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Add support for additional media types #18054

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merged 14 commits into from
May 20, 2024
Merged

Add support for additional media types #18054

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99e1fc8
Add support for Ogg, Webm, Mpeg, Mpga, M4a, Mov, Avi, Wmv, and Wma me…
arash77 Apr 23, 2024
541939f
Add support for Ogg, Webm, Mpeg, Mpga, M4a, Mov, Avi, Wmv, and Wma me…
arash77 Apr 23, 2024
498e095
Update media datatypes
arash77 Apr 23, 2024
f420c97
Refactor media datatype sniffing logic in media.py
arash77 Apr 23, 2024
1cfc63e
Refactor media datatype sniffing logic in media.py
arash77 Apr 23, 2024
e64cb60
Update media datatypes and using magic numbers as main idinifier of f…
arash77 Apr 25, 2024
de6f00c
Refactor media datatype sniffing logic in media.py
arash77 Apr 25, 2024
e50f829
change the order of file check, change names to meaningful names
arash77 Apr 25, 2024
371e227
Fix typo in datatype sniffing logic for H5 files
arash77 Apr 25, 2024
230b734
Refactor media datatype sniffing logic
arash77 Apr 25, 2024
d7673ab
Sorting imports
arash77 Apr 25, 2024
a7e9775
Refactor media datatype sniffing logic in media.py
arash77 Apr 29, 2024
85c1db5
using magic bit as fallback
arash77 May 2, 2024
ef45b49
remove unnecessary list
arash77 May 3, 2024
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14 changes: 13 additions & 1 deletion lib/galaxy/config/sample/datatypes_conf.xml.sample
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Original file line number Diff line number Diff line change
Expand Up @@ -931,10 +931,16 @@
<!-- media datatypes -->
<datatype extension="wav" type="galaxy.datatypes.media:Wav" display_in_upload="true" mimetype="audio/wav"/>
<datatype extension="mp3" type="galaxy.datatypes.media:Mp3" display_in_upload="true" mimetype="audio/mp3"/>
<datatype extension="ogg" type="galaxy.datatypes.media:Ogg" display_in_upload="true" mimetype="audio/ogg"/>
<datatype extension="wma" type="galaxy.datatypes.media:Wma" display_in_upload="true" mimetype="audio/x-ms-wma"/>
<datatype extension="mkv" type="galaxy.datatypes.media:Mkv" display_in_upload="true" mimetype="video/mkv"/>
<datatype extension="mp4" type="galaxy.datatypes.media:Mp4" display_in_upload="true" mimetype="video/mp4"/>
<datatype extension="flv" type="galaxy.datatypes.media:Flv" display_in_upload="true" mimetype="video/flv"/>
<datatype extension="webm" type="galaxy.datatypes.media:Webm" display_in_upload="true" mimetype="video/webm"/>
<datatype extension="mpg" type="galaxy.datatypes.media:Mpg" display_in_upload="true" mimetype="video/mpeg"/>
<datatype extension="mov" type="galaxy.datatypes.media:Mov" display_in_upload="true" mimetype="video/quicktime"/>
<datatype extension="avi" type="galaxy.datatypes.media:Avi" display_in_upload="true" mimetype="video/x-msvideo"/>
<datatype extension="wmv" type="galaxy.datatypes.media:Wmv" display_in_upload="true" mimetype="video/x-ms-wmv"/>
<!-- speech datatypes -->
<datatype extension="textgrid" type="galaxy.datatypes.speech:TextGrid" display_in_upload="true" mimetype="text/plain"/>
<datatype extension="par" type="galaxy.datatypes.speech:BPF" display_in_upload="true" mimetype="text/plain-bas"/>
Expand Down Expand Up @@ -1241,11 +1247,17 @@
<sniffer type="galaxy.datatypes.images:Nifti2" />
<sniffer type="galaxy.datatypes.images:Star" />
<sniffer type="galaxy.datatypes.media:Wav"/>
<sniffer type="galaxy.datatypes.media:Mkv"/>
<sniffer type="galaxy.datatypes.media:Mp3"/>
<sniffer type="galaxy.datatypes.media:Mp4"/>
<sniffer type="galaxy.datatypes.media:Flv"/>
<sniffer type="galaxy.datatypes.media:Ogg"/>
<sniffer type="galaxy.datatypes.media:Mpg"/>
<sniffer type="galaxy.datatypes.media:Mov"/>
<sniffer type="galaxy.datatypes.media:Avi"/>
<sniffer type="galaxy.datatypes.media:Wmv"/>
<sniffer type="galaxy.datatypes.media:Wma"/>
<sniffer type="galaxy.datatypes.media:Webm"/>
<sniffer type="galaxy.datatypes.media:Mkv"/>
<sniffer type="galaxy.datatypes.speech:TextGrid" />
<sniffer type="galaxy.datatypes.speech:BPF" />
<sniffer type="galaxy.datatypes.larch:FEFFInput" />
Expand Down
177 changes: 168 additions & 9 deletions lib/galaxy/datatypes/media.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import wave
from functools import lru_cache
from typing import (
cast,
List,
Tuple,
)
Expand Down Expand Up @@ -32,6 +33,97 @@ def ffprobe(path):
return data["format"], data["streams"]


