Re: Loading IntAct data using psi source

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Re: Loading IntAct data using psi source

Julie Sullivan
Hi Deepak,

I just tried to load IntAct data for cow, and it was successful.

1. Can you verify your project XML entry is correct. Should look like this:

http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/

2. Maybe the config file is formatted weirdly (e.g. some whitespace /
tabs somewhere). I don't think the reading in of the config file is very
robust. Can you try to delete all the config, except for cow? And make
sure there is no extra spaces. Try that?

Let me know what you find!
Julie

On 04/11/14 16:30, Deepak Unni wrote:

> Hi Julie,
>
> I am trying to load the IntAct data ( in PSI-MI 2.5 format) using the
> PSI source and I noticed couple of issues.
>
> Firstly, no information from the XML seems to load into the tables such
> as gene, interaction, interactiondetail, etc (as defined in
> *psi_additions.xml*).
>
> Secondly, I tried tinkering with the *PsiConverter.java* and noticed
> that the psi-intact_config.properties file is not read properly.
>
> I added the following lines to *psi-intact_config.properties*,
>
> 9913.identifier = primaryIdentifier
> 9913.datasource = uniprotkb
>
> But in the *PsiConverter.java*,
> /if (config.get(organism) == null)/ condition evaluates as 'true' and
> the 'identifier' defaults to DEFAULT_IDENTIFIER ('symbol') and
> 'datasource' defaults to DEFAULT_DATASOURCE ("").
>
>
> Am I missing some configuration?
>
> Thanks and best regards,
>
> Deepak Unni
>
> Research Analyst,
> S104A Animal Science Research Center,
> University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Deepak Unni
Hi Julie,

I removed everything from the config properties file except the lines for 9913.

The entry in project.xml is as follows,

    <source name="psi-intact" type="psi" dump="true">
      <property name="src.data.dir" location="/Users/Deepak/Intermine/bovinemine_test_data/IntAct"/>
      <property name="intact.organisms" value="9913"/>
    </source>

I tried loading the IntAct data again and it is 'successful' but there are no corresponding tables populated in the database.

Thanks,

Deepak

On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan <[hidden email]> wrote:
Hi Deepak,

I just tried to load IntAct data for cow, and it was successful.

1. Can you verify your project XML entry is correct. Should look like this:

http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/

2. Maybe the config file is formatted weirdly (e.g. some whitespace / tabs somewhere). I don't think the reading in of the config file is very robust. Can you try to delete all the config, except for cow? And make sure there is no extra spaces. Try that?

Let me know what you find!
Julie

On 04/11/14 16:30, Deepak Unni wrote:
Hi Julie,

I am trying to load the IntAct data ( in PSI-MI 2.5 format) using the
PSI source and I noticed couple of issues.

Firstly, no information from the XML seems to load into the tables such
as gene, interaction, interactiondetail, etc (as defined in
*psi_additions.xml*).

Secondly, I tried tinkering with the *PsiConverter.java* and noticed
that the psi-intact_config.properties file is not read properly.

I added the following lines to *psi-intact_config.properties*,

9913.identifier = primaryIdentifier
9913.datasource = uniprotkb

But in the *PsiConverter.java*,
/if (config.get(organism) == null)/ condition evaluates as 'true' and
the 'identifier' defaults to DEFAULT_IDENTIFIER ('symbol') and
'datasource' defaults to DEFAULT_DATASOURCE ("").


Am I missing some configuration?

Thanks and best regards,

Deepak Unni

Research Analyst,
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Julie Sullivan
Which files are you loading? I was successful with `bovin_02.xml`. I
didn't try `bovin_01.xml`, I assumed that would work too.

On 05/11/14 13:19, Deepak Unni wrote:

