-
-
-
-
-
-
JavaScript JSON convertors for Cytoscape 3.0 file formats
-
-
-
-
-
-
Project Idea:
-
-
-
-
The project title is: JavaScript JSON convertors for
-Cytoscape 3.0 file formats.
-
-
The idea is based upon suggested Idea 19: JavaScript JSON
-convertors for graph file formats, but I would like to drop the word “graph”
-from it, because this project will support virtually all formats accepted by
-Cytoscape 3.0 .
-
-
Synopsis:
-
-
-
-
This project deals with the conversion of different graph
-and other formats used in Cytoscape 3.0 to Json used in cytoscape.js and vice
-versa.
-
-
Cytoscape 3.0 accepts file formats like xgmml, graphml, gml,
-nnf, sif, xls, sif, csv whereas cytoscape.js currently accepts only json
-representations of the data. It is not an easy task to create json
-representation of a required graph by hand. This is where this project comes
-in. I will develop some converters using JavaScript which will automate this generation
-of json representation. Cytoscape-web, the predecessor of Cytoscape.js
-supported only sif files, but this project will support import and export to
-all the formats mentioned earlier.
-
-
Implementation details:
-
-
-
-
The Cytoscape 3.0 file formats that will be supported are:
-
-
Xgmml, Graphml, Sif, Nnf, Gml (,Csv, Xlsx).
-
-
They are arranged according to their priority and so this is
-the order in which their json converters will be implemented. The last two (in
-bracket) will be kept as extras, meaning that they will be implemented only if
-the project is finished well before the deadline (see the timeline for details)
-.
-
-
![]()
-
-
Now, this is how I plan to deal with each of them.
-
-
1.
-Xgmml: This is the top priority format and hence will be dealt with
-first. Xml parsers available in native javascript and jquery will be used for
-parsing the xgmml file. Then some JavaScript code (using looping and if needed,
-regular expressions) will deal with the parsed xml file to convert them
-correctly into javascript variables and objects. Finally, they can be used to
-generate its json representation. (Maybe, take some inspiration from this
-library in Gremlin (written in java): https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library
-)
-
-
This required some separate
-functions which can:
-
-
·
-convert parsed xml to jS variables and objects
-
-
·
-create xml from given jS variables and objects
-
-
·
-save given jS variables and objects as json
-
-
·
-convert json into given jS variables and objects
-
-
-
-
2. Graphml:
-Graphml is also a xml-based format, so the implementation process is same as
-that of the previous one. Only the code will be different to take care of the
-syntax difference of these formats.
-
-
-
-
Before I move on to the other ones, here
-is a small chart for reference:
-
-
-
-
![]()
-
-
3. Sif
-and Nnf: Very simple jS code needs to be written to take care of these file
-formats. There is already a python-based implementation of these converters
-(written by me) available at https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py
- . Nnf files will be stripped off its network information and treated just
-like a Sif file (Possible problem with multi-network files ??)
-
-
4. GML:
-A custom-made parser needs to be built based on regular expressions (native js
-or possibly using xregexp library http://xregexp.com/
-). The rest of the plan is the same as that of xgmml, only this new parser will
-be used.
-
-
Few words on the extras:
-
-
These extras will be done only if there is ample time left
-after the completion of the whole project, so there is no way that they will
-harm the main project. I am aware that new GSOC applicants like me tend to
-propose a lot more than they can actually complete, so I have tried not to fall
-in that trap. But these extras are here, because I plan to do them in the
-future, within or after GSOC. Also, as a side note, in future, I wish to
-release this codes as a separate jS library for converting customized-xml
-formats into json (I hope my mentoring org will allow this).
-
-
5. Csv:
-Use any well-documented csv parser and rest is the same.
-
-
6. Xlsx:
-This is the most challenging part. I wouldn’t have tried this if there was no
-cross-browser external library to read and write xlsx format. But thankfully
-and quite surprisingly, there is one called Xlsx.js https://github.com/stephen-hardy/xlsx.js
-. I am not much sure if I can pull off this part, but I am still including this
-in the proposal mostly for my inspiration than anything else. Also, I know that
-the Cytoscape project originally supported .xls, but I think its best kept to
-Microsoft Excel for converting .xls into .xlsx .
-
-
-
-
Timeline:
-
-
-
-
1.
-Before June 17 :
-
-
o Learn
-more about:
-
-
o Jquery,
-xregexp, csv-parser, json, xlsx.js and the graph formats.
-
-
o Set up
-development environment
-
-
2.
-June 17 – July 6 (18 days): Implement xgmml converter
-
-
o June 17 –
-June 29 (12 days): Implement xgmml parser
-
-
o July 30 –
-July 5 (6 days): Rest of the converter
-
-
3.
-July 5 – July 7 (3 days): Test converter with different xgmml
-files.
-
-
4.
