Changed repo and updated, now errors everywhere

[oldgristmill]

Hi all--

It's been a long while since I gave my Birdnet-Pi installation any attention and so finally switched over to this repo from the original and ran an update, but now I'm getting errors everywhere! I'm not a coder, but can follow instructions well... any suggestions on how to debug/fix this?

A few examples:

On the Overview page I get

Fatal error: Uncaught Error: Call to a member function fetchArray() on bool in /home/pi/BirdNET-Pi/scripts/overview.php:160 Stack trace: #0 /home/pi/BirdNET-Pi/scripts/overview.php(198): get_chart_data() #1 {main} thrown in /home/pi/BirdNET-Pi/scripts/overview.php on line 160
and
Fatal error: Uncaught Error: Call to a member function fetchArray() on bool in /home/pi/BirdNET-Pi/scripts/todays_detections.php:32 Stack trace: #0 {main} thrown in /home/pi/BirdNET-Pi/scripts/todays_detections.php on line 32

As well as a note that says "Your system is currently processing a backlog of audio. This can take several hours before normal functionality of your BirdNET-Pi resumes."

In Weekly Report I get:

Warning: SQLite3Stmt::execute(): Unable to execute statement: database disk image is malformed in /home/pi/BirdNET-Pi/scripts/weekly_report.php on line 183

Fatal error: Uncaught Error: Call to a member function fetchArray() on bool in /home/pi/BirdNET-Pi/scripts/weekly_report.php:184 Stack trace: #0 /home/pi/BirdNET-Pi/homepage/views.php(132): include() #1 {main} thrown in /home/pi/BirdNET-Pi/scripts/weekly_report.php on line 184

In Species Stats I get:

DatabaseError: database disk image is malformed
Traceback:
File "/home/pi/BirdNET-Pi/birdnet/lib/python3.9/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 565, in _run_script
    exec(code, module.__dict__)
File "/home/pi/BirdNET-Pi/scripts/plotly_streamlit.py", line 66, in <module>
    df2 = get_data(conn)
File "/home/pi/BirdNET-Pi/scripts/plotly_streamlit.py", line 61, in get_data
    df1 = pd.read_sql("SELECT * FROM detections", con=conn)
File "/home/pi/BirdNET-Pi/birdnet/lib/python3.9/site-packages/pandas/io/sql.py", line 567, in read_sql
    return pandas_sql.read_query(
File "/home/pi/BirdNET-Pi/birdnet/lib/python3.9/site-packages/pandas/io/sql.py", line 2097, in read_query
    data = self._fetchall_as_list(cursor)
File "/home/pi/BirdNET-Pi/birdnet/lib/python3.9/site-packages/pandas/io/sql.py", line 2111, in _fetchall_as_list
    result = cur.fetchall()

[alexbelgium]

Hi, how did you upgrade, did you follow the instructions in https://github.com/Nachtzuster/BirdNET-Pi?tab=readme-ov-file#migrating ?

If yes it might be easier for you to just start back from a clean install again (using bookworm)...

In all case I would highly advise you to backup your files before moving further - for example downloading the content of your sdcard in order to be sure to save your files such as :
"$HOME/BirdNET-Pi/birdnet.conf"
"$HOME/BirdNET-Pi/scripts/birds.db"
"$HOME/BirdNET-Pi/scripts/disk_check_exclude.txt"
"$HOME/BirdNET-Pi/apprise.txt"
"$HOME/BirdNET-Pi/BirdDB.txt"
"$HOME/BirdNET-Pi/exclude_species_list.txt"
"$HOME/BirdNET-Pi/include_species_list.txt"
"$HOME/BirdNET-Pi/IdentifiedSoFar.txt"
"$HOME/BirdSongs/Extracted/Charts"
"$HOME/BirdSongs/Extracted/By_Date"

[oldgristmill]

Whe nI realized it wasn't created properly, I did a search on the repo to see if there was db file I could just plop in, but found the script instead and ran it. Everything works now, so the problem must be with the old DB... I'm gonna have to see if I can see an obvious problem with it... Not sure where to start looking though--probably table names.

[alexbelgium]

Can you open it with the embedded database maintenance tool? As long as it's in the same location as the normal db you should be able to open it just by typing it's name instead of birds.db. There are tools that could allow to fix it, or recreate it from the Birds.txt that in the end is just a duplicate of the sqlite database

[oldgristmill]

The structure and the indexes look the same with both databases, so the problem must be in the data. I'll have to check into that later...

[oldgristmill]

Probably the easiest, at this point, is just to rebuild the database from the birdsdb.txt file. Is there a script for that? I'll go looking, but if you know, please let me know.

[alexbelgium]

I think you need to import the csv into phpmyadmin (the sqlite administration tool) but I never tried it. If you post your sqlite perhaps someone will have an idea to fix it (not sure if it contains confidential data - I think it's just bird observations however there is your gps location). Or if you post your txt file (after changing all your gps coordinates to a fixed value that you can easily change back to something else later)