location of tomcat server and path of webapp - e.g. access
> http://localhost:8080/malariamine
> webapp.deploy.url=http://insectmine.org:8080
> webapp.path=fawmine
>
> # tomcat username and password needed to deploy webapp
> webapp.manager=manager
> webapp.password=xxxx
>
> # 'Home' link
> webapp.baseurl=http://insectmine.org:8080
>
> # account name for superuser (who can edit appearance and publish
> templates)
> superuser.account=[hidden email]
> superuser.initialPassword=xxxx
>
> # run with no associated web site
> project.standalone=true
>
> # details for sending login e-mails
> mail.host=localhost
> mail.from=[hidden email]
> mail.subject=Welcome to FAWMine
> mail.text="Dear users\nYou have successfully created an account on
> FAWMine. Please don't hesitate to feed back any of your suggestions for
> the improvement of FAWMine.\nBest,\nPengcheng Yang\n"
>
> # text that appears in the header and elsewhere
> project.title=FAWMine
> project.subTitle=An integrated Omics data warehouse for FAW,
> <i>Spodoptera frugiperda </i>
> project.releaseVersion=1.0
>
> # various URLs use this as the prefix
> project.sitePrefix=http://insectmine.org:8080/fawmine
> project.helpLocation=http://www.flymine.org/help
>
> # recipient of feedback form located on bottom of every page
> feedback.destination = [hidden email]
>
> inline.collections.in.tables = true
>
>
>
> On 2020-2-10 20:04, sergio contrino wrote:
>> dear Pengcheng,
>> have you installed jbrowse (as illustrated here
>> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
>> ?
>> if you did already, could you send us also your fawnmine.properties in
>> your .intermine directory?
>> thanks!
>> sergio
>>
>>
>> On 10/02/2020 04:15, Pengcheng Yang wrote:
>>> Dear InterMiners,
>>>
>>> The FAWmine has been successfully deployed
>>> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work
>>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
>>> with the following message:
>>>
>>> It said that "Could not load reference sequence definitions.
>>> RequestError: Unable to load
>>> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
>>> status: 404.".
>>>
>>> I have committed the project to github for your checking
>>> https://github.com/pengchy/fawmine and
>>> https://github.com/pengchy/fawmine-bio-sources.
>>>
>>> Thank you and best,
>>>
>>> Pengcheng Yang
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang
Dear sergio,

I have add the link to the jbrose installation in the web.properties
file. In the gene report page
(http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got the
JBrowse link that center on that gene
(http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene).
In this link, you could find that the JBrowse installation directory is
"http://insectmine.org/jbrowse/".

Thank you for your kind help.

pengcheng

On 2020-2-10 22:46, sergio contrino wrote:

> dear Pengcheng,
> please add the link to your jbrowse installation in the properties file.
>
> jbrowse.install.url = http://your.jbrowse/installation
>
> (unless it is already in your mine web.properties)
> please let me know
> thanks
> sergio
>
>
> On 10/02/2020 14:10, Pengcheng Yang wrote:
>> Hi sergio,
>>
>> Thank you for your reply. Below is the content of my
>> fawmine.properties and fawmine.properties.beta in the ~/.intermine
>> directory.
>>
>> best,
>>
>> Pengcheng
>>
>>
>> ====================== fawmine.properties =========================
>> # if true will log details about execution time of every query
>> os.production.verboseQueryLog=true
>>
>> # Access to the postgres database to build into and access from the
>> webapp
>> db.production.datasource.serverName=localhost
>> db.production.datasource.databaseName=fawmine
>> db.production.datasource.user=postgres
>> db.production.datasource.password=xxxx
>>
>> # Temporary database used during the build process, this is re-built
>> # as sources are loaded and can be discarded once the warehouse build
>> is complete
>> # It uses the InterMine 'items' metadata format to describe objects.
>>
>> # common target items database
>> db.common-tgt-items.datasource.serverName=localhost
>> db.common-tgt-items.datasource.databaseName=items-fawmine
>> db.common-tgt-items.datasource.user=postgres
>> db.common-tgt-items.datasource.password=xxxx
>>
>> ================= fawmine.properties.beta================
>>
>> # Access to the postgres database to build into and access from the
>> webapp
>> db.production.datasource.serverName=localhost
>> db.production.datasource.databaseName=fawminebeta
>> db.production.datasource.user=postgres
>> db.production.datasource.password=xxxx
>>
>> # Temporary database used during the build process, this is re-built
>> # as sources are loaded and can be discarded once the warehouse build
>> is complete
>> # It uses the InterMine 'items' metadata format to describe objects.
>>
>> # common target items database
>> db.common-tgt-items.datasource.serverName=localhost
>> db.common-tgt-items.datasource.databaseName=items-fawminebeta
>> db.common-tgt-items.datasource.user=postgres
>> db.common-tgt-items.datasource.password=xxxx
>>
>>
>> # userprofile database - used by the webapp to store logins, query
>> history,
>> # saved bags, templates and tags.
>> db.userprofile-production.datasource.serverName=localhost
>> db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
>>
>> db.userprofile-production.datasource.user=postgres
>> db.userprofile-production.datasource.password=xxxx
>>
>> # files for ID resolvers
>> #resolver.file.rootpath=/DATA/idresolver
>>
>> #####################
>> # webapp properties #
>> #####################
>>
>> # Web application deployment properties
>>
>> # location of tomcat server and path of webapp - e.g. access
>> http://localhost:8080/malariamine
>> webapp.deploy.url=http://insectmine.org:8080
>> webapp.path=fawmine
>>
>> # tomcat username and password needed to deploy webapp
>> webapp.manager=manager
>> webapp.password=xxxx
>>
>> # 'Home' link
>> webapp.baseurl=http://insectmine.org:8080
>>
>> # account name for superuser (who can edit appearance and publish
>> templates)
>> superuser.account=[hidden email]
>> superuser.initialPassword=xxxx
>>
>> # run with no associated web site
>> project.standalone=true
>>
>> # details for sending login e-mails
>> mail.host=localhost
>> mail.from=[hidden email]
>> mail.subject=Welcome to FAWMine
>> mail.text="Dear users\nYou have successfully created an account on
>> FAWMine. Please don't hesitate to feed back any of your suggestions
>> for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"
>>
>> # text that appears in the header and elsewhere
>> project.title=FAWMine
>> project.subTitle=An integrated Omics data warehouse for FAW,
>> <i>Spodoptera frugiperda </i>
>> project.releaseVersion=1.0
>>
>> # various URLs use this as the prefix
>> project.sitePrefix=http://insectmine.org:8080/fawmine
>> project.helpLocation=http://www.flymine.org/help
>>
>> # recipient of feedback form located on bottom of every page
>> feedback.destination = [hidden email]
>>
>> inline.collections.in.tables = true
>>
>>
>>
>> On 2020-2-10 20:04, sergio contrino wrote:
>>> dear Pengcheng,
>>> have you installed jbrowse (as illustrated here
>>> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
>>> ?
>>> if you did already, could you send us also your fawnmine.properties
>>> in your .intermine directory?
>>> thanks!
>>> sergio
>>>
>>>
>>> On 10/02/2020 04:15, Pengcheng Yang wrote:
>>>> Dear InterMiners,
>>>>
>>>> The FAWmine has been successfully deployed
>>>> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't
>>>> work
>>>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
>>>> with the following message:
>>>>
>>>> It said that "Could not load reference sequence definitions.
>>>> RequestError: Unable to load
>>>> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
>>>> status: 404.".
>>>>
>>>> I have committed the project to github for your checking
>>>> https://github.com/pengchy/fawmine and
>>>> https://github.com/pengchy/fawmine-bio-sources.
>>>>
>>>> Thank you and best,
>>>>
>>>> Pengcheng Yang
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>
>>>
>>
>

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Re: JBrowse problem: Could not load reference sequence definitions

sergio contrino-2
dear pengcheng

i think you are missing the setup of your mine datasources in the
jbrowse installation. you would need to just edit one file,
jbrowse_conf.json

please check the
Point JBrowse at your InterMine
section in
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/

your jbrowse url should return something like ours
https://jbrowse.intermine.org
(i assume with only one reference to fawnmine)
thanks
sergio

On 10/02/2020 15:48, Pengcheng Yang wrote:

> Dear sergio,
>
> I have add the link to the jbrose installation in the web.properties
> file. In the gene report page
> (http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got the
> JBrowse link that center on that gene
> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene).
> In this link, you could find that the JBrowse installation directory is
> "http://insectmine.org/jbrowse/".
>
> Thank you for your kind help.
>
> pengcheng
>
> On 2020-2-10 22:46, sergio contrino wrote:
>> dear Pengcheng,
>> please add the link to your jbrowse installation in the properties file.
>>
>> jbrowse.install.url = http://your.jbrowse/installation
>>
>> (unless it is already in your mine web.properties)
>> please let me know
>> thanks
>> sergio
>>
>>
>> On 10/02/2020 14:10, Pengcheng Yang wrote:
>>> Hi sergio,
>>>
>>> Thank you for your reply. Below is the content of my
>>> fawmine.properties and fawmine.properties.beta in the ~/.intermine
>>> directory.
>>>
>>> best,
>>>
>>> Pengcheng
>>>
>>>
>>> ====================== fawmine.properties =========================
>>> # if true will log details about execution time of every query
>>> os.production.verboseQueryLog=true
>>>
>>> # Access to the postgres database to build into and access from the
>>> webapp
>>> db.production.datasource.serverName=localhost
>>> db.production.datasource.databaseName=fawmine
>>> db.production.datasource.user=postgres
>>> db.production.datasource.password=xxxx
>>>
>>> # Temporary database used during the build process, this is re-built
>>> # as sources are loaded and can be discarded once the warehouse build
>>> is complete
>>> # It uses the InterMine 'items' metadata format to describe objects.
>>>
>>> # common target items database
>>> db.common-tgt-items.datasource.serverName=localhost
>>> db.common-tgt-items.datasource.databaseName=items-fawmine
>>> db.common-tgt-items.datasource.user=postgres
>>> db.common-tgt-items.datasource.password=xxxx
>>>
>>> ================= fawmine.properties.beta================
>>>
>>> # Access to the postgres database to build into and access from the
>>> webapp
>>> db.production.datasource.serverName=localhost
>>> db.production.datasource.databaseName=fawminebeta
>>> db.production.datasource.user=postgres
>>> db.production.datasource.password=xxxx
>>>
>>> # Temporary database used during the build process, this is re-built
>>> # as sources are loaded and can be discarded once the warehouse build
>>> is complete
>>> # It uses the InterMine 'items' metadata format to describe objects.
>>>
>>> # common target items database
>>> db.common-tgt-items.datasource.serverName=localhost
>>> db.common-tgt-items.datasource.databaseName=items-fawminebeta
>>> db.common-tgt-items.datasource.user=postgres
>>> db.common-tgt-items.datasource.password=xxxx
>>>
>>>
>>> # userprofile database - used by the webapp to store logins, query
>>> history,
>>> # saved bags, templates and tags.
>>> db.userprofile-production.datasource.serverName=localhost
>>> db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
>>>
>>> db.userprofile-production.datasource.user=postgres
>>> db.userprofile-production.datasource.password=xxxx
>>>
>>> # files for ID resolvers
>>> #resolver.file.rootpath=/DATA/idresolver
>>>
>>> #####################
>>> # webapp properties #
>>> #####################
>>>
>>> # Web application deployment properties
>>>
>>> # location of tomcat server and path of webapp - e.g. access
>>> http://localhost:8080/malariamine
>>> webapp.deploy.url=http://insectmine.org:8080
>>> webapp.path=fawmine
>>>
>>> # tomcat username and password needed to deploy webapp
>>> webapp.manager=manager
>>> webapp.password=xxxx
>>>
>>> # 'Home' link
>>> webapp.baseurl=http://insectmine.org:8080
>>>
>>> # account name for superuser (who can edit appearance and publish
>>> templates)
>>> superuser.account=[hidden email]
>>> superuser.initialPassword=xxxx
>>>
>>> # run with no associated web site
>>> project.standalone=true
>>>
>>> # details for sending login e-mails
>>> mail.host=localhost
>>> mail.from=[hidden email]
>>> mail.subject=Welcome to FAWMine
>>> mail.text="Dear users\nYou have successfully created an account on
>>> FAWMine. Please don't hesitate to feed back any of your suggestions
>>> for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"
>>>
>>> # text that appears in the header and elsewhere
>>> project.title=FAWMine
>>> project.subTitle=An integrated Omics data warehouse for FAW,
>>> <i>Spodoptera frugiperda </i>
>>> project.releaseVersion=1.0
>>>
>>> # various URLs use this as the prefix
>>> project.sitePrefix=http://insectmine.org:8080/fawmine
>>> project.helpLocation=http://www.flymine.org/help
>>>
>>> # recipient of feedback form located on bottom of every page
>>> feedback.destination = [hidden email]
>>>
>>> inline.collections.in.tables = true
>>>
>>>
>>>
>>> On 2020-2-10 20:04, sergio contrino wrote:
>>>> dear Pengcheng,
>>>> have you installed jbrowse (as illustrated here
>>>> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
>>>> ?
>>>> if you did already, could you send us also your fawnmine.properties
>>>> in your .intermine directory?
>>>> thanks!
>>>> sergio
>>>>
>>>>
>>>> On 10/02/2020 04:15, Pengcheng Yang wrote:
>>>>> Dear InterMiners,
>>>>>
>>>>> The FAWmine has been successfully deployed
>>>>> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't
>>>>> work
>>>>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
>>>>> with the following message:
>>>>>
>>>>> It said that "Could not load reference sequence definitions.
>>>>> RequestError: Unable to load
>>>>> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
>>>>> status: 404.".
>>>>>
>>>>> I have committed the project to github for your checking
>>>>> https://github.com/pengchy/fawmine and
>>>>> https://github.com/pengchy/fawmine-bio-sources.
>>>>>
>>>>> Thank you and best,
>>>>>
>>>>> Pengcheng Yang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>
>>>>
>>>
>>
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang
Dear Sergio,

Thank you for your suggestions. I have made following tests. Jbrowse worked for LocustMine but failed for FAWMine. The difference between these two mines that may be a reason for this problem is the key for Organism data model in FAWMine is organism.taxonid, while in FAWMine the key are organism.taxonid and organism.strainName. Could this be the reason?

1. Added the following content to jbrowse_conf.json file, actually, this action equal to visit http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108.

        "datasets": {
                     "FAWMine-7108": {
                                         "url": "?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108",
                                        "name": "FAWMine"
                                 }
        }


I got the following error message(s):

Error message(s):


2. I have also checked the sample_data/json/volvox, it works, which indicate that the jbrowse installation is OK.

3. I have also tested another InterMine implementation LocustMine supported by the same InterMine/postgres/apache service through the following links:
and this
both worked well.

gives the same error as "Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404.".

Best,
Pengcheng

On 2020-2-11 0:57, sergio contrino wrote:
dear pengcheng

i think you are missing the setup of your mine datasources in the jbrowse installation. you would need to just edit one file, jbrowse_conf.json

please check the
Point JBrowse at your InterMine
section in
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/

your jbrowse url should return something like ours
https://jbrowse.intermine.org
(i assume with only one reference to fawnmine)
thanks
sergio

On 10/02/2020 15:48, Pengcheng Yang wrote:
Dear sergio,

I have add the link to the jbrose installation in the web.properties file. In the gene report page (http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got the JBrowse link that center on that gene (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene). In this link, you could find that the JBrowse installation directory is "http://insectmine.org/jbrowse/".