magic_number = {
"mp4": {
"offset": 4,
"string": ["ftypisom", "ftypmp42", "ftypMSNV"],
},
"flv": {"offset": 0, "string": ["FLV"]},
"mkv": {"offset": 0, "hex": ["1A 45 DF A3"]},
"webm": {"offset": 0, "hex": ["1A 45 DF A3"]},
"mov": {"offset": 4, "string": ["ftypqt", "moov"]},
"wav": {"offset": 8, "string": ["WAVE"]},
"mp3": {
"offset": 0,
"hex": [
"49 44 33",
"FF E0",
"FF E1",
"FF E2",
"FF E3",
"FF E4",
"FF E5",
"FF E6",
"FF E7",
"FF E8",
"FF E9",
"FF EA",
"FF EB",
"FF EC",
"FF ED",
"FF EE",
"FF EF",
"FF F0",
"FF F1",
"FF F2",
"FF F3",
"FF F4",
"FF F5",
"FF F6",
"FF F7",
"FF F8",
"FF F9",
"FF FA",
"FF FB",
"FF FC",
"FF FD",
"FF FE",
"FF FF",
],
},
"ogg": {"offset": 0, "string": ["OggS"]},
"wma": {"offset": 0, "hex": ["30 26 B2 75"]},
"wmv": {"offset": 0, "hex": ["30 26 B2 75"]},
"avi": {"offset": 8, "string": ["AVI"]},
"mpg": {
"offset": 0,
"hex": [
"00 00 01 B0",
"00 00 01 B1",
"00 00 01 B3",
"00 00 01 B4",
"00 00 01 B5",
"00 00 01 B6",
"00 00 01 B7",
"00 00 01 B8",
"00 00 01 B9",
"00 00 01 BA",
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are these all seen in practice? Wikipedia's list suggests it should be a much reduced set

00 00 01 BA
00 00 01 B3

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I was using this source:
https://www.garykessler.net/library/file_sigs.html

00 00 01 Bx ....
MPEG, MPG MPEG video file
Trailer:
00 00 01 B7 (...·)

