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ParasiteTracker / tpt-reporting

Terrestrial Parasite Tracking Reporting Methods
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generate-report.sh not creating expected results on Mac #6

Closed seltmann closed 4 years ago

seltmann commented 4 years ago

@jhpoelen I am still getting unexpected results with the report script on Mac. I did update.

Screen Shot 2020-02-05 at 1 50 54 PM
jhpoelen commented 4 years ago

Thanks for sharing. Which version of elton are you using? elton version . If not 0.7.6 or higher, then please new version install via https://github.com/globalbioticinteractions/elton/#install .

Then, re-run the report using: ./generate-report.sh | tee report.log

and attach report.log to this issue. Thanks for being patient.

jhpoelen commented 4 years ago

Just noticed a bug in the report archive constructions (see https://github.com/ParasiteTracker/tpt-reporting/commit/7a65ed953c126478dd37f14603953758ab26df1b) , am rebuilding using travis.

jhpoelen commented 4 years ago

I checked the report zip in tpt-reporting and it contained the expected content. Please verify/ confirm.

seltmann commented 4 years ago

@jhpoelen using version fa95b07

indexed_interactions_by_collection.tsv is not reporting any data review_summary.tsv and review_summary_by_collection.tsv not reporting any data indexed_interactions_simple.tsv and review_comments.tsv both null

Screen Shot 2020-02-08 at 5 32 02 PM

Log contents: using elton version 0.5.15 checking github api limits.checking github api limits......................................................................................................................................................................................................checking github api limits......checking github api limits.checking github api limits.checking github api limits.

---- distinct review comments by type ---- distinctReviewCommentCount type comment

---- indexed interaction record count by institutionCode, collectionId, collectionCode, and interaction type ---- institutionCode collectionId collectionCode sourceCitation indexedInteractionRecordCount interactionTypeName interactionTypeId

---- distinct review comment count by institution, collection and review comment type ---- institutionCode collectionId collectionCode sourceCitation distinctReviewCommentCount type comment

For more information, see /Users/katjaseltmann/Documents/elton/TPT-report/tpt-reporting//Users/katjaseltmann/Documents/elton/TPT-report/tpt-reporting/output/2020-02-08

Cannot create report because no interaction records were found. Please check log.

jhpoelen commented 4 years ago

Thanks for sharing the details on your report run!

Looks like you are using an older elton version (v0.5.15). I've made some improvement to elton and the report generation script since, so please install v0.8.4 (https://github.com/globalbioticinteractions/elton#install) and get latest version of tpt-reporting repo and try again.

Thanks for being patient as we are figuring out how to make this easier to use.

seltmann commented 4 years ago

@jhpoelen Updated and ran the reports. Log:

Screen Shot 2020-02-12 at 3 20 46 PM

review_summary_by_collection.tsv and review_summary.tsv are still blank.

jhpoelen commented 4 years ago

Weird. Must be a mac thing. Let me use travis to test on mac also. Thanks for being patient.

jhpoelen commented 4 years ago

@seltmann looks like the travis Mac builder is happy now (see https://travis-ci.org/ParasiteTracker/tpt-reporting/jobs/649754690). Please update your script and confirm that it now runs on your mac.

In case you were wondering: the root cause was the tool zcat - fix was to do cat bla.txt | gunzip instead of just zcat bla.txt

seltmann commented 4 years ago

@jhpoelen with the new update the review_summary_by_collection.tsv and review_summary.tsv are working. Closing issue.