> Hi Julie,
>
> I removed everything from the config properties file except the lines
> for 9913.
>
> The entry in project.xml is as follows,
>
>      <source name="psi-intact" type="psi" dump="true">
>        <property name="src.data.dir"
> location="/Users/Deepak/Intermine/bovinemine_test_data/IntAct"/>
>        <property name="intact.organisms" value="9913"/>
>      </source>
>
> I tried loading the IntAct data again and it is 'successful' but there
> are no corresponding tables populated in the database.
>
> Thanks,
>
> Deepak
>
> On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Deepak,
>
>     I just tried to load IntAct data for cow, and it was successful.
>
>     1. Can you verify your project XML entry is correct. Should look
>     like this:
>
>     http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
>     <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>
>
>     2. Maybe the config file is formatted weirdly (e.g. some whitespace
>     / tabs somewhere). I don't think the reading in of the config file
>     is very robust. Can you try to delete all the config, except for
>     cow? And make sure there is no extra spaces. Try that?
>
>     Let me know what you find!
>     Julie
>
>     On 04/11/14 16:30, Deepak Unni wrote:
>
>         Hi Julie,
>
>         I am trying to load the IntAct data ( in PSI-MI 2.5 format)
>         using the
>         PSI source and I noticed couple of issues.
>
>         Firstly, no information from the XML seems to load into the
>         tables such
>         as gene, interaction, interactiondetail, etc (as defined in
>         *psi_additions.xml*).
>
>         Secondly, I tried tinkering with the *PsiConverter.java* and noticed
>         that the psi-intact_config.properties file is not read properly.
>
>         I added the following lines to *psi-intact_config.properties*__,
>
>         9913.identifier = primaryIdentifier
>         9913.datasource = uniprotkb
>
>         But in the *PsiConverter.java*,
>         /if (config.get(organism) == null)/ condition evaluates as
>         'true' and
>         the 'identifier' defaults to DEFAULT_IDENTIFIER ('symbol') and
>         'datasource' defaults to DEFAULT_DATASOURCE ("").
>
>
>         Am I missing some configuration?
>
>         Thanks and best regards,
>
>         Deepak Unni
>
>         Research Analyst,
>         S104A Animal Science Research Center,
>         University of Missouri, Columbia
>
>
>
>
> --
> Research Analyst
> S104A Animal Science Research Center,
> University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Deepak Unni
Hi Julie,

Previously I was trying to load both bovin_01.xml and bovin_02.xml.
I tried again with just bovin_02.xml and yet I couldn't see the interaction tables being populated.

I will give it a try on a different machine just to see if I can reproduce the same issue.
I apologize for not doing that earlier.


Thanks,

Deepak


On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan <[hidden email]> wrote:
Which files are you loading? I was successful with `bovin_02.xml`. I didn't try `bovin_01.xml`, I assumed that would work too.

On 05/11/14 13:19, Deepak Unni wrote:
Hi Julie,

I removed everything from the config properties file except the lines
for 9913.

The entry in project.xml is as follows,

     <source name="psi-intact" type="psi" dump="true">
       <property name="src.data.dir"
location="/Users/Deepak/Intermine/bovinemine_test_data/IntAct"/>
       <property name="intact.organisms" value="9913"/>
     </source>

I tried loading the IntAct data again and it is 'successful' but there
are no corresponding tables populated in the database.

Thanks,

Deepak

On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Deepak,

    I just tried to load IntAct data for cow, and it was successful.

    1. Can you verify your project XML entry is correct. Should look
    like this:

    http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
    <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>

    2. Maybe the config file is formatted weirdly (e.g. some whitespace
    / tabs somewhere). I don't think the reading in of the config file
    is very robust. Can you try to delete all the config, except for
    cow? And make sure there is no extra spaces. Try that?

    Let me know what you find!
    Julie

    On 04/11/14 16:30, Deepak Unni wrote:

        Hi Julie,

        I am trying to load the IntAct data ( in PSI-MI 2.5 format)
        using the
        PSI source and I noticed couple of issues.

        Firstly, no information from the XML seems to load into the
        tables such
        as gene, interaction, interactiondetail, etc (as defined in
        *psi_additions.xml*).

        Secondly, I tried tinkering with the *PsiConverter.java* and noticed
        that the psi-intact_config.properties file is not read properly.

        I added the following lines to *psi-intact_config.properties*__,

        9913.identifier = primaryIdentifier
        9913.datasource = uniprotkb

        But in the *PsiConverter.java*,
        /if (config.get(organism) == null)/ condition evaluates as
        'true' and
        the 'identifier' defaults to DEFAULT_IDENTIFIER ('symbol') and
        'datasource' defaults to DEFAULT_DATASOURCE ("").


        Am I missing some configuration?

        Thanks and best regards,

        Deepak Unni

        Research Analyst,
        S104A Animal Science Research Center,
        University of Missouri, Columbia




--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Julie Sullivan
Hi Deepak

Okay, let me know what happens! Honestly, I didn't run the build, I just
ran the unit test. Maybe try that too?