Thank you for your kind help.

pengcheng

On 2020-2-10 22:46, sergio contrino wrote:
dear Pengcheng,
please add the link to your jbrowse installation in the properties file.

jbrowse.install.url = http://your.jbrowse/installation

(unless it is already in your mine web.properties)
please let me know
thanks
sergio


On 10/02/2020 14:10, Pengcheng Yang wrote:
Hi sergio,

Thank you for your reply. Below is the content of my fawmine.properties and fawmine.properties.beta in the ~/.intermine directory.

best,

Pengcheng


====================== fawmine.properties =========================
# if true will log details about execution time of every query
os.production.verboseQueryLog=true

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawmine
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawmine
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx

================= fawmine.properties.beta================

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawminebeta
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawminebeta
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx


# userprofile database - used by the webapp to store logins, query history,
# saved bags, templates and tags.
db.userprofile-production.datasource.serverName=localhost
db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
db.userprofile-production.datasource.user=postgres
db.userprofile-production.datasource.password=xxxx

# files for ID resolvers
#resolver.file.rootpath=/DATA/idresolver

#####################
# webapp properties #
#####################

# Web application deployment properties

# location of tomcat server and path of webapp - e.g. access http://localhost:8080/malariamine
webapp.deploy.url=http://insectmine.org:8080
webapp.path=fawmine

# tomcat username and password needed to deploy webapp
webapp.manager=manager
webapp.password=xxxx

# 'Home' link
webapp.baseurl=http://insectmine.org:8080

# account name for superuser (who can edit appearance and publish templates)
[hidden email]
superuser.initialPassword=xxxx

# run with no associated web site
project.standalone=true

# details for sending login e-mails
mail.host=localhost
[hidden email]
mail.subject=Welcome to FAWMine
mail.text="Dear users\nYou have successfully created an account on FAWMine. Please don't hesitate to feed back any of your suggestions for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"

# text that appears in the header and elsewhere
project.title=FAWMine
project.subTitle=An integrated Omics data warehouse for FAW, <i>Spodoptera frugiperda </i>
project.releaseVersion=1.0

# various URLs use this as the prefix
project.sitePrefix=http://insectmine.org:8080/fawmine
project.helpLocation=http://www.flymine.org/help

# recipient of feedback form located on bottom of every page
feedback.destination = [hidden email]

inline.collections.in.tables = true



On 2020-2-10 20:04, sergio contrino wrote:
dear Pengcheng,
have you installed jbrowse (as illustrated here https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/) ?
if you did already, could you send us also your fawnmine.properties in your .intermine directory?
thanks!
sergio


On 10/02/2020 04:15, Pengcheng Yang wrote:
Dear InterMiners,

The FAWmine has been successfully deployed (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108) with the following message:

It said that "Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404.".

I have committed the project to github for your checking https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources.

Thank you and best,

Pengcheng Yang



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Re: JBrowse problem: Could not load reference sequence definitions

sergio contrino-2
dear Pengcheng,
yes, at the moment we cannot refer jbrowse to a specific strain of an
organism. we have added now a ticket for that.
i wanted to check your fawnmine this morning (to see if you could just
use the taxonid for now) but i think it is down.
thanks
sergio

https://github.com/intermine/intermine/issues/2202

On 11/02/2020 03:40, Pengcheng Yang wrote:

> Dear Sergio,
>
> Thank you for your suggestions. I have made following tests. Jbrowse
> worked for LocustMine but failed for FAWMine. The difference between
> these two mines that may be a reason for this problem is the key for
> Organism data model in FAWMine is organism.taxonid, while in FAWMine the
> key are organism.taxonid and organism.strainName. Could this be the reason?
>
> 1. Added the following content to jbrowse_conf.json file, actually, this
> action equal to visit
> http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108.
>
>
> "datasets": {
>                       "FAWMine-7108": {
>                                           "url":
> "?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108",
>                                          "name": "FAWMine"
>                                   }
>          }
>
> I got the following error message(s):
>
>
>     Error message(s):
>
> RequestError: Unable to load
> http://www.insectmine.org:8080/query/service/jbrowse/config/7108/trackList.json?v=0.8755048746520337 
> status: 0.
>
> 2. I have also checked the sample_data/json/volvox, it works, which
> indicate that the jbrowse installation is OK.
> http://insectmine.org/jbrowse/?data=sample_data/json/volvox
>
> 3. I have also tested another InterMine implementation LocustMine
> supported by the same InterMine/postgres/apache service through the
> following links:
> 3.1http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004,
> this link gives the same error message as
> http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108 
> <http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004>
> 3.2
> insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004
> and this
> http://insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004&loc=scaffold2825:148457..283758&tracks=LocustMine-7004-Gene
> both worked well.
>
> 4. Testing the link:
> http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/fawmine/service/jbrowse/config/7108
> gives the same error as "/Could not load reference sequence definitions.
> RequestError: Unable to load
> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
> status: 404./".
>
> Best,
> Pengcheng
>
> On 2020-2-11 0:57, sergio contrino wrote:
>> dear pengcheng
>>
>> i think you are missing the setup of your mine datasources in the
>> jbrowse installation. you would need to just edit one file,
>> jbrowse_conf.json
>>
>> please check the
>> Point JBrowse at your InterMine
>> section in
>> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/ 
>>
>>
>> your jbrowse url should return something like ours
>> https://jbrowse.intermine.org
>> (i assume with only one reference to fawnmine)
>> thanks
>> sergio
>>
>> On 10/02/2020 15:48, Pengcheng Yang wrote:
>>> Dear sergio,
>>>
>>> I have add the link to the jbrose installation in the web.properties
>>> file. In the gene report page
>>> (http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got
>>> the JBrowse link that center on that gene
>>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene).
>>> In this link, you could find that the JBrowse installation directory
>>> is "http://insectmine.org/jbrowse/".
>>>
>>> Thank you for your kind help.
>>>
>>> pengcheng
>>>
>>> On 2020-2-10 22:46, sergio contrino wrote:
>>>> dear Pengcheng,
>>>> please add the link to your jbrowse installation in the properties
>>>> file.
>>>>
>>>> jbrowse.install.url = http://your.jbrowse/installation
>>>>
>>>> (unless it is already in your mine web.properties)
>>>> please let me know
>>>> thanks
>>>> sergio
>>>>
>>>>
>>>> On 10/02/2020 14:10, Pengcheng Yang wrote:
>>>>> Hi sergio,
>>>>>
>>>>> Thank you for your reply. Below is the content of my
>>>>> fawmine.properties and fawmine.properties.beta in the ~/.intermine
>>>>> directory.
>>>>>
>>>>> best,
>>>>>
>>>>> Pengcheng
>>>>>
>>>>>
>>>>> ====================== fawmine.properties =========================
>>>>> # if true will log details about execution time of every query
>>>>> os.production.verboseQueryLog=true
>>>>>
>>>>> # Access to the postgres database to build into and access from the
>>>>> webapp
>>>>> db.production.datasource.serverName=localhost
>>>>> db.production.datasource.databaseName=fawmine
>>>>> db.production.datasource.user=postgres
>>>>> db.production.datasource.password=xxxx
>>>>>
>>>>> # Temporary database used during the build process, this is re-built
>>>>> # as sources are loaded and can be discarded once the warehouse
>>>>> build is complete
>>>>> # It uses the InterMine 'items' metadata format to describe objects.
>>>>>
>>>>> # common target items database
>>>>> db.common-tgt-items.datasource.serverName=localhost
>>>>> db.common-tgt-items.datasource.databaseName=items-fawmine
>>>>> db.common-tgt-items.datasource.user=postgres
>>>>> db.common-tgt-items.datasource.password=xxxx
>>>>>
>>>>> ================= fawmine.properties.beta================
>>>>>
>>>>> # Access to the postgres database to build into and access from the
>>>>> webapp
>>>>> db.production.datasource.serverName=localhost
>>>>> db.production.datasource.databaseName=fawminebeta
>>>>> db.production.datasource.user=postgres
>>>>> db.production.datasource.password=xxxx
>>>>>
>>>>> # Temporary database used during the build process, this is re-built
>>>>> # as sources are loaded and can be discarded once the warehouse
>>>>> build is complete
>>>>> # It uses the InterMine 'items' metadata format to describe objects.
>>>>>
>>>>> # common target items database
>>>>> db.common-tgt-items.datasource.serverName=localhost
>>>>> db.common-tgt-items.datasource.databaseName=items-fawminebeta
>>>>> db.common-tgt-items.datasource.user=postgres
>>>>> db.common-tgt-items.datasource.password=xxxx
>>>>>
>>>>>
>>>>> # userprofile database - used by the webapp to store logins, query
>>>>> history,
>>>>> # saved bags, templates and tags.
>>>>> db.userprofile-production.datasource.serverName=localhost
>>>>> db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
>>>>>
>>>>> db.userprofile-production.datasource.user=postgres
>>>>> db.userprofile-production.datasource.password=xxxx
>>>>>
>>>>> # files for ID resolvers
>>>>> #resolver.file.rootpath=/DATA/idresolver
>>>>>
>>>>> #####################
>>>>> # webapp properties #
>>>>> #####################
>>>>>
>>>>> # Web application deployment properties
>>>>>
>>>>> # location of tomcat server and path of webapp - e.g. access
>>>>> http://localhost:8080/malariamine
>>>>> webapp.deploy.url=http://insectmine.org:8080
>>>>> webapp.path=fawmine
>>>>>
>>>>> # tomcat username and password needed to deploy webapp
>>>>> webapp.manager=manager
>>>>> webapp.password=xxxx
>>>>>
>>>>> # 'Home' link
>>>>> webapp.baseurl=http://insectmine.org:8080
>>>>>
>>>>> # account name for superuser (who can edit appearance and publish
>>>>> templates)
>>>>> superuser.account=[hidden email]
>>>>> superuser.initialPassword=xxxx
>>>>>
>>>>> # run with no associated web site
>>>>> project.standalone=true
>>>>>
>>>>> # details for sending login e-mails
>>>>> mail.host=localhost
>>>>> mail.from=[hidden email]
>>>>> mail.subject=Welcome to FAWMine
>>>>> mail.text="Dear users\nYou have successfully created an account on
>>>>> FAWMine. Please don't hesitate to feed back any of your suggestions
>>>>> for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"
>>>>>
>>>>> # text that appears in the header and elsewhere
>>>>> project.title=FAWMine
>>>>> project.subTitle=An integrated Omics data warehouse for FAW,
>>>>> <i>Spodoptera frugiperda </i>
>>>>> project.releaseVersion=1.0
>>>>>
>>>>> # various URLs use this as the prefix
>>>>> project.sitePrefix=http://insectmine.org:8080/fawmine
>>>>> project.helpLocation=http://www.flymine.org/help
>>>>>
>>>>> # recipient of feedback form located on bottom of every page
>>>>> feedback.destination = [hidden email]
>>>>>
>>>>> inline.collections.in.tables = true
>>>>>
>>>>>
>>>>>
>>>>> On 2020-2-10 20:04, sergio contrino wrote:
>>>>>> dear Pengcheng,
>>>>>> have you installed jbrowse (as illustrated here
>>>>>> https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/)
>>>>>> ?
>>>>>> if you did already, could you send us also your
>>>>>> fawnmine.properties in your .intermine directory?
>>>>>> thanks!
>>>>>> sergio
>>>>>>
>>>>>>
>>>>>> On 10/02/2020 04:15, Pengcheng Yang wrote:
>>>>>>> Dear InterMiners,
>>>>>>>
>>>>>>> The FAWmine has been successfully deployed
>>>>>>> (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't
>>>>>>> work
>>>>>>> (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108)
>>>>>>> with the following message:
>>>>>>>
>>>>>>> It said that "Could not load reference sequence definitions.
>>>>>>> RequestError: Unable to load
>>>>>>> http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json 
>>>>>>> status: 404.".
>>>>>>>
>>>>>>> I have committed the project to github for your checking
>>>>>>> https://github.com/pengchy/fawmine and
>>>>>>> https://github.com/pengchy/fawmine-bio-sources.
>>>>>>>
>>>>>>> Thank you and best,
>>>>>>>
>>>>>>> Pengcheng Yang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang

Dear Sergio,

I have reloaded the data to FAWMine (7108) with the key of Organism was setting to taxonId, the same as LocustMine (7004). However, it is pity that both

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/query/service/jbrowse/config/7004

and

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/query/service/jbrowse/config/7108

do not work and return the same error messages:

Error message(s):

In addition, http://insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004 worked before this reloading data, now still displaying "Loading..." status after several minutes.

Maybe I have mistaken some steps, I will double check the loading the deploying steps. Any progress will be send to you and this list later.

Best,

Pengcheng


On 2020-2-11 18:57, sergio contrino wrote:
dear Pengcheng,
yes, at the moment we cannot refer jbrowse to a specific strain of an organism. we have added now a ticket for that.
i wanted to check your fawnmine this morning (to see if you could just use the taxonid for now) but i think it is down.
thanks
sergio

https://github.com/intermine/intermine/issues/2202

On 11/02/2020 03:40, Pengcheng Yang wrote:
Dear Sergio,

Thank you for your suggestions. I have made following tests. Jbrowse worked for LocustMine but failed for FAWMine. The difference between these two mines that may be a reason for this problem is the key for Organism data model in FAWMine is organism.taxonid, while in FAWMine the key are organism.taxonid and organism.strainName. Could this be the reason?

1. Added the following content to jbrowse_conf.json file, actually, this action equal to visit http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108.

"datasets": {
                      "FAWMine-7108": {
                                          "url": "?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108",
                                         "name": "FAWMine"
                                  }
         }

I got the following error message(s):


    Error message(s):

RequestError: Unable to load http://www.insectmine.org:8080/query/service/jbrowse/config/7108/trackList.json?v=0.8755048746520337 status: 0.

2. I have also checked the sample_data/json/volvox, it works, which indicate that the jbrowse installation is OK.
http://insectmine.org/jbrowse/?data=sample_data/json/volvox

3. I have also tested another InterMine implementation LocustMine supported by the same InterMine/postgres/apache service through the following links:
3.1http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004, this link gives the same error message as http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108 <http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004>
3.2 insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004
and this
http://insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004&loc=scaffold2825:148457..283758&tracks=LocustMine-7004-Gene
both worked well.

4. Testing the link: http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/fawmine/service/jbrowse/config/7108
gives the same error as "/Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404./".

Best,
Pengcheng

On 2020-2-11 0:57, sergio contrino wrote:
dear pengcheng

i think you are missing the setup of your mine datasources in the jbrowse installation. you would need to just edit one file, jbrowse_conf.json

please check the
Point JBrowse at your InterMine
section in
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/

your jbrowse url should return something like ours
https://jbrowse.intermine.org
(i assume with only one reference to fawnmine)
thanks
sergio

On 10/02/2020 15:48, Pengcheng Yang wrote:
Dear sergio,

I have add the link to the jbrose installation in the web.properties file. In the gene report page (http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got the JBrowse link that center on that gene (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene). In this link, you could find that the JBrowse installation directory is "http://insectmine.org/jbrowse/".

