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cPath: old Pathway Commons portal engine

Home Page: http://www.pathwaycommons.org/pc/

License: Other

Python 0.32% Perl 0.51% Shell 0.35% XSLT 0.73% Java 44.11% HTML 5.34% Web Ontology Language 41.02% CSS 0.90% JavaScript 6.23% TeX 0.49%

cpath1's Introduction

CREATE CYTOSCAPE WEBSTART
-------------------------

0) Update cpath2.jar
- in coreplugins/cPath2, update plugin.props, and make sure that the plugin is pointing to the correct URL.
  for example:  cpath2.server_url=http://awabi.cbio.mskcc.org/pc/webservice.do
- regenerate the jar:  ant jar

1) Run cytoscape webstart ant task:

- update build.xml and replace all storepass attributes with your storepass (see Ben for password)
- update build.xml and replace all alias attributes with your alias (alias="cbio")
- make sure code signing keystore file, .keystore is located in your home directory
- type: "ant -DwebstartURL=http://yourdomain.com webstart" on commandline inside cytoscape dir
  example:  ant -DwebstartURL=http://cerami.bscb.cornell.edu/ webstart
  example:  ant -DwebstartURL=http://192.168.0.4/ webstart

2) Move signed cytoscape files into cpath tree:

- move files in build/webstart to $CPATH_ROOT/web/jsp/cytoscape
- restore the original cytoscape.props file in $CPATH_ROOT/web/jsp/cytoscape (if you just clobbered it), and modify as needed
- verify that $CPATH_ROOT/src/org/mskcc/pathdb/servlet/CytoscapeJnlpServlet.java, writeJNLPData() references all required jars
  (this can be done by comparing servlet with $CPATH_ROOT/web/jsp/cytoscape/cy1.jnlp

3) Done!

cpath1's People

Contributors

armish avatar igorrodchenkov avatar onursumer avatar

Watchers

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Forkers

tramyn

cpath1's Issues

Tabs on pathway page are squished

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1.  Go to a pathway page, e.g.
http://awabi.cbio.mskcc.org/pc-demo/record2.do?id=604467 (FOXA1
transcription factor network)

What is the expected output? What do you see instead?

1.  The tabs are all squished up at the top.  See attached screenshot.

Original issue reported on code.google.com by [email protected] on 12 Oct 2009 at 3:42

Attachments:

Copied from original issue: PathwayCommons/cpath2#24

Filter Summary is missing on the home page

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1.Click on the global filter settings link in the search box
2. Set the custom filters by selecting some of the oganisms
3. Return to home page

What is the expected output? What do you see instead?
Per Feature 6 on the feature matrix, there should be a summary of the
filter settings on the home page as well

What version of the product are you using? On what operating system?
Prototype at http://awabi.cbio.mskcc.org/pc-demo/
on iMac

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 9 Sep 2009 at 6:28

Copied from original issue: PathwayCommons/cpath2#13

pathway participants number is actually the number of molecules

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1. Search for pathways, using "BRCA1".
2. On the results page, right to a pathway, read the number of participants. 

What is the expected output? What do you see instead?
How about to have  [34 interactions, 49 molecules] instead of the  [49 
participants]
("participants there actually mean only molecules")

What version of the product are you using? On what operating system?
test (pc-demo)

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 2 Oct 2009 at 2:39

Copied from original issue: PathwayCommons/cpath2#22

search by SIR2 - no hits

From @GoogleCodeExporter on March 16, 2015 20:17

This issue seems to be a full-text index/query bug.

What steps will reproduce the problem?
1. pathwaycommons.org
2. search (does not matter pathways or molecules) for Sir2 or SIR2

What is the expected output? What do you see instead?
SIR2 (yeast) must be in top hits; there must be some pathway hits too

Searching by SIR* - success!

Originally reported by user:

On Fri, Feb 15, 2013 at 12:53 PM, <[email protected]> wrote:
We are working on yeast genes related to replicative lifespan extension (i.e. 
Sir2). When we enter Sir2 into the search box, it finds nothing. This is really 
odd as this is a very important gene in yeast.

When we are looking for pathways, for example, the tor pathway, we can't find 
that.

When we are building interaction networks in cytoscape, it only builds networks 
from proteins and we need networks from genes.

Any help would be most gratefully appreciated
Dr. Tarynn M. Witten

Original issue reported on code.google.com by [email protected] on 15 Feb 2013 at 6:16

Copied from original issue: PathwayCommons/cpath2#154

Molecules Tab does not Make Sense

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1.  Search for NCOA3 (Find Pathways)
2.  Click "Pathway: FOXA1 transcription factor network"
3.  Click the "Molecules" tab

What is the expected output? What do you see instead?