Here's the docs on how to run InterMine tests:

http://intermine.readthedocs.org/en/latest/get-started/intermine-tests/

You have to create a couple databases, and add a properties file.

I copied bovin_02.xml over to here:

https://github.com/intermine/intermine/tree/emma/bio/sources/psi/test/resources

I changed the test to read in this new file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L47

And I wrote the output to a tmp file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L51-L52

I ran the unit test using Eclipse. But you can run on the command line
by running the "ant" command in the bio/sources/psi/test directory.

My temp file the test created had cow genes, interactions etc.
Everything I would expect. Try that?

Julie

On 05/11/14 13:29, Deepak Unni wrote:

> Hi Julie,
>
> Previously I was trying to load both bovin_01.xml and bovin_02.xml.
> I tried again with just bovin_02.xml and yet I couldn't see the
> interaction tables being populated.
>
> I will give it a try on a different machine just to see if I can
> reproduce the same issue.
> I apologize for not doing that earlier.
>
>
> Thanks,
>
> Deepak
>
>
> On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Which files are you loading? I was successful with `bovin_02.xml`. I
>     didn't try `bovin_01.xml`, I assumed that would work too.
>
>     On 05/11/14 13:19, Deepak Unni wrote:
>
>         Hi Julie,
>
>         I removed everything from the config properties file except the
>         lines
>         for 9913.
>
>         The entry in project.xml is as follows,
>
>               <source name="psi-intact" type="psi" dump="true">
>                 <property name="src.data.dir"
>         location="/Users/Deepak/__Intermine/bovinemine_test___data/IntAct"/>
>                 <property name="intact.organisms" value="9913"/>
>               </source>
>
>         I tried loading the IntAct data again and it is 'successful' but
>         there
>         are no corresponding tables populated in the database.
>
>         Thanks,
>
>         Deepak
>
>         On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan
>         <[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>              Hi Deepak,
>
>              I just tried to load IntAct data for cow, and it was
>         successful.
>
>              1. Can you verify your project XML entry is correct. Should
>         look
>              like this:
>
>         http://intermine.readthedocs.____org/en/latest/database/data-____sources/library/interactions/____intact/
>
>         <http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
>         <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>>
>
>              2. Maybe the config file is formatted weirdly (e.g. some
>         whitespace
>              / tabs somewhere). I don't think the reading in of the
>         config file
>              is very robust. Can you try to delete all the config,
>         except for
>              cow? And make sure there is no extra spaces. Try that?
>
>              Let me know what you find!
>              Julie
>
>              On 04/11/14 16:30, Deepak Unni wrote:
>
>                  Hi Julie,
>
>                  I am trying to load the IntAct data ( in PSI-MI 2.5 format)
>                  using the
>                  PSI source and I noticed couple of issues.
>
>                  Firstly, no information from the XML seems to load into the
>                  tables such
>                  as gene, interaction, interactiondetail, etc (as defined in
>                  *psi_additions.xml*).
>
>                  Secondly, I tried tinkering with the
>         *PsiConverter.java* and noticed
>                  that the psi-intact_config.properties file is not read
>         properly.
>
>                  I added the following lines to
>         *psi-intact_config.properties*____,
>
>                  9913.identifier = primaryIdentifier
>                  9913.datasource = uniprotkb
>
>                  But in the *PsiConverter.java*,
>                  /if (config.get(organism) == null)/ condition evaluates as
>                  'true' and
>                  the 'identifier' defaults to DEFAULT_IDENTIFIER
>         ('symbol') and
>                  'datasource' defaults to DEFAULT_DATASOURCE ("").
>
>
>                  Am I missing some configuration?
>
>                  Thanks and best regards,
>
>                  Deepak Unni
>
>                  Research Analyst,
>                  S104A Animal Science Research Center,
>                  University of Missouri, Columbia
>
>
>
>
>         --
>         Research Analyst
>         S104A Animal Science Research Center,
>         University of Missouri, Columbia
>
>
>
>
> --
> Research Analyst
> S104A Animal Science Research Center,
> University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Deepak Unni
Thanks Julie.

Will try both options and get back to you :)



On Wed, Nov 5, 2014 at 7:35 AM, Julie Sullivan <[hidden email]> wrote:
Hi Deepak

Okay, let me know what happens! Honestly, I didn't run the build, I just ran the unit test. Maybe try that too?

