1 new exercise: protein-translation #125

kapitaali · 2024-04-16T15:18:59Z

Adding 1 new exercise to COBOL track: protein-translation

Based on last pull request attempt, all GOBACKs have been removed from code.

github-actions · 2024-04-16T15:19:14Z

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kapitaali · 2024-04-16T15:21:51Z

Forgot config.json once again, but it has been fixed in my branch.

axtens · 2024-04-17T09:19:56Z

I've sent a pile of comments via the forum. See https://forum.exercism.org/t/requirements-for-cut-and-proof-ci-cob-files/10818

kotp

The suggested changes are to make lines consistent throughout.

exercises/practice/protein-translation/bin/fetch-cobolcheck.ps1

exercises/practice/protein-translation/src/protein-translation.cob

axtens · 2024-04-18T03:33:10Z

@ErikSchierboom still have the appveyor issue COBOL / Test (Windows) / ci (pull_request). A separate issue in COBOL / Test / ci (pull_request)

axtens · 2024-04-18T03:36:02Z

We could stand to remove some of the DISPLAY statements in the various proof.ci.cob files as they clutter up the test runs

axtens · 2024-04-18T03:42:49Z

@kapitaali tests are failing ... but you knew that

ErikSchierboom · 2024-04-18T05:45:28Z

Checking protein-translation practice exercise...
Cobolcheck not found, try to fetch it.
CobolCheck: INFO 2024-04-18T03:35:18.670116Z INF001: Attempting to load config from config.properties.
CobolCheck: INFO 2024-04-18T03:35:18.670267Z INF002: Loaded config successfully from config.properties.
CobolCheck: INFO 2024-04-18T03:35:18.670289Z INF003: Cobol-Check starting
CobolCheck: INFO 2024-04-18T03:35:18.670298Z INF005: Log level is INFO.
CobolCheck: INFO 2024-04-18T03:35:18.670306Z INF006: Configuration settings: production.
CobolCheck: INFO 2024-04-18T03:35:18.670637Z INF014: Error log for the test suite parser is set to: /home/runner/work/cobol/cobol/exercises/practice/protein-translation/ParserErrorLog.txt.
CobolCheck: INFO 2024-04-18T03:35:18.670897Z INF013: Output for generated COBOL test program is set to: /home/runner/work/cobol/cobol/exercises/practice/protein-translation/test.cob.
CobolCheck: INFO 2024-04-18T03:35:18.678179Z INF012: Successfully generated COBOL test program for src/protein-translation.
CobolCheck: INFO 2024-04-18T03:35:18.678224Z INF004: Cobol-Check terminating: 0
COMPILE AND RUN TEST
test.cob: in paragraph 'UT-AFTER-EACH':
test.cob:791: error: syntax error, unexpected PERFORM
protein-translation: proof solution did not pass the tests

That makes it appear like there is a syntax error somewhere in protein-translation.

@ErikSchierboom still have the appveyor issue COBOL / Test (Windows) / ci (pull_request)

Feel free to try and fix that, I don't have much time for that.

axtens · 2024-04-18T08:06:11Z

Feel free to try and fix that, I don't have much time for that.

Righto. I did get feedback from @GitMensch about that. See #126 (comment) but I'll see what I can do about it in the meantime

axtens · 2024-04-18T08:31:47Z

The compiler error is being caused by cobolcheck not properly parsing

AFTER-EACH
	MOVE SPACES TO WS-PROTEIN
END-AFTER

therefore, remove that from the CUT file and explicitly INITIALIZE WS-PROTEIN at the top of the relevant paragraphs.

axtens · 2024-04-18T08:53:22Z

This passes all the tests.

       IDENTIFICATION DIVISION.
       PROGRAM-ID. PROTEIN-TRANSLATION.
       AUTHOR. kapitaali.
       ENVIRONMENT DIVISION.
       DATA DIVISION.
       WORKING-STORAGE SECTION.
       01 WS-INPUT                  PIC X(60).
       01 WS-PROTEIN                PIC X(120).
       01 WS-ERROR                  PIC X(60). 
       01 WS-CODON                  PIC XXX.   
       01 WS-AMINOACID              PIC X(14).
       01 SLICES.
         03 SLICE PIC XXX OCCURS 20 TIMES 
            INDEXED BY SLICED.