-July 8 – July 25 (18 days): Implement graphml converter
-
-
o July 8 –
-July 19 (12 days): Implement graphml parser
-
-
o July 20 –
-July 25 (6 days): Rest of the converter
-
-
5.
- July 26 – July 28 (3 days): Test graphml converter
-
-
6.
-July 29 (Mid-term evaluation): Deliver fully-implemented xgmml
-and graphml parser.
-
-
7.
-July 30: Take a day off from coding and analyze what went right
-and wrong in the first-term. (How about a blog post? :D)
-
-
8.
-July 31 – August 2 (3 days): Implement and test Sif and Nnf
-converter.
-
-
9.
-August 3 – August 20 (18 days): Implement Gml converter (First 12
-days for the parser).
-
-
10.
-August 21 – August 23 (3 days): Test Gml converter
-
-
11.
-August 24 – August 27 (4 days): Put all the converters together
-and test them (Packaging).
-
-
12.
-August 28 – September 3 (10 days): Prepare documentation and add
-inline comments in the code.
-
-
13.
-September 4 – September 16 (13 days): Buffer time (If everything
-is working, work on the extras)
-
-
(Feedback will be obtained for all the converters from the
-community and they will be of more importance than the extras)
-
-
Possible hurdles:
-
-
-
-
1.
-Json handler in Cytoscape.js might not be able to handle objects
-within the “data” section. If so, request the developer or send a patch to the
-core project so that it is supported.
-
-
2.
-Make sure the regular-expression based Gml parser is not buggy.
-
-
3.
-The input graph formats might not be well-formed (if manually
-created). (Maybe, add a xml-checker and discard non well-formed files. Such a
-checker might not be possible in case of non-xml based formats. )
-
-
What can I bring to the team?
-
-
-
-
ü
-Yes, I am committed in working hard for this GSOC project this
-summer. I do not have any other commitment during the summer other than my
-college internals for the next session which should be held near the end of
-August or the start of September. I am not yet sure about the date, but I will
-ask for a one-week break during that time. I hope it won’t be much of a
-problem.
-
-
ü
-Being my first GSOC project, I am also super-excited about it,
-can’t wait to have a fruitful summer this year.
-
-
ü
-I wish to learn some more about the core Cytoscape project but as
-I am not a Java developer, I wish to linger with the Cytoscape.js project.
-
-
+
+
+
+
+
+
JavaScript JSON convertors for Cytoscape 3.0 file formats
+
+
+
+
+
+
Project Idea:
+
+
+
+
The project title is: JavaScript JSON convertors for
+Cytoscape 3.0 file formats.
+
+
The idea is based
+upon suggested Idea 19: JavaScript JSON convertors for graph file formats, but
+I would like to drop the word “graph” from it, because this project will
+support virtually all formats accepted by Cytoscape 3.0 .
+
+
Synopsis:
+
+
+
+
This project deals with the conversion of different graph
+and other formats
+used in Cytoscape 3.0 to Json used in cytoscape.js and vice versa.
+
+
Cytoscape 3.0 accepts file formats like xgmml, graphml, gml,
+nnf, sif, xls, sif, csv whereas cytoscape.js currently accepts only json
+representations of the data. It is not an easy task to create json
+representation of a required graph by hand. This is where this project comes
+in. I will develop some converters using JavaScript which will automate this generation
+of json representation. Cytoscape-web,
+the predecessor of Cytoscape.js supported only sif files, but this project will
+support import and export to all the formats mentioned earlier.
+
+
Implementation details:
+
+
+
+
The Cytoscape 3.0 file formats that will be supported are:
+
+
Xgmml, Graphml, Sif, Nnf, Gml (,Csv,
+Xlsx).
+
+
They are arranged according to their priority and so this is
+the order in which their json converters will be implemented. The last two (in
+bracket) will be kept as extras, meaning that they will be implemented only if
+the project is finished well before the deadline (see the timeline for details) .
+
+
![]()
+
+
Now, this is how I plan to deal with each of them.
+
+
1.
+Xgmml: This is the top priority format and hence
+will be dealt with first. Xml parsers available in native javascript
+and jquery will be used for parsing the xgmml file.
+Then some JavaScript code (using looping and if needed, regular expressions)
+will deal with the parsed xml file to convert them correctly into javascript variables and objects. Finally, they can be used
+to generate its json representation. (Maybe, take some inspiration from this
+library in Gremlin (written in java): https://github.com/tinkerpop/blueprints/wiki/GraphSON-Reader-and-Writer-Library
+)
+
+
This required some separate
+functions which can:
+
+
·
+convert parsed xml to jS
+variables and objects
+
+
·
+create xml from given jS
+variables and objects
+
+
·
+save given jS
+variables and objects as json
+
+
·
+convert json into given jS
+variables and objects
+
+
+
+
2.
