The bacting from egonw

BioclipsePlatformManager

~~public void planet() throws BioclipseException {~~ reason: GUI
~~public void wiki() throws BioclipseException {~~ reason: GUI
public String logfileLocation() {
~~public void bugTracker() throws BioclipseException {~~ reason: GUI
public String download(String url, IProgressMonitor monitor)
public String download(String url, String mimeType,
public IFile downloadAsFile(String url, IFile target,
public IFile downloadAsFile(String url, String mimeType, IFile target,
public IFile downloadAsFile(String url, String mimeType, IFile target,
public byte[] sparqlRemote(
~~public void openURL(URL url) throws BioclipseException {~~ reason: GUI
public boolean isOnline() {
public String version() {
public void requireVersion( String version ) throws BioclipseException {
public void assumeOnline() throws BioclipseException {
public void requireVersion( String lowerVersionBound,
public String fullPath(IFile file) {

figure out compile issues

as reported by @arcuri82 in #11. At this moment I cannot reproduce the failing to compile because of the missing JavaDoc (see also #22).

Eclipse Public License 1.0 (EPL-1.0) has been superseded

I have a question regarding the license. Why is this repository under Eclipse Public License 1.0 (EPL-1.0), when it's been superseded by Eclipse Public License 2.0 (EPL-2.0)?

Not a major issue or anything like that, but maybe you can explain that to me?

Thanks!

Add Maven installation link

For users that do not have Maven installed (but Ant for example), add a link to page explaining installation: https://www.baeldung.com/install-maven-on-windows-linux-mac (worked fine for me).

Installation tries to sign with gpg and fails

Dear @egonw,

when attempting to install with mvn clean install I run into:

[INFO] --- maven-gpg-plugin:1.5:sign (sign-artifacts) @ bacting ---
gpg: no default secret key: No secret key
gpg: signing failed: No secret key

The installation should not try to sign keys, or?
Am I missing something?

clarify Spring

From #11:

What is "Spring approaches"? Are you referring to the Spring Framework (https://spring.io/)?

ponder about JavaScript examples

Explore GraalVM to run JavaScript with Bacting managers.

Goal: version 2.0

This version will be able to run all Bioclipse scripts publishing in peer reviewed journal articles.

figure out a more robust installation instructions for Windows

... because even installing Groovy seems tricky :(

Split into two repositories

One for Bacting and one for Bioclipse-NG.

oscar.extractText() and .findResolvedNamedEntities()

Method described in this 2011 paper.

Plugin source code is available from: https://github.com/bioclipse/bioclipse.oscar

Example use

A short code example where the API method is used.

// Demo showing the Oscar text mining functionality

var html = "<html><body>Benzene and toluene.</body></html>";

var text = oscar.extractText(html);
var mols = oscar.findResolvedNamedEntities(text);

var file = "/Oscar Demo/extractedMols.sdf";
cdk.saveSDFile(file, mols);
ui.open(file);

a bit more about Bioclipse

From #11:

provide URL to original Bioclipse, besides tha academic reference to (Spjuth et al., 2007).
Furthermore, should add 2-3 sentences specifying what Bioclipse does.

Extract specific tasks from JOSS reviews:

#10
#11

add a section on making releases

From #10 (comment):

I suggest that you also very quickly add a section on making releases. I doubt
that any maintainers want to read the paper to find out how releases should be
created.

check if paper can be updated for progress monitoring

@egonw mean with missing progress monitoring

See: openjournals/joss-reviews#2558

install.md file not found

The install.md file in the README is not present.

Update copyright description

Copyright is now up to 2018, should read 2019:

CDKManager.loadMolecule with Scyjava does not work

Bacting API method with unexpected output

loadMolecule did not work when importing CDKManager with scyjava.

Expected Output

kegg_sdf will be a data object for the given input

Actual Output

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-14-9f73bc61576b> in <module>()
----> 1 kegg_sdf = cdk.loadMolecule("./kegg.sdf")

TypeError: No matching overloads found for net.bioclipse.managers.CDKManager.loadMolecule(str), options are:
	public net.bioclipse.cdk.domain.ICDKMolecule net.bioclipse.managers.CDKManager.loadMolecule(java.io.InputStream,org.openscience.cdk.io.formats.IChemFormat) throws net.bioclipse.core.business.BioclipseException,java.io.IOException

Additional context

You can reproduce the error with https://colab.research.google.com/drive/1RwXBVgClncDwascTbhhsFkuzPmgFl6ar?usp=sharing

ponder about JPython and JavaScript examples

As asked about in #11

Update SPARQL instructions

See https://www.wikipathways.org/index.php/Help:WikiPathways_SPARQL_queries#Bioclipse

add issue templates

port request
bug report

From #10 (comment)

CDKDebugManager

public String diff(ICDKMolecule mol, ICDKMolecule mol) {
public String debug(ICDKMolecule mol) {
public String getManagerName() {
public String perceiveSybylAtomTypes(IMolecule mol)
public String perceiveCDKAtomTypes(IMolecule mol)
public String listWriterOptions(IChemFormat format) {
public String listReaderOptions(IChemFormat format) {

ADD Licence file

Licence is only mentioned in README, would create a separate file for this repo.