Only one of the molecules, e.g. AP1 is listed as coming from NCI.  I am not
even sure why we are showing the data source here.

We should simplify this page by removing the data source entirely.  It's
very confusing as it is.

Original issue reported on code.google.com by [email protected] on 12 Oct 2009 at 3:45

Copied from original issue: PathwayCommons/cpath2#25

Searching for "brca1 complex" results in many exact matches

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1.  Searched for "brca1 complex"

What is the expected output? What do you see instead?

Under exact matches, I see:  Exact Matches: BRCA1 [Homo sapiens]  NFKBIA
[Homo sapiens]  FRAP1 [Homo sapiens]  NFATC1 [Homo sapiens]  THOC4 [Homo
sapiens]  NUP214 [Homo sapiens]  IGFALS [Homo sapiens]  BIRC3 [Homo
sapiens]  YY1 [Homo sapiens]  SAP30 [Homo sapiens]  

Only one of these is really an exact match.  But, I am not even sue if we
should be showing any of these.

What version of the product are you using? On what operating system?


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 2 Oct 2009 at 1:19

Copied from original issue: PathwayCommons/cpath2#18

Issues related to moving the old PC service and db to another host

Trying to run PC portal on another machine (99% seems to work), when accessing a page -
http://beta.pathwaycommons.org/pc/record2.do?id=139997

Also, logos are not displayed on http://beta.pathwaycommons.org/pc/dbSources.do page (
despite, e.g., http://beta.pathwaycommons.org/pc/jsp/images/database/db_45.png image URLs work.)

bigger neighborhood map was once different from the mini-map

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1. go to http://www.pathwaycommons.org/pc/record2.do?id=9422
2. click on the "Neighborhood Map"

What is the expected output? What do you see instead?
 The picture in the bigger window is not the same as in the mini-map. 

What version of the product are you using? On what operating system?
 pathwaycommons.org web site (October 15, 2009 release); Safari 4.0.5.

Please provide any additional information below.
 I could not reproduce this issue again (it's probably a browser's problem...)

Original issue reported on code.google.com by [email protected] on 7 Jun 2010 at 10:29

Copied from original issue: PathwayCommons/cpath2#33

no filter summary on Home page

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1. set Global filter, e.g., to include Human, Mouse, Rat...
2. return to the home page
3. also, do search, look at the results page, under the top-right search box

What is the expected output? What do you see instead?
Global filters summary on both pages, like
"Current filters: 3 Organisms, All Data Sources. Set filters."

It is absent from the home page.

Please use labels and text to provide additional information.

Original issue reported on code.google.com by [email protected] on 1 Oct 2009 at 1:08

  • Merged into: #13

Copied from original issue: PathwayCommons/cpath2#16

Search Results: Not Enough Space between Search Tabs and Exact Matches, IE Specific

Issue by GoogleCodeExporter
Monday Mar 16, 2015 at 20:14 GMT
Originally opened as PathwayCommons/cpath2#7

What steps will reproduce the problem?
1. Search for BRCA1

What is the expected output? What do you see instead?

Not Enough Space between Search Tabs and Exact Matches

Please use labels and text to provide additional information.

Original issue reported on code.google.com by [email protected] on 3 Sep 2009 at 6:36

Useless interaction names being displayed in biopax view of PC plugin for Cytoscape

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1. Download NGAL interactions from PC and view in biopax mode

Some of the small squares representing interactions have useless labels. 
We should probably suppress all labels of interactions.

What version of the product are you using? On what operating system?
-Cytoscape 2.3, Mac OS X

Original issue reported on code.google.com by [email protected] on 28 Dec 2009 at 1:32

Copied from original issue: PathwayCommons/cpath2#30

The border of the search box is not clearly visible in Windows IE.

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1. Go to the home page.
2.
3.

What is the expected output? What do you see instead?
When compared with Firefox, the border on the search box (within 
large_search_box) is not clearly 
visible.

Please use labels and text to provide additional information.

Original issue reported on code.google.com by [email protected] on 1 Oct 2009 at 5:46

Copied from original issue: PathwayCommons/cpath2#17

Reactome EntitySets in PC Gene Set download

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1.Search the pathway commons web interface for "The proton buffering model"
2.Click on Molecules (there are 5 molecules) including the EntitySet UCP
3.Click on Gene Set in Downloads 
(http://www.pathwaycommons.org/pc/record2.do?id=717015#)


What is the expected output? What do you see instead?
The gene set should contain the gene from the xrefs from the entities in the 
molecules tab. These entitySet molecules should be in the gene set.