Thank you for your kind help.

pengcheng

On 2020-2-10 22:46, sergio contrino wrote:
dear Pengcheng,
please add the link to your jbrowse installation in the properties file.

jbrowse.install.url = http://your.jbrowse/installation

(unless it is already in your mine web.properties)
please let me know
thanks
sergio


On 10/02/2020 14:10, Pengcheng Yang wrote:
Hi sergio,

Thank you for your reply. Below is the content of my fawmine.properties and fawmine.properties.beta in the ~/.intermine directory.

best,

Pengcheng


====================== fawmine.properties =========================
# if true will log details about execution time of every query
os.production.verboseQueryLog=true

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawmine
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawmine
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx

================= fawmine.properties.beta================

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawminebeta
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawminebeta
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx


# userprofile database - used by the webapp to store logins, query history,
# saved bags, templates and tags.
db.userprofile-production.datasource.serverName=localhost
db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
db.userprofile-production.datasource.user=postgres
db.userprofile-production.datasource.password=xxxx

# files for ID resolvers
#resolver.file.rootpath=/DATA/idresolver

#####################
# webapp properties #
#####################

# Web application deployment properties

# location of tomcat server and path of webapp - e.g. access http://localhost:8080/malariamine
webapp.deploy.url=http://insectmine.org:8080
webapp.path=fawmine

# tomcat username and password needed to deploy webapp
webapp.manager=manager
webapp.password=xxxx

# 'Home' link
webapp.baseurl=http://insectmine.org:8080

# account name for superuser (who can edit appearance and publish templates)
[hidden email]
superuser.initialPassword=xxxx

# run with no associated web site
project.standalone=true

# details for sending login e-mails
mail.host=localhost
[hidden email]
mail.subject=Welcome to FAWMine
mail.text="Dear users\nYou have successfully created an account on FAWMine. Please don't hesitate to feed back any of your suggestions for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"

# text that appears in the header and elsewhere
project.title=FAWMine
project.subTitle=An integrated Omics data warehouse for FAW, <i>Spodoptera frugiperda </i>
project.releaseVersion=1.0

# various URLs use this as the prefix
project.sitePrefix=http://insectmine.org:8080/fawmine
project.helpLocation=http://www.flymine.org/help

# recipient of feedback form located on bottom of every page
feedback.destination = [hidden email]

inline.collections.in.tables = true



On 2020-2-10 20:04, sergio contrino wrote:
dear Pengcheng,
have you installed jbrowse (as illustrated here https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/) ?
if you did already, could you send us also your fawnmine.properties in your .intermine directory?
thanks!
sergio


On 10/02/2020 04:15, Pengcheng Yang wrote:
Dear InterMiners,

The FAWmine has been successfully deployed (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108) with the following message:

It said that "Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404.".

I have committed the project to github for your checking https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources.

Thank you and best,

Pengcheng Yang



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Re: JBrowse problem: Could not load reference sequence definitions

Pengcheng Yang

Dear Sergio,

Update

The following link work well now:

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/locustmine/service/jbrowse/config/7004

But the following link still failed:

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108

best,

Pengcheng


On 2020-2-11 23:25, Pengcheng Yang wrote:

Dear Sergio,

I have reloaded the data to FAWMine (7108) with the key of Organism was setting to taxonId, the same as LocustMine (7004). However, it is pity that both

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/query/service/jbrowse/config/7004

and

http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/query/service/jbrowse/config/7108

do not work and return the same error messages:

Error message(s):

In addition, http://insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004 worked before this reloading data, now still displaying "Loading..." status after several minutes.

Maybe I have mistaken some steps, I will double check the loading the deploying steps. Any progress will be send to you and this list later.

Best,

Pengcheng


On 2020-2-11 18:57, sergio contrino wrote:
dear Pengcheng,
yes, at the moment we cannot refer jbrowse to a specific strain of an organism. we have added now a ticket for that.
i wanted to check your fawnmine this morning (to see if you could just use the taxonid for now) but i think it is down.
thanks
sergio

https://github.com/intermine/intermine/issues/2202

On 11/02/2020 03:40, Pengcheng Yang wrote:
Dear Sergio,

Thank you for your suggestions. I have made following tests. Jbrowse worked for LocustMine but failed for FAWMine. The difference between these two mines that may be a reason for this problem is the key for Organism data model in FAWMine is organism.taxonid, while in FAWMine the key are organism.taxonid and organism.strainName. Could this be the reason?

1. Added the following content to jbrowse_conf.json file, actually, this action equal to visit http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108.

"datasets": {
                      "FAWMine-7108": {
                                          "url": "?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108",
                                         "name": "FAWMine"
                                  }
         }

I got the following error message(s):


    Error message(s):

RequestError: Unable to load http://www.insectmine.org:8080/query/service/jbrowse/config/7108/trackList.json?v=0.8755048746520337 status: 0.

2. I have also checked the sample_data/json/volvox, it works, which indicate that the jbrowse installation is OK.
http://insectmine.org/jbrowse/?data=sample_data/json/volvox

3. I have also tested another InterMine implementation LocustMine supported by the same InterMine/postgres/apache service through the following links:
3.1http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004, this link gives the same error message as http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7108 <http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/query/service/jbrowse/config/7004>
3.2 insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004
and this
http://insectmine.org/jbrowse/?data=http://locustmine.org:8080/locustmine/service/jbrowse/config/7004&loc=scaffold2825:148457..283758&tracks=LocustMine-7004-Gene
both worked well.