Update Copyright info in HEADER

From #11:

"All code in the /bioclipse/ folder": I do not see such folder.

This content in the "Copyright and authors" section is outdated (predates the split into a separate folder).

ChemspiderManager

public IFile loadCompound(int csid, IFile target, IProgressMonitor monitor)
public List resolve(String inchiKey, IProgressMonitor monitor)
public String downloadAsString(Integer csid, IProgressMonitor monitor)
public IMolecule download(Integer csid, IProgressMonitor monitor)
public List similaritySearch(IMolecule mol, Float tanimoto, IProgressMonitor monitor)
public List exactSearch(IMolecule mol, IProgressMonitor monitor)
public List substructureSearch(IMolecule mol, IProgressMonitor monitor)
public List simpleSearch(IMolecule mol, IProgressMonitor monitor)

add missing JavaDoc

To fix the warnings during compilation:

[WARNING] Javadoc Warnings
[WARNING] /home/egonw/var/Projects/hub/bacting/managers-cheminfo/net.bioclipse.managers.inchi/src/main/java/net/bioclipse/managers/InChIManager.java:157: warning - @param argument "inchikey" is not a parameter name.
[WARNING] /home/egonw/var/Projects/hub/bacting/managers-cheminfo/net.bioclipse.managers.inchi/src/main/java/net/bioclipse/managers/InChIManager.java:177: warning - @param argument "inchikey" is not a parameter name.

BridgedbManager.loadRelationalDatabase with Scyjava does not work

Bacting API method with unexpected output

loadRelationalDatabase did not work when importing BridgedbManager with scyjava.

See

Expected Output

test will be IDMapper object

Actual Output

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-9-eee82142c20a> in <module>()
----> 1 test = bdbClass.loadRelationalDatabase("./metabolites_20210109.bridge")

TypeError: No matching overloads found for *static* net.bioclipse.managers.BridgedbManager.loadRelationalDatabase(str), options are:
	public org.bridgedb.IDMapper net.bioclipse.managers.BridgedbManager.loadRelationalDatabase(java.lang.String) throws net.bioclipse.core.business.BioclipseException

Additional context

You can reproduce this with https://colab.research.google.com/drive/1hs-yuKl_pOCIkUl5DM4h_Ecyp6rI2cOx?usp=sharing

README does not state in 1-2 sentences what Bacting is about

From #10 (comment):

The README does not state in 1-2 sentences what Bacting is about. I suggest
that you add 1-2 sentences from your JOSS paper so that viewers of this repository
know at a glance what it is about.

Documentation lacks a few key issues

I have a couple of suggestions regarding the documentation:

The README does not state in 1-2 sentences what Bacting is about. I suggest that you add 1-2 sentences from your JOSS paper so that viewers of this repository know at a glance what it is about.
Please mention the supported Java versions (CI pipeline gives me the answer, but still...)
Please state more clearly which features of the original API are not covered. I assume that the readers of the README are interested in this information and don't want to make a diff themselves.
I suggest that you also very quickly add a section on making releases. I doubt that any maintainers want to read the paper to find out how releases should be created.
Please add some community guidelines on how to contribute. I suggest a contributing.md file with a couple of sentences, maybe a code of conduct, some issue and PR templates etc. Feel free to ask me if you need clarification here.

Goal: Version 1.0

This version has the significant part implemented of:

Where significant is at least 30%.

WikidataManager

hasMolecule(InChI inchi)
getEntityID(InChI inchi)
getMolecule(InChI inchi) which returns an IMolecule

PathvisioManager

public String exportPNG(String pathwayFile)
public Set queryWikipathways(String label)
public String getGPML(String pathwayID)

ReportManager

public IReport createReport()
public String asHTML(IReport report)

state more clearly which features of the original API are not covered

From #10 (comment):

Please state more clearly which features of the original API are not covered. I assume that
the readers of the README are interested in this information and don't want to make a diff
themselves.

IcebearManager

public List findInfo(IMolecule mol) throws BioclipseException
public List findInfo(String uri) throws BioclipseException
public String saveAsHTML(List stores, String filename) throws BioclipseException, CoreException
public List getProperties(IRDFStore store) throws BioclipseException, CoreException;

set up Bacting bundle with everything

Like the CDK bundle.

port xml.validate(IFile file, IProgressMonitor monitor)

This issue is specifically about porting a single Bioclipse methods to the XMLManager of Bacting.
The goal is that the API (manager method) call is identical in Bacting as it is in Bioclipse 2.6.2.