+Graphml:
+Graphml is also a xml-based format, so the
+implementation process is same as that of the previous one. Only the code will
+be different to take care of the syntax difference of these formats.
+
+
+
+
Before I move on to the other ones, here is a
+small chart for reference:
+
+
+
+
![]()
+
+
3.
+Sif and Nnf: Very simple jS
+code needs to be written to take care of these file formats. There is already a
+python-based implementation of these converters (written by me) available at https://github.com/bendtherules/GSOC_13/tree/master/nnf_and_sif_to_json_py
+ . Nnf files will be stripped off its
+network information and treated just like a Sif file (Possible problem with
+multi-network files ??)
+
+
4.
+GML: A
+custom-made parser needs to be built based on regular expressions (native js or possibly using xregexp
+library http://xregexp.com/ ). The rest of
+the plan is the same as that of xgmml, only this new
+parser will be used.
+
+
Few words on the extras:
+
+
These extras will be done only if there is ample time left
+after the completion of the whole project, so there is no way that they will
+harm the main project. I am aware that new GSOC applicants like me tend to
+propose a lot more than they can actually complete, so I have tried not to fall
+in that trap. But these extras are here, because I plan to do them in the
+future, within or after GSOC. Also, as a
+side note, in future, I wish to release this codes as a separate jS library for converting customized-xml formats into json
+(I hope my mentoring org will allow this).
+
+
5.
+Csv: Use
+any well-documented csv parser and rest is the same.
+
+
6.
+Xlsx: This is the most challenging part. I
+wouldn’t have tried this if there was no cross-browser external library to read
+and write xlsx format. But thankfully and quite surprisingly, there is one
+called Xlsx.js https://github.com/stephen-hardy/xlsx.js
+. I am not much sure if I can pull off this part, but I am still including this
+in the proposal mostly for my inspiration than anything else. Also, I know that
+the Cytoscape project originally supported .xls, but I think its best kept to
+Microsoft Excel for converting .xls into .xlsx .
+
+
+
+
Timeline:
+
+
+
+
1. Before
+June 17 :
+
+
o Learn
+more about:
+
+
o Jquery, xregexp, csv-parser, json, xlsx.js and the graph formats.
+
+
o Set
+up development environment
+
+
2. June
+17 – July 6 (18 days): Implement xgmml converter
+
+
o June
+17 – June 29 (12 days): Implement xgmml parser
+
+
o July
+30 – July 5 (6 days): Rest of the converter
+
+
3. July
+5 – July 7 (3 days): Test converter with different xgmml files.
+
+
4. July
+8 – July 25 (18 days): Implement graphml converter
+
+
o July 8 – July 19 (12 days): Implement graphml
+parser
+
+
o July
+20 – July 25 (6 days): Rest of the converter
+
+
5. July 26 – July 28 (3 days): Test graphml converter
+
+
6. July
+29 (Mid-term evaluation): Deliver
+fully-implemented xgmml and graphml parser.
+
+
7. July
+30: Take a day off from coding and analyze what went right and wrong in the
+first-term. (How about a blog post? :D)
+
+
8. July
+31 – August 2 (3 days): Implement and test Sif and Nnf converter.
+
+
9. August
+3 – August 20 (18 days): Implement Gml converter (First 12 days for the
+parser).
+
+
10. August
+21 – August 23 (3 days): Test Gml converter
+
+
11. August
+24 – August 27 (4 days): Put all the converters
+together and test them (Packaging).
+
+
12. August
+28 – September 3 (10 days): Prepare documentation and add inline comments in
+the code.
+
+
13. September
+4 – September 16 (13 days): Buffer time (If everything is working, work on the
+extras)
+
+
(Feedback will be obtained for all the converters from the
+community and they will be of more importance than the extras)
+
+
Possible hurdles:
+
+
+
+
1. Json
+handler in Cytoscape.js might not be able to handle objects within the “data”
+section. If so, request the developer or send a patch to the core project so
+that it is supported.
+
+
2. Make
+sure the regular-expression based Gml parser is not buggy.
+
+
3. The
+input graph formats might not be well-formed (if manually created). (Maybe, add
+a xml-checker and discard non well-formed files. Such
+a checker might not be possible in case of non-xml based formats. )
+
+
What can I bring to the team?
+
+
+
+
ü
+Yes, I am committed in working hard for this
+GSOC project this summer. I do not have
+any other commitment during the summer other than my college internals for the
+next session which should be held near the end of August or the start of
+September. I am not yet sure about the date, but I will ask for a one-week
+break during that time. I hope it won’t be much of a problem.
+
+
ü
+Being my first GSOC project, I am also
+super-excited about it, can’t wait to have a fruitful summer this year.
+
+
ü
+I wish to learn some more about the core
+Cytoscape project but as I am not a Java developer, I
+wish to linger with the Cytoscape.js project.
+
+