Here's the docs on how to run InterMine tests:

http://intermine.readthedocs.org/en/latest/get-started/intermine-tests/

You have to create a couple databases, and add a properties file.

I copied bovin_02.xml over to here:

https://github.com/intermine/intermine/tree/emma/bio/sources/psi/test/resources

I changed the test to read in this new file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L47

And I wrote the output to a tmp file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L51-L52

I ran the unit test using Eclipse. But you can run on the command line by running the "ant" command in the bio/sources/psi/test directory.

My temp file the test created had cow genes, interactions etc. Everything I would expect. Try that?

Julie

On 05/11/14 13:29, Deepak Unni wrote:
Hi Julie,

Previously I was trying to load both bovin_01.xml and bovin_02.xml.
I tried again with just bovin_02.xml and yet I couldn't see the
interaction tables being populated.

I will give it a try on a different machine just to see if I can
reproduce the same issue.
I apologize for not doing that earlier.


Thanks,

Deepak


On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Which files are you loading? I was successful with `bovin_02.xml`. I
    didn't try `bovin_01.xml`, I assumed that would work too.

    On 05/11/14 13:19, Deepak Unni wrote:

        Hi Julie,

        I removed everything from the config properties file except the
        lines
        for 9913.

        The entry in project.xml is as follows,

              <source name="psi-intact" type="psi" dump="true">
                <property name="src.data.dir"
        location="/Users/Deepak/__Intermine/bovinemine_test___data/IntAct"/>
                <property name="intact.organisms" value="9913"/>
              </source>

        I tried loading the IntAct data again and it is 'successful' but
        there
        are no corresponding tables populated in the database.

        Thanks,

        Deepak

        On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan
        <[hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Deepak,

             I just tried to load IntAct data for cow, and it was
        successful.

             1. Can you verify your project XML entry is correct. Should
        look
             like this:

        http://intermine.readthedocs.____org/en/latest/database/data-____sources/library/interactions/____intact/


        <http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
        <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>>

             2. Maybe the config file is formatted weirdly (e.g. some
        whitespace
             / tabs somewhere). I don't think the reading in of the
        config file
             is very robust. Can you try to delete all the config,
        except for
             cow? And make sure there is no extra spaces. Try that?

             Let me know what you find!
             Julie

             On 04/11/14 16:30, Deepak Unni wrote:

                 Hi Julie,

                 I am trying to load the IntAct data ( in PSI-MI 2.5 format)
                 using the
                 PSI source and I noticed couple of issues.

                 Firstly, no information from the XML seems to load into the
                 tables such
                 as gene, interaction, interactiondetail, etc (as defined in
                 *psi_additions.xml*).

                 Secondly, I tried tinkering with the
        *PsiConverter.java* and noticed
                 that the psi-intact_config.properties file is not read
        properly.

                 I added the following lines to
        *psi-intact_config.properties*____,

                 9913.identifier = primaryIdentifier
                 9913.datasource = uniprotkb

                 But in the *PsiConverter.java*,
                 /if (config.get(organism) == null)/ condition evaluates as
                 'true' and
                 the 'identifier' defaults to DEFAULT_IDENTIFIER
        ('symbol') and
                 'datasource' defaults to DEFAULT_DATASOURCE ("").


                 Am I missing some configuration?

                 Thanks and best regards,

                 Deepak Unni

                 Research Analyst,
                 S104A Animal Science Research Center,
                 University of Missouri, Columbia




        --
        Research Analyst
        S104A Animal Science Research Center,
        University of Missouri, Columbia




--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

_______________________________________________
dev mailing list
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http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: Loading IntAct data using psi source

Deepak Unni
Hi Julie,

In your test output XML, did you see any entry for class 'Gene'?

The reason I ask is because I tried the PSI test just like you suggested and I did get an output XML.
This XML had entries for class 'Comment', 'Publication' and 'InteractionTerm' but I couldn't find any entry for class 'Gene' or 'Interaction'.

Thanks,

Deepak

On Wed, Nov 5, 2014 at 7:37 AM, Deepak Unni <[hidden email]> wrote:
Thanks Julie.

Will try both options and get back to you :)



On Wed, Nov 5, 2014 at 7:35 AM, Julie Sullivan <[hidden email]> wrote:
Hi Deepak

Okay, let me know what happens! Honestly, I didn't run the build, I just ran the unit test. Maybe try that too?

Here's the docs on how to run InterMine tests:

http://intermine.readthedocs.org/en/latest/get-started/intermine-tests/

You have to create a couple databases, and add a properties file.

I copied bovin_02.xml over to here:

https://github.com/intermine/intermine/tree/emma/bio/sources/psi/test/resources

I changed the test to read in this new file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L47

And I wrote the output to a tmp file:

https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L51-L52

I ran the unit test using Eclipse. But you can run on the command line by running the "ant" command in the bio/sources/psi/test directory.

My temp file the test created had cow genes, interactions etc. Everything I would expect. Try that?

Julie

On 05/11/14 13:29, Deepak Unni wrote:
Hi Julie,

Previously I was trying to load both bovin_01.xml and bovin_02.xml.
I tried again with just bovin_02.xml and yet I couldn't see the
interaction tables being populated.

I will give it a try on a different machine just to see if I can
reproduce the same issue.
I apologize for not doing that earlier.


Thanks,

Deepak


On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Which files are you loading? I was successful with `bovin_02.xml`. I
    didn't try `bovin_01.xml`, I assumed that would work too.

    On 05/11/14 13:19, Deepak Unni wrote:

        Hi Julie,

        I removed everything from the config properties file except the
        lines
        for 9913.

        The entry in project.xml is as follows,

              <source name="psi-intact" type="psi" dump="true">
                <property name="src.data.dir"
        location="/Users/Deepak/__Intermine/bovinemine_test___data/IntAct"/>
                <property name="intact.organisms" value="9913"/>
              </source>

        I tried loading the IntAct data again and it is 'successful' but
        there
        are no corresponding tables populated in the database.

        Thanks,

        Deepak

        On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan
        <[hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Deepak,

             I just tried to load IntAct data for cow, and it was
        successful.

             1. Can you verify your project XML entry is correct. Should
        look
             like this:

        http://intermine.readthedocs.____org/en/latest/database/data-____sources/library/interactions/____intact/


        <http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
        <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>>

             2. Maybe the config file is formatted weirdly (e.g. some
        whitespace
             / tabs somewhere). I don't think the reading in of the
        config file
             is very robust. Can you try to delete all the config,
        except for
             cow? And make sure there is no extra spaces. Try that?

             Let me know what you find!
             Julie

             On 04/11/14 16:30, Deepak Unni wrote:

                 Hi Julie,

                 I am trying to load the IntAct data ( in PSI-MI 2.5 format)
                 using the
                 PSI source and I noticed couple of issues.

                 Firstly, no information from the XML seems to load into the
                 tables such
                 as gene, interaction, interactiondetail, etc (as defined in
                 *psi_additions.xml*).

                 Secondly, I tried tinkering with the
        *PsiConverter.java* and noticed
                 that the psi-intact_config.properties file is not read
        properly.

                 I added the following lines to
        *psi-intact_config.properties*____,

                 9913.identifier = primaryIdentifier
                 9913.datasource = uniprotkb

                 But in the *PsiConverter.java*,
                 /if (config.get(organism) == null)/ condition evaluates as
                 'true' and
                 the 'identifier' defaults to DEFAULT_IDENTIFIER
        ('symbol') and
                 'datasource' defaults to DEFAULT_DATASOURCE ("").


                 Am I missing some configuration?

                 Thanks and best regards,

                 Deepak Unni

                 Research Analyst,
                 S104A Animal Science Research Center,
                 University of Missouri, Columbia




        --
        Research Analyst
        S104A Animal Science Research Center,
        University of Missouri, Columbia




--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Julie Sullivan
Sorry, I changed from fly to cow:

https://github.com/intermine/intermine/blob/beta/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L37

Change that from dmel to be 9913

https://github.com/intermine/intermine/blob/beta/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L38-L40

delete these lines

Try that?

