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Rename source and sink to empty set #658

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ugurdogrusoz opened this issue Apr 11, 2021 · 5 comments
Open

Rename source and sink to empty set #658

ugurdogrusoz opened this issue Apr 11, 2021 · 5 comments

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@ugurdogrusoz
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ugurdogrusoz commented Apr 11, 2021 •
edited

The latest SBGN PD names these nodes "Empty set", so let's rename them. Let's review other node (glyphs) and edge (archs) types as well.
msalihaltun added a commit to iVis-at-Bilkent/sbgnviz.js that referenced this issue Jun 1, 2021
@msalihaltun
Rename source and sink to empty set
ed33cfc 
  iVis-at-Bilkent/newt#658
msalihaltun added a commit to iVis-at-Bilkent/chise.js that referenced this issue Jun 1, 2021
@msalihaltun
Rename source and sink to empty set
522b431 
  iVis-at-Bilkent/newt#658
msalihaltun added a commit that referenced this issue Jun 1, 2021
@msalihaltun
Rename source and sink to empty set #658
290adf6
@msalihaltun
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The related tests failed because the link in the test points to master version of one of our files which had the source and sink to empty set change.

@ugurdogrusoz
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Let's find out whether "source and sink" should be used in SBGNML's when reading and writing with the UI using "empty set".

@msalihaltun msalihaltun mentioned this issue Jun 2, 2021
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@ugurdogrusoz
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ugurdogrusoz commented Jun 2, 2021 •
edited

Let's accept both "source and sink", "empty set", and "emptyset" when reading. For writing, let's keep using "source and sink" since SBGNML is still outdated in this respect. The UI should refer to the node with the new name "empty set" though.

msalihaltun added a commit that referenced this issue Jun 2, 2021
@msalihaltun
Fix #658
42d892c 
  Address #658 (comment)

  Rename changes in sample files back to 'source and sink' since that's
  what we use now for reading and writing.

  Should also fix the failing test.
@ugurdogrusoz
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This map with a single process passes the checks in public Newt but not the daily build. Could this be related to not renaming / using the new node class name?
Screenshot 2021-06-07 111403

msalihaltun added a commit that referenced this issue Jun 7, 2021
@msalihaltun
Undo node class name changes in validation files
734adfe 
  Addressing #658 (comment)
@ugurdogrusoz
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Since SBGNML, other tools, validator, etc. might be referring to the old name, let's keep this issue open for a while.

@ugurdogrusoz ugurdogrusoz removed their assignment Jun 7, 2021
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@ugurdogrusoz @msalihaltun