What version of the product are you using? On what operating system?
-
Email from pc-info
Please provide any additional information below.
Here is another pathway---the proton buffering model pathway from 
Reactome---that is appears to be a problem. You do not list any genes in this 
pathway, but it should contain genes UCP1, UCP2 and UCP3. (At least according 
to the NCBI BioSystems database.) Any idea what is going on here? Thanks!

Peter Carbonetto, Ph.D.
Postdoctoral Fellow
Dept. of Human Genetics
University of Chicago

Original issue reported on code.google.com by [email protected] on 14 Jan 2011 at 8:07

Copied from original issue: PathwayCommons/cpath2#38

Organism filter will remove interactions at pathwaycommons.org

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1. Set organism limit to Homo Sapiens ( or any other organism)
2. Search for an protein or pathway


What is the expected output? What do you see instead?

Expected output is to list pathways and interactions. They are not
currently listed.

This is a difficult problem since the interactions does NOT have an
organism in BioPAX. One of the two logical rules should be used ( TBD):

The interaction should be displayed if
at least one of its participants belongs to the selected organism(s), 

OR alternatively

all of its participants with the exception of small molecules and base
class physical entites belong to the selected organim(s).

Original issue reported on code.google.com by emekdemir on 28 Sep 2009 at 5:25

Copied from original issue: PathwayCommons/cpath2#15

original data batch download: wrong file extension

From @GoogleCodeExporter on March 16, 2015 20:15

What steps will reproduce the problem?
1. http://awabi.cbio.mskcc.org/pc-demo/dbSnapshot.do?snapshot_id=5
2. click "Download BioPAX"
3. browser starts auto-download....

What is the expected output? What do you see instead?
Homo_sapience.owl (locally unpacked, ~60Mb, or maybe a zipped one with. e.g., 
.zip or .tar 
extension)

Instead, it starts download Homo_sapience.owl.gz file, then unpacks it to 
produce the 
Homo_sapience.owl, which is still a binary file (look like a zip archive)!

What version of the product are you using? On what operating system?
Mac OS 10.5.8 and Safari 4.0.4

Please provide any additional information below.
I haven't tested on a different platform.

Original issue reported on code.google.com by [email protected] on 10 Dec 2009 at 10:25

Copied from original issue: PathwayCommons/cpath2#29

The Message Under the Search Box Contains Syntax Errors

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1. open the home page
2. read under the search box

- "..you will get back a list of proteins.." - correct English would be "the 
list of" (because this is the 
specific list that contains...)

- ".. and a list pathways that contain the BRCA1 gene." - - correct is "the 
list of".
 ("of " is also missing)

Original issue reported on code.google.com by [email protected] on 6 Sep 2009 at 3:52

Copied from original issue: PathwayCommons/cpath2#11

Search Results: Search Meter not Centered, IE Specific

Issue by GoogleCodeExporter
Monday Mar 16, 2015 at 20:14 GMT
Originally opened as PathwayCommons/cpath2#8

What steps will reproduce the problem?
1. Search for BRCA1

What is the expected output? What do you see instead?

The search results green meter boxes are not centered vertically within the
search results table.

Please use labels and text to provide additional information.

Original issue reported on code.google.com by [email protected] on 3 Sep 2009 at 6:37

Reactome biopax export causes issue with gene set export

From @GoogleCodeExporter on March 16, 2015 20:15

The gene set output from Reactome pathways is sometimes wrong. Many
pathways of only 1-2 genes get converted to gene sets with 100s of genes.

The issue is that reactome has next-steps which reference other pathways.
We should not traverse these when creating gene sets.  It may make sense to
never traverse pathway steps and instead just collect genes from all
interactions in the pathway, though this will need to be checked to ensure
it covers all cases.

Original issue reported on code.google.com by [email protected] on 3 Dec 2009 at 9:38

Copied from original issue: PathwayCommons/cpath2#28

Null Pointer Exception Occurs When Searching for "dna repair"

From @GoogleCodeExporter on March 16, 2015 20:14

What steps will reproduce the problem?
1.  I searched for "dna repair"  

What is the expected output? What do you see instead?

I got a NullPointerException:

java.lang.NullPointerException
    at
org.apache.jsp.WEB_002dINF.jsp.pages.search.biopax_005fsearch_jsp._jspService(bi
opax_005fsearch_jsp.java:364)
    at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:94)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:856)


What version of the product are you using? On what operating system?


Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 2 Oct 2009 at 1:23

Copied from original issue: PathwayCommons/cpath2#19

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