4. Testing the link: http://insectmine.org/jbrowse/?data=http://www.insectmine.org:8080/fawmine/service/jbrowse/config/7108
gives the same error as "/Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404./".

Best,
Pengcheng

On 2020-2-11 0:57, sergio contrino wrote:
dear pengcheng

i think you are missing the setup of your mine datasources in the jbrowse installation. you would need to just edit one file, jbrowse_conf.json

please check the
Point JBrowse at your InterMine
section in
https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/

your jbrowse url should return something like ours
https://jbrowse.intermine.org
(i assume with only one reference to fawnmine)
thanks
sergio

On 10/02/2020 15:48, Pengcheng Yang wrote:
Dear sergio,

I have add the link to the jbrose installation in the web.properties file. In the gene report page (http://www.insectmine.org:8080/fawmine/gene:SFR01273), you can got the JBrowse link that center on that gene (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108&loc=chr6:11620871..11621874&tracks=FAWMine-7108-Gene). In this link, you could find that the JBrowse installation directory is "http://insectmine.org/jbrowse/".

Thank you for your kind help.

pengcheng

On 2020-2-10 22:46, sergio contrino wrote:
dear Pengcheng,
please add the link to your jbrowse installation in the properties file.

jbrowse.install.url = http://your.jbrowse/installation

(unless it is already in your mine web.properties)
please let me know
thanks
sergio


On 10/02/2020 14:10, Pengcheng Yang wrote:
Hi sergio,

Thank you for your reply. Below is the content of my fawmine.properties and fawmine.properties.beta in the ~/.intermine directory.

best,

Pengcheng


====================== fawmine.properties =========================
# if true will log details about execution time of every query
os.production.verboseQueryLog=true

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawmine
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawmine
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx

================= fawmine.properties.beta================

# Access to the postgres database to build into and access from the webapp
db.production.datasource.serverName=localhost
db.production.datasource.databaseName=fawminebeta
db.production.datasource.user=postgres
db.production.datasource.password=xxxx

# Temporary database used during the build process, this is re-built
# as sources are loaded and can be discarded once the warehouse build is complete
# It uses the InterMine 'items' metadata format to describe objects.

# common target items database
db.common-tgt-items.datasource.serverName=localhost
db.common-tgt-items.datasource.databaseName=items-fawminebeta
db.common-tgt-items.datasource.user=postgres
db.common-tgt-items.datasource.password=xxxx


# userprofile database - used by the webapp to store logins, query history,
# saved bags, templates and tags.
db.userprofile-production.datasource.serverName=localhost
db.userprofile-production.datasource.databaseName=userprofile-fawminebeta
db.userprofile-production.datasource.user=postgres
db.userprofile-production.datasource.password=xxxx

# files for ID resolvers
#resolver.file.rootpath=/DATA/idresolver

#####################
# webapp properties #
#####################

# Web application deployment properties

# location of tomcat server and path of webapp - e.g. access http://localhost:8080/malariamine
webapp.deploy.url=http://insectmine.org:8080
webapp.path=fawmine

# tomcat username and password needed to deploy webapp
webapp.manager=manager
webapp.password=xxxx

# 'Home' link
webapp.baseurl=http://insectmine.org:8080

# account name for superuser (who can edit appearance and publish templates)
[hidden email]
superuser.initialPassword=xxxx

# run with no associated web site
project.standalone=true

# details for sending login e-mails
mail.host=localhost
[hidden email]
mail.subject=Welcome to FAWMine
mail.text="Dear users\nYou have successfully created an account on FAWMine. Please don't hesitate to feed back any of your suggestions for the improvement of FAWMine.\nBest,\nPengcheng Yang\n"

# text that appears in the header and elsewhere
project.title=FAWMine
project.subTitle=An integrated Omics data warehouse for FAW, <i>Spodoptera frugiperda </i>
project.releaseVersion=1.0

# various URLs use this as the prefix
project.sitePrefix=http://insectmine.org:8080/fawmine
project.helpLocation=http://www.flymine.org/help

# recipient of feedback form located on bottom of every page
feedback.destination = [hidden email]

inline.collections.in.tables = true



On 2020-2-10 20:04, sergio contrino wrote:
dear Pengcheng,
have you installed jbrowse (as illustrated here https://intermine.readthedocs.io/en/latest/webapp/third-party-tools/jbrowse/) ?
if you did already, could you send us also your fawnmine.properties in your .intermine directory?
thanks!
sergio


On 10/02/2020 04:15, Pengcheng Yang wrote:
Dear InterMiners,

The FAWmine has been successfully deployed (http://www.insectmine.org:8080/fawmine), but the JBrowse didn't work (http://insectmine.org/jbrowse/?data=http://insectmine.org:8080/fawmine/service/jbrowse/config/7108) with the following message:

It said that "Could not load reference sequence definitions. RequestError: Unable to load http://insectmine.org:8080/fawmine/service/jbrowse/config/7108/seq/refSeqs.json status: 404.".

I have committed the project to github for your checking https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources.

Thank you and best,

Pengcheng Yang



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev








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[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

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