On 05/11/14 16:24, Deepak Unni wrote:

> Hi Julie,
>
> In your test output XML, did you see any entry for class 'Gene'?
>
> The reason I ask is because I tried the PSI test just like you suggested
> and I did get an output XML.
> This XML had entries for class 'Comment', 'Publication' and
> 'InteractionTerm' but I couldn't find any entry for class 'Gene' or
> 'Interaction'.
>
> Thanks,
>
> Deepak
>
> On Wed, Nov 5, 2014 at 7:37 AM, Deepak Unni <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Thanks Julie.
>
>     Will try both options and get back to you :)
>
>
>
>     On Wed, Nov 5, 2014 at 7:35 AM, Julie Sullivan <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>         Hi Deepak
>
>         Okay, let me know what happens! Honestly, I didn't run the
>         build, I just ran the unit test. Maybe try that too?
>
>         Here's the docs on how to run InterMine tests:
>
>         http://intermine.readthedocs.__org/en/latest/get-started/__intermine-tests/
>         <http://intermine.readthedocs.org/en/latest/get-started/intermine-tests/>
>
>         You have to create a couple databases, and add a properties file.
>
>         I copied bovin_02.xml over to here:
>
>         https://github.com/intermine/__intermine/tree/emma/bio/__sources/psi/test/resources
>         <https://github.com/intermine/intermine/tree/emma/bio/sources/psi/test/resources>
>
>         I changed the test to read in this new file:
>
>         https://github.com/intermine/__intermine/blob/emma/bio/__sources/psi/test/src/org/__intermine/bio/dataconversion/__PsiConverterTest.java#L47
>         <https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L47>
>
>         And I wrote the output to a tmp file:
>
>         https://github.com/intermine/__intermine/blob/emma/bio/__sources/psi/test/src/org/__intermine/bio/dataconversion/__PsiConverterTest.java#L51-L52
>         <https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L51-L52>
>
>         I ran the unit test using Eclipse. But you can run on the
>         command line by running the "ant" command in the
>         bio/sources/psi/test directory.
>
>         My temp file the test created had cow genes, interactions etc.
>         Everything I would expect. Try that?
>
>         Julie
>
>         On 05/11/14 13:29, Deepak Unni wrote:
>
>             Hi Julie,
>
>             Previously I was trying to load both bovin_01.xml and
>             bovin_02.xml.
>             I tried again with just bovin_02.xml and yet I couldn't see the
>             interaction tables being populated.
>
>             I will give it a try on a different machine just to see if I can
>             reproduce the same issue.
>             I apologize for not doing that earlier.
>
>
>             Thanks,
>
>             Deepak
>
>
>             On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan
>             <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>                  Which files are you loading? I was successful with
>             `bovin_02.xml`. I
>                  didn't try `bovin_01.xml`, I assumed that would work too.
>
>                  On 05/11/14 13:19, Deepak Unni wrote:
>
>                      Hi Julie,
>
>                      I removed everything from the config properties
>             file except the
>                      lines
>                      for 9913.
>
>                      The entry in project.xml is as follows,
>
>                            <source name="psi-intact" type="psi" dump="true">
>                              <property name="src.data.dir"
>
>             location="/Users/Deepak/____Intermine/bovinemine_test_____data/IntAct"/>
>                              <property name="intact.organisms"
>             value="9913"/>
>                            </source>
>
>                      I tried loading the IntAct data again and it is
>             'successful' but
>                      there
>                      are no corresponding tables populated in the database.
>
>                      Thanks,
>
>                      Deepak
>
>                      On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan
>                      <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>
>                      <mailto:[hidden email]
>             <mailto:[hidden email]> <mailto:[hidden email]
>             <mailto:[hidden email]>>>> wrote:
>
>                           Hi Deepak,
>
>                           I just tried to load IntAct data for cow, and
>             it was
>                      successful.
>
>                           1. Can you verify your project XML entry is
>             correct. Should
>                      look
>                           like this:
>
>             http://intermine.readthedocs.______org/en/latest/database/__data-____sources/library/__interactions/____intact/
>
>
>
>             <http://intermine.readthedocs.____org/en/latest/database/data-____sources/library/__interactions/__intact/
>
>             <http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
>             <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>>>
>
>                           2. Maybe the config file is formatted weirdly
>             (e.g. some
>                      whitespace
>                           / tabs somewhere). I don't think the reading
>             in of the
>                      config file
>                           is very robust. Can you try to delete all the
>             config,
>                      except for
>                           cow? And make sure there is no extra spaces.
>             Try that?
>
>                           Let me know what you find!
>                           Julie
>
>                           On 04/11/14 16:30, Deepak Unni wrote:
>
>                               Hi Julie,
>
>                               I am trying to load the IntAct data ( in
>             PSI-MI 2.5 format)
>                               using the
>                               PSI source and I noticed couple of issues.
>
>                               Firstly, no information from the XML seems
>             to load into the
>                               tables such
>                               as gene, interaction, interactiondetail,
>             etc (as defined in
>                               *psi_additions.xml*).
>
>                               Secondly, I tried tinkering with the
>                      *PsiConverter.java* and noticed
>                               that the psi-intact_config.properties file
>             is not read
>                      properly.
>
>                               I added the following lines to
>                      *psi-intact_config.properties*______,
>
>                               9913.identifier = primaryIdentifier
>                               9913.datasource = uniprotkb
>
>                               But in the *PsiConverter.java*,
>                               /if (config.get(organism) == null)/
>             condition evaluates as
>                               'true' and
>                               the 'identifier' defaults to
>             DEFAULT_IDENTIFIER
>                      ('symbol') and
>                               'datasource' defaults to
>             DEFAULT_DATASOURCE ("").
>
>
>                               Am I missing some configuration?
>
>                               Thanks and best regards,
>
>                               Deepak Unni
>
>                               Research Analyst,
>                               S104A Animal Science Research Center,
>                               University of Missouri, Columbia
>
>
>
>
>                      --
>                      Research Analyst
>                      S104A Animal Science Research Center,
>                      University of Missouri, Columbia
>
>
>
>
>             --
>             Research Analyst
>             S104A Animal Science Research Center,
>             University of Missouri, Columbia
>
>
>
>
>     --
>     Research Analyst
>     S104A Animal Science Research Center,
>     University of Missouri, Columbia
>
>
>
>
> --
> Research Analyst
> S104A Animal Science Research Center,
> University of Missouri, Columbia