"00 00 01 BB",
"00 00 01 BC",
"00 00 01 BD",
"00 00 01 BE",
"00 00 01 BF",
],
},
}


def _get_file_format_from_magic_number(filename: str, file_ext: str):
with open(filename, "rb") as f:
f.seek(cast(int, magic_number[file_ext]["offset"]))
head = f.read(8)
if "string" in magic_number[file_ext]:
string_check = any(
head.startswith(string_code.encode("iso-8859-1"))
for string_code in cast(List[str], magic_number[file_ext]["string"])
)
if "hex" in magic_number[file_ext]:
hex_check = any(
head.startswith(bytes.fromhex(hex_code)) for hex_code in cast(List[str], magic_number[file_ext]["hex"])
)
return string_check or hex_check


class Audio(Binary):
MetadataElement(
name="duration",
Expand Down Expand Up @@ -183,8 +275,11 @@ class Mkv(Video):
def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "matroska" in metadata["format_name"].split(",")
return False
vp_check = any(
stream["codec_name"] in ["av1", "vp8", "vp9"] for stream in streams if stream["codec_type"] == "video"
)
return "matroska" in metadata["format_name"].split(",") and not vp_check
return _get_file_format_from_magic_number(filename, "mkv")


class Mp4(Video):
Expand All @@ -200,8 +295,8 @@ class Mp4(Video):
def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "mp4" in metadata["format_name"].split(",")
return False
return "mp4" in metadata["format_name"].split(",") and _get_file_format_from_magic_number(filename, "mp4")
return _get_file_format_from_magic_number(filename, "mp4")


class Flv(Video):
Expand All @@ -211,7 +306,7 @@ def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "flv" in metadata["format_name"].split(",")
return False
return _get_file_format_from_magic_number(filename, "flv")


class Mpg(Video):
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Expand All @@ -221,7 +316,7 @@ def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "mpegvideo" in metadata["format_name"].split(",")
return False
return _get_file_format_from_magic_number(filename, "mpg")


class Mp3(Audio):
Expand All @@ -240,7 +335,7 @@ def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "mp3" in metadata["format_name"].split(",")
return False
return _get_file_format_from_magic_number(filename, "mp3")
Comment on lines -243 to +338
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but yes cases like this, instead of return False, just return _get_file_format_from_magic_number(filename, "mp3") and keeping the ffprobe would potentially be good.



class Wav(Audio):
Expand Down Expand Up @@ -274,8 +369,7 @@ def get_mime(self) -> str:
return "audio/wav"

def sniff(self, filename: str) -> bool:
with wave.open(filename, "rb"):
return True
return _get_file_format_from_magic_number(filename, "wav")

def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
"""Set the metadata for this dataset from the file contents."""
Expand All @@ -287,3 +381,68 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
dataset.metadata.nchannels = fd.getnchannels()
except wave.Error:
pass


class Ogg(Audio):
file_ext = "ogg"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "ogg" in metadata["format_name"].split(",")
return _get_file_format_from_magic_number(filename, "ogg")


class Webm(Video):
file_ext = "webm"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
vp_check = any(
stream["codec_name"] in ["av1", "vp8", "vp9"] for stream in streams if stream["codec_type"] == "video"
)
return "webm" in metadata["format_name"].split(",") and vp_check
return _get_file_format_from_magic_number(filename, "webm")


class Mov(Video):
file_ext = "mov"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "mov" in metadata["format_name"].split(",") and _get_file_format_from_magic_number(filename, "mov")
return _get_file_format_from_magic_number(filename, "mov")


class Avi(Video):
file_ext = "avi"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
return "avi" in metadata["format_name"].split(",")
return _get_file_format_from_magic_number(filename, "avi")


class Wmv(Video):
file_ext = "wmv"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
is_video = "video" in [stream["codec_type"] for stream in streams]
return "asf" in metadata["format_name"].split(",") and is_video
return _get_file_format_from_magic_number(filename, "wmv")


class Wma(Audio):
file_ext = "wma"

def sniff(self, filename: str) -> bool:
if which("ffprobe"):
metadata, streams = ffprobe(filename)
is_audio = "video" not in [stream["codec_type"] for stream in streams]
return "asf" in metadata["format_name"].split(",") and is_audio
return _get_file_format_from_magic_number(filename, "wma")
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