Mahlet G. Tadesse

21 papers Journal 9Unranked 12
YearRankTypeTitle / Venue / Authors
2023 conf
BIBM
Yichen Guo, Marie Denis, Rency S. Varghese, Sidharth S. Jain, Mahlet G. Tadesse, Habtom W. Ressom
2022 conf
EMBC
Marie Denis, Rency S. Varghese, Megan E. Barefoot, Mahlet G. Tadesse, Habtom W. Ressom
2020 J jnl
BMC Medical Informatics Decis. Mak.
Xiangdong Gu, Mahlet G. Tadesse, Andrea S. Foulkes, Yunsheng Ma, Raji Balasubramanian
2020 conf
EMBC
Rency S. Varghese, Yuan Zhou, Yifan Chen, Megan E. Barefoot, Mahlet G. Tadesse, Habtom W. Ressom
2016 J jnl
Bioinform.
Marie Denis, Mahlet G. Tadesse
2016 conf
EMBC
Habtom W. Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R. Nezami Ranjbar, Ehwang Song, Rency S. Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G. Tadesse, Yehia Mechref
2015 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom
2013 conf
BCB
Krithika Bhuvaneshwar, Michael Harris, Thanemozhi Natarajan, Laura Sheahan, Difei Wang, Subha Madhavan, Mahlet G. Tadesse, John Deeken
2013 J jnl
Bioinform.
Tsung-Heng Tsai, Mahlet G. Tadesse, Cristina Di Poto, Lewis K. Pannell, Yehia Mechref, Yue Joseph Wang, Habtom W. Ressom
2013 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Tsung-Heng Tsai, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom
2013 conf
BIBM
Yiming Zuo, Guoqiang Yu, Mahlet G. Tadesse, Habtom W. Ressom
2012 conf
BIBM Workshops
Mohammad R. Nezami Ranjbar, Yi Zhao, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom
2012 conf
GENSiPS
Jinlian Wang, Hongyan Yuan, Mahlet G. Tadesse, Habtom W. Ressom
2012 conf
GENSiPS
Mohammad R. Nezami Ranjbar, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom
2012 conf
GENSiPS
Yi Zhao, Tsung-Heng Tsai, Cristina Di Poto, Lewis K. Pannell, Mahlet G. Tadesse, Habtom W. Ressom
2011 conf
BIBM
Tsung-Heng Tsai, Mahlet G. Tadesse, Yue Joseph Wang, Habtom W. Ressom
2011 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Getachew K. Befekadu, Mahlet G. Tadesse, Tsung-Heng Tsai, Habtom W. Ressom
2009 J jnl
Autom.
Habtom W. Ressom, Getachew K. Befekadu, Mahlet G. Tadesse
2008 conf
BIOCOMP
Getachew K. Befekadu, Mahlet G. Tadesse, Habtom W. Ressom
2006 J jnl
Bioinform.
Naijun Sha, Mahlet G. Tadesse, Marina Vannucci
2004 J jnl
Bioinform.
Mahlet G. Tadesse, Marina Vannucci, Pietro Liò
redb/extractors/js