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Re: Loading IntAct data using psi source

Deepak Unni
Hi Julie,

I modified the lines but now I get no output XML after running ant.

The modified PsiConverterTest.java and the stack trace is at https://gist.github.com/deepakunni3/1c444bd968244d27b005

Thanks,

Deepak

On Wed, Nov 5, 2014 at 10:30 AM, Julie Sullivan <[hidden email]> wrote:
Sorry, I changed from fly to cow:

https://github.com/intermine/intermine/blob/beta/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L37

Change that from dmel to be 9913

https://github.com/intermine/intermine/blob/beta/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L38-L40

delete these lines

Try that?

On 05/11/14 16:24, Deepak Unni wrote:
Hi Julie,

In your test output XML, did you see any entry for class 'Gene'?

The reason I ask is because I tried the PSI test just like you suggested
and I did get an output XML.
This XML had entries for class 'Comment', 'Publication' and
'InteractionTerm' but I couldn't find any entry for class 'Gene' or
'Interaction'.

Thanks,

Deepak

On Wed, Nov 5, 2014 at 7:37 AM, Deepak Unni <[hidden email]
<mailto:[hidden email]>> wrote:

    Thanks Julie.

    Will try both options and get back to you :)



    On Wed, Nov 5, 2014 at 7:35 AM, Julie Sullivan <[hidden email]
    <mailto:[hidden email]>> wrote:

        Hi Deepak

        Okay, let me know what happens! Honestly, I didn't run the
        build, I just ran the unit test. Maybe try that too?

        Here's the docs on how to run InterMine tests:

        http://intermine.readthedocs.__org/en/latest/get-started/__intermine-tests/
        <http://intermine.readthedocs.org/en/latest/get-started/intermine-tests/>

        You have to create a couple databases, and add a properties file.

        I copied bovin_02.xml over to here:

        https://github.com/intermine/__intermine/tree/emma/bio/__sources/psi/test/resources
        <https://github.com/intermine/intermine/tree/emma/bio/sources/psi/test/resources>

        I changed the test to read in this new file:

        https://github.com/intermine/__intermine/blob/emma/bio/__sources/psi/test/src/org/__intermine/bio/dataconversion/__PsiConverterTest.java#L47
        <https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L47>

        And I wrote the output to a tmp file:

        https://github.com/intermine/__intermine/blob/emma/bio/__sources/psi/test/src/org/__intermine/bio/dataconversion/__PsiConverterTest.java#L51-L52
        <https://github.com/intermine/intermine/blob/emma/bio/sources/psi/test/src/org/intermine/bio/dataconversion/PsiConverterTest.java#L51-L52>

        I ran the unit test using Eclipse. But you can run on the
        command line by running the "ant" command in the
        bio/sources/psi/test directory.