       PROCEDURE DIVISION.
       TRANSLATE-CODON.
           INITIALIZE WS-PROTEIN WS-ERROR WS-CODON WS-AMINOACID.
           MOVE WS-INPUT TO SLICES.
           SET SLICED TO 1.
           PERFORM WITH TEST BEFORE UNTIL SLICE(SLICED) = SPACE
               MOVE SLICE(SLICED) TO WS-CODON
               PERFORM CHECK-CODON
               SET SLICED UP BY  1
           END-PERFORM.
           IF WS-AMINOACID = "ERROR" 
             MOVE "Invalid codon" TO WS-ERROR
           ELSE 
             MOVE WS-AMINOACID TO WS-PROTEIN.
           EXIT PARAGRAPH.
           
       CHECK-CODON.
           MOVE SPACES TO WS-AMINOACID.
           EVALUATE WS-CODON 
              WHEN SPACE MOVE SPACE TO WS-AMINOACID
              WHEN "AUG" MOVE "Methionine" TO WS-AMINOACID
              WHEN "UUU" MOVE "Phenylalanine" TO WS-AMINOACID
              WHEN "UUC" MOVE "Phenylalanine" TO WS-AMINOACID
              WHEN "UUA" MOVE "Leucine" TO WS-AMINOACID
              WHEN "UUG" MOVE "Leucine" TO WS-AMINOACID
              WHEN "UCU" MOVE "Serine" TO WS-AMINOACID
              WHEN "UCC" MOVE "Serine" TO WS-AMINOACID
              WHEN "UCA" MOVE "Serine" TO WS-AMINOACID
              WHEN "UCG" MOVE "Serine" TO WS-AMINOACID
              WHEN "UAU" MOVE "Tyrosine" TO WS-AMINOACID
              WHEN "UAC" MOVE "Tyrosine" TO WS-AMINOACID
              WHEN "UGU" MOVE "Cysteine" TO WS-AMINOACID
              WHEN "UGC" MOVE "Cysteine" TO WS-AMINOACID
              WHEN "UGG" MOVE "Tryptophan" TO WS-AMINOACID
              WHEN "UAA" MOVE "STOP" TO WS-AMINOACID
              WHEN "UAG" MOVE "STOP" TO WS-AMINOACID
              WHEN "UGA" MOVE "STOP" TO WS-AMINOACID
              WHEN OTHER MOVE "ERROR" TO WS-AMINOACID
           END-EVALUATE.
           EXIT PARAGRAPH.

       TRANSLATE-RNA.
           INITIALIZE WS-PROTEIN WS-ERROR WS-CODON WS-AMINOACID.
           MOVE WS-INPUT TO SLICES.
           SET SLICED TO 1.
           PERFORM WITH TEST AFTER UNTIL SLICE(SLICED) = SPACE
               MOVE SLICE(SLICED) TO WS-CODON
               PERFORM CHECK-CODON
               IF WS-AMINOACID = "STOP"
                 EXIT PERFORM
               END-IF
               IF WS-AMINOACID = "ERROR"
                 MOVE ",ERROR" TO WS-PROTEIN
                 EXIT PERFORM
               END-IF
               STRING WS-PROTEIN DELIMITED BY SPACE 
                 "," DELIMITED BY SIZE
                 WS-AMINOACID DELIMITED BY SPACE 
                 INTO WS-PROTEIN
               END-STRING
               SET SLICED UP BY 1
           END-PERFORM.
           MOVE WS-PROTEIN(2:) TO WS-PROTEIN.
           IF WS-PROTEIN = "ERROR"
             MOVE "Invalid codon" TO WS-ERROR.
           EXIT PARAGRAPH.

GitMensch · 2024-04-18T09:19:40Z

If this is also about good COBOL, I'd recommend to drop the EXIT PARAGRAPH - that is seldom used and at the end of the paragraph makes no sense at all.