This issue is about porting xml.validate(IFile file, IProgressMonitor monitor). In Bacting, the
manager method signature should therefore be xml.validate(String file) where the String value is the
Bioclipse Project filename, like /SomeProject/someFile.txt.

This issue provides some pointers to get your going:

read the CONTRIBUTING.md
find the Bioclipse source code (here: validate)
create the new method with the same implementation as in the Bioclipse code
create new test methods that test as many lines in the new method as possible
check if the JavaDoc is complete

JOSS review 2558: first set of comments

First set of comments for JOSS submission 2558.

PAPER:

The paper looks fine. I only have a few minor comments.

Summary: provide URL to original Bioclipse, besides tha academic reference to (Spjuth et al., 2007). Furthermore, should add 2-3 sentences specifying what Bioclipse does.
What is "Spring approaches"? Are you referring to the Spring Framework (https://spring.io/)?
Why there is the section for "Grabbing Bacting from Groovy"? Isn't that something more fitting for the Readme in repository instead of the paper? Furthermore, if you discuss it for Groovy, why not for JavaScript and Python as well?

README

"Bacting := acting as the Bioclipse TNG": what is TNG?
"If you use this software, please cite the Bioclipse 2 paper"
But this tool is called Bacting.
What is the relation between Bioclipse 2 and Bacting. Did you just re-named Bioclipse 2 into Bacting? If so, this should be clarified.
"Bacting is a Java-based, open-source platform..." however, the example is in Groovy. Why not Java? And what is that example doing? (Could add 1-2 sentences saying what it should be for)
In the Readme, need a full working example to show what Bacting can do. I see the "For a description of the API, I refer to the book", but you still need some full examples here.
Note that JOSS explicitly requires: "Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)."
"All code in the /bioclipse/ folder": I do not see such folder.

CODE:

"mvn clean install -Dgpg.skip" fails the build, due to
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-javadoc-plugin:3.2.0:jar (attach-javadocs) on project managers-ui: MavenReportException: Error while generating Javadoc:
[ERROR] Exit code: 1 - /Users/foo/WEB/joss/bacting/managers-core/src/main/java/net/bioclipse/managers/BioclipseManager.java:89: warning: no description for @throws
[ERROR] * @throws BioclipseException

as it is now, I cannot run the code, as I cannot compile it, nor follow an example to try it out.

The groupId is "io.github.egonw.bacting", which is the package used in some modules, e.g. "bacting-core". However, most of the code is under "net.bioclipse.managers".
Why? Shouldn't it be "io.github.egonw.bacting.managers"?
Or is this related to "All Bacting scripts will be backwards compatible with Bioclipse"?
That would make sense for Groovy.
But, in such case, what about Python and JavaScript? Or are those not supported in Bacting? This needs to be clarified in the documentation.
There are some test cases, but I do not see any check on coverage. Could add JaCoCo (https://www.eclemma.org/jacoco/), and then publish the results on some services like CodeCov (https://codecov.io/). This can then be automated in Travis with a simple:

after_success:
- bash <(curl -s https://codecov.io/bash)

You can then also add a badge in Readme for GitHub to display (eg, as you already do for "build-passing" for Travis).

BiojavaManager

InChIManager

public void generate( IMolecule molecule,
public void generate( IMolecule molecule, String options,
public List options() {
public String load() {
public boolean isLoaded() {
public boolean checkKey(String inchikey) throws BioclipseException {
public boolean check(String inchi) throws BioclipseException {
public boolean checkStrict(String inchi) throws BioclipseException {
public boolean isAvailable() {

XmlManager

public boolean isWellFormed(IFile file, IProgressMonitor monitor)
public boolean isValid(IFile file, IProgressMonitor monitor)
public List validate(IFile file, IProgressMonitor monitor)
public List validateAgainstXMLSchema(
public List validateAgainstRelaxNG(
public List validateAgainstSchematron(
public List listNamespaces(IFile file) throws BioclipseException {

set up JaCoCo code coverage testing

See #11

OpsinManager

public ICDKMolecule parseIUPACName(String iupacName, IProgressMonitor monitor)
public String parseIUPACNameAsCML(String iupacName, IProgressMonitor monitor)
public String parseIUPACNameAsSMILES(String iupacName, IProgressMonitor monitor)

egonw / bacting Goto Github PK

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oscar.extractText() and .findResolvedNamedEntities()

Example use

Bacting API method with unexpected output

Expected Output

Actual Output

Additional context

Bacting API method with unexpected output

Expected Output

Actual Output

Additional context

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