        My temp file the test created had cow genes, interactions etc.
        Everything I would expect. Try that?

        Julie

        On 05/11/14 13:29, Deepak Unni wrote:

            Hi Julie,

            Previously I was trying to load both bovin_01.xml and
            bovin_02.xml.
            I tried again with just bovin_02.xml and yet I couldn't see the
            interaction tables being populated.

            I will give it a try on a different machine just to see if I can
            reproduce the same issue.
            I apologize for not doing that earlier.


            Thanks,

            Deepak


            On Wed, Nov 5, 2014 at 7:23 AM, Julie Sullivan
            <[hidden email] <mailto:[hidden email]>
            <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

                 Which files are you loading? I was successful with
            `bovin_02.xml`. I
                 didn't try `bovin_01.xml`, I assumed that would work too.

                 On 05/11/14 13:19, Deepak Unni wrote:

                     Hi Julie,

                     I removed everything from the config properties
            file except the
                     lines
                     for 9913.

                     The entry in project.xml is as follows,

                           <source name="psi-intact" type="psi" dump="true">
                             <property name="src.data.dir"

            location="/Users/Deepak/____Intermine/bovinemine_test_____data/IntAct"/>
                             <property name="intact.organisms"
            value="9913"/>
                           </source>

                     I tried loading the IntAct data again and it is
            'successful' but
                     there
                     are no corresponding tables populated in the database.

                     Thanks,

                     Deepak

                     On Wed, Nov 5, 2014 at 5:37 AM, Julie Sullivan
                     <[hidden email] <mailto:[hidden email]>
            <mailto:[hidden email] <mailto:[hidden email]>>
                     <mailto:[hidden email]
            <mailto:[hidden email]> <mailto:[hidden email]
            <mailto:[hidden email]>>>> wrote:

                          Hi Deepak,

                          I just tried to load IntAct data for cow, and
            it was
                     successful.

                          1. Can you verify your project XML entry is
            correct. Should
                     look
                          like this:

            http://intermine.readthedocs.______org/en/latest/database/__data-____sources/library/__interactions/____intact/



            <http://intermine.readthedocs.____org/en/latest/database/data-____sources/library/__interactions/__intact/


            <http://intermine.readthedocs.__org/en/latest/database/data-__sources/library/interactions/__intact/
            <http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/intact/>>>

                          2. Maybe the config file is formatted weirdly
            (e.g. some
                     whitespace
                          / tabs somewhere). I don't think the reading
            in of the
                     config file
                          is very robust. Can you try to delete all the
            config,
                     except for
                          cow? And make sure there is no extra spaces.
            Try that?

                          Let me know what you find!
                          Julie

                          On 04/11/14 16:30, Deepak Unni wrote:

                              Hi Julie,

                              I am trying to load the IntAct data ( in
            PSI-MI 2.5 format)
                              using the
                              PSI source and I noticed couple of issues.

                              Firstly, no information from the XML seems
            to load into the
                              tables such
                              as gene, interaction, interactiondetail,
            etc (as defined in
                              *psi_additions.xml*).

                              Secondly, I tried tinkering with the
                     *PsiConverter.java* and noticed
                              that the psi-intact_config.properties file
            is not read
                     properly.

                              I added the following lines to
                     *psi-intact_config.properties*______,


                              9913.identifier = primaryIdentifier
                              9913.datasource = uniprotkb

                              But in the *PsiConverter.java*,
                              /if (config.get(organism) == null)/
            condition evaluates as
                              'true' and
                              the 'identifier' defaults to
            DEFAULT_IDENTIFIER
                     ('symbol') and
                              'datasource' defaults to
            DEFAULT_DATASOURCE ("").


                              Am I missing some configuration?

                              Thanks and best regards,

                              Deepak Unni

                              Research Analyst,
                              S104A Animal Science Research Center,
                              University of Missouri, Columbia




                     --
                     Research Analyst
                     S104A Animal Science Research Center,
                     University of Missouri, Columbia




            --
            Research Analyst
            S104A Animal Science Research Center,
            University of Missouri, Columbia




    --
    Research Analyst
    S104A Animal Science Research Center,
    University of Missouri, Columbia




--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia



--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

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