The complete "fall through" would commonly be seen as bad style. It may should be adjusted to instead of

       TRANSLATE-CODON.
           INITIALIZE WS-PROTEIN WS-ERROR WS-CODON WS-AMINOACID.
           MOVE WS-INPUT TO SLICES.
           SET SLICED TO 1.
           PERFORM WITH TEST BEFORE UNTIL SLICE(SLICED) = SPACE
               MOVE SLICE(SLICED) TO WS-CODON
               PERFORM CHECK-CODON
               SET SLICED UP BY  1
           END-PERFORM.
           IF WS-AMINOACID = "ERROR" 
             MOVE "Invalid codon" TO WS-ERROR
           ELSE 
             MOVE WS-AMINOACID TO WS-PROTEIN.
           EXIT PARAGRAPH.

be:

       TRANSLATE-MAIN.
           INITIALIZE WS-PROTEIN WS-ERROR WS-CODON WS-AMINOACID.
           MOVE WS-INPUT TO SLICES.

           PERFORM TRANSLATE-CODON.
           IF WS-AMINOACID = "ERROR" 
             MOVE "Invalid codon" TO WS-ERROR
             GOBACK.

           MOVE WS-AMINOACID TO WS-PROTEIN.
           PERFORM TRANSLATE-RNA.

           GOBACK.

       TRANSLATE-CODON.
           SET SLICED TO 1.
           PERFORM WITH TEST BEFORE UNTIL SLICE(SLICED) = SPACE
               MOVE SLICE(SLICED) TO WS-CODON
               PERFORM CHECK-CODON
               SET SLICED UP BY  1
           END-PERFORM.

kapitaali · 2024-04-18T09:45:01Z

If this is also about good COBOL, I'd recommend to drop the EXIT PARAGRAPH - that is seldom used and at the end of the paragraph makes no sense at all.

it wasn't about good COBOL last time I submitted exercises, the only requirement was that the code passes the tests

GOBACKs supposedly messed up something with testing, so I removed them and used EXIT PARAGRAPH

for good COBOL I would appreciate a style guide

ErikSchierboom · 2024-04-18T09:50:21Z

it wasn't about good COBOL last time I submitted exercises, the only requirement was that the code passes the tests

That is still 100% the case.

GitMensch · 2024-04-18T10:01:17Z

GOBACKs supposedly messed up something with testing, so I removed them and used EXIT PARAGRAPH

GOBACK gets you to the caller (which may be the operating system), you'd only use one if you don't want to "fall out of the program", either in the current fall-through state at the very end, or with a "main" paragraph PERFORMing the other paragraphs at its end, similar as in your example.

As noted: EXIT PARAGRAPH in this code doesn't do anything here, because it gets you directly before the next paragraph - which is the exact place where this statement is.

The rest is a style question and in COBOL those are commonly set fixed in the team/working place (you will find a bunch of those heavily disagreeing; and there may be one where the fall-through is preferred [I've so far just met styles where this was allowed within sections, but not for the whole program]).

axtens · 2024-04-18T20:25:49Z

We've found that GOBACK and STOP RUN confuse COBOLCHECK

GitMensch · 2024-04-18T20:29:37Z

I'm not sure what you reference with COBOLCHECK, but it seems that part is buggy and may should be improved?

axtens · 2024-04-18T22:27:11Z

FYI https://openmainframeproject.org/projects/cobol-check/
github: https://github.com/openmainframeproject/cobol-check/

I'm sure the author would appreciate help improving the tool

axtens · 2024-04-19T13:48:33Z

As asked in the forum, How do I rebase #125 so that it uses the new setup? I thought this was what was needed

bugmagnet@bugmagnet-wasta:~/Projects/Everything_Exercism/exercism-tracks/cobol$ git pull upstream main
remote: Enumerating objects: 1, done.
remote: Counting objects: 100% (1/1), done.
remote: Total 1 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (1/1), 927 bytes | 927.00 KiB/s, done.
From https://github.com/exercism/cobol
 * branch            main       -> FETCH_HEAD
   be1cc08..40ed166  main       -> upstream/main
Successfully rebased and updated refs/heads/protein-translation.

Co-authored-by: Victor Goff <keeperotphones@gmail.com>

….cob Co-authored-by: Victor Goff <keeperotphones@gmail.com>

…cism#126)

…ism#127)

* Add file patterns * Update files keys

* Pre-fetch cobolcheck * Use home dir * Fetch cobolcheck on windows * Allow for pre-installed cobolcheck

* from appveyor to sourceforge * different server * 7z * 7z * yaml issue fixed * slashes * 7z oddities * directories * $HOME ? * atbash tweak * cache management fix * commented out extraneous DISPLAY in proof.ci.cob files * eol issue * line ends fixed * strangenesses * SPACE instead of "" in CUT files * Trim additional line * Debug * Try simplify environment variables * More debugging * More tweaking * Fix path * Fix path * Fix path * Fix env * Streamline * eof is lf * acronym * acronym * sqrt * Fix paths * Fix cache path --------- Co-authored-by: Erik Schierboom <erik_schierboom@hotmail.com>

* Try fix caching * Try fix cache path * Try include cobolcheck * Try include cobolcheck * Use home dir * Use home dir

function all intrinsic on its own line

* Try install * CONCAT -> CONCATENATE * CONCATENATE is two-fer --------- Co-authored-by: Bruce Axtens <bruce.axtens@gmail.com>

axtens · 2024-04-19T14:28:34Z

@kotp all the CI passes. Lots of hard work done by @ErikSchierboom

axtens · 2024-04-19T23:40:04Z

@ErikSchierboom why can't I merge this?

ErikSchierboom · 2024-04-20T07:49:23Z

A maintainer has to approve it first

adding protein-translation

e2ecc24

github-actions bot closed this Apr 16, 2024

fixed config.json for protein-translation

215293b

axtens reopened this Apr 16, 2024

kotp approved these changes Apr 18, 2024

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exercises/practice/protein-translation/bin/fetch-cobolcheck.ps1 Outdated Show resolved Hide resolved

exercises/practice/protein-translation/src/protein-translation.cob Outdated Show resolved Hide resolved

fixing .cut file + proof

1850875

axtens and others added 6 commits April 19, 2024 22:24

Update exercises/practice/protein-translation/bin/fetch-cobolcheck.ps1

a90f979

Co-authored-by: Victor Goff <keeperotphones@gmail.com>

Update exercises/practice/protein-translation/src/protein-translation…

90fccb4

….cob Co-authored-by: Victor Goff <keeperotphones@gmail.com>

Sync the scrabble-score exercise's docs with the latest data. (exer…

9c05dc0

…cism#126)

Sync the all-your-base exercise's docs with the latest data. (exerc…

4f16df4

…ism#127)

Simplify test workflow (exercism#129)

dcfbb3c

Format config.json file (exercism#131)

ea143ac

ErikSchierboom and others added 6 commits April 19, 2024 22:24

file patterns (exercism#132)

aaedb5b

* Add file patterns * Update files keys

Pre-fetch cobolcheck (exercism#130)

6da8588

* Pre-fetch cobolcheck * Use home dir * Fetch cobolcheck on windows * Allow for pre-installed cobolcheck

Try fix Windows caching (exercism#133)

08f3786

* Try fix caching * Try fix cache path * Try include cobolcheck * Try include cobolcheck * Use home dir * Use home dir

Update proof.ci.cob (exercism#135)

2efc20e

function all intrinsic on its own line

Cache on linux (exercism#134)

3291be3

* Try install * CONCAT -> CONCATENATE * CONCATENATE is two-fer --------- Co-authored-by: Bruce Axtens <bruce.axtens@gmail.com>

axtens force-pushed the protein-translation branch from 24b25eb to 3291be3 Compare April 19, 2024 14:24

axtens requested a review from kotp April 19, 2024 14:27

kotp approved these changes Apr 19, 2024

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axtens self-requested a review April 20, 2024 11:24

axtens approved these changes Apr 20, 2024

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axtens merged commit 835af7f into exercism:main Apr 20, 2024
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1 new exercise: protein-translation #125

1 new exercise: protein-translation #125

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1 new exercise: protein-translation #125

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