Support for new error types

[hasanbalci]

Support below error codes:

• 1. pd10001: ID needs to be unique
• 2. pd10002: An arc source/target should be a glyph defined in the diagram
• 3. pd10110: Modulation arc must have target reference to PN classes
• 4. pd10127: Arc with class equivalence arc must have source reference to glyph of EPN classes
• 5. pd10128: Arc with class equivalence arc must have target reference to glyph of classes 'tag', 'submap' or 'terminal'
• 6. pd10141: All process nodes should have at least one input and at least one ouput

[YusufZiyaOzgul]

@ugurdogrusoz @hasanbalci for item 3, modulation arc target is connected to one of the nearby PN's as a resolution, for item 4, equivalence arc source is connected to one of the nearby EPN's as a resolution, for item 5, equivalence arc target is connected to one of the nearby 'tag', 'submap' or 'terminal'. for item 6, process is connected to one of the nearby EPN's as an input with class consumption arc if input is missing, process is connected to one of the nearby EPN's as output with class production arc if output is missing.

[hasanbalci]

@YusufZiyaOzgul For item 6, please see #27.

[hasanbalci]

For item 3, 4, 5 and 6, fix explanations should be corrected. Currently, it always says "Fix of another error resolved this error." when these error types are resolved, even though we select one of the suggested choices. But the fixes work correctly for these items except item 6. So we should fix the fix problem in item 6 and explanations for items 3, 4, 5 and 6.

[YusufZiyaOzgul]

For item 3, 4, 5 and 6, fix explanations should be corrected. Currently, it always says "Fix of another error resolved this error." when these error types are resolved, even though we select one of the suggested choices. But the fixes work correctly for these items except item 6. So we should fix the fix problem in item 6 and explanations for items 3, 4, 5 and 6.

@hasanbalci @ugurdogrusoz fix explanations are added for item 3,4,5,6 and now it works correct. the resolve for item 6 works correct now. pd10001 and pd10002 is handled now. If these occur, SyBValS does nothing and return error message.

[hasanbalci]

The fix explanations for item 3, 4, 5, 6 and resolve for item 6 are now correctly working. But for pd10001 and pd10002, cannot we add errors like in the other cases? When these errors exist, we can still load the maps and apply validation, but only the node with non-unique id or the arc without source or target is not drawn. So I think if these errors exist we can continue to validation as before, but we can add these errors to the error list shown on the left panel. @ugurdogrusoz What do you think?

[ugurdogrusoz]

The fix explanations for item 3, 4, 5, 6 and resolve for item 6 are now correctly working. But for pd10001 and pd10002, cannot we add errors like in the other cases? When these errors exist, we can still load the maps and apply validation, but only the node with non-unique id or the arc without source or target is not drawn. So I think if these errors exist we can continue to validation as before, but we can add these errors to the error list shown on the left panel. @ugurdogrusoz What do you think?

We can do it like @hasanbalci suggests if not very difficult.

[ugurdogrusoz]

Let's try solving items 1 & 2 as discussed over Skype.

[YusufZiyaOzgul]

Let's try solving items 1 & 2 as discussed over Skype.

@ugurdogrusoz @hasanbalci these items are solved as discussed.

[hasanbalci]

@YusufZiyaOzgul For pattern pd10141, please make sure that we only suggest nodes from EPN class.

[hasanbalci]

For pattern pd10001, can we print the error only one time for each id that is not unique? Currently if there are two nodes
with the same id, we see the error twice.

test_file.sbgn.txt In this file, there is no glyph with the source id of the consumption edge, therefore it doesn't add the edge, but it doesn't show error with pattern pd10002.

[hasanbalci]

@YusufZiyaOzgul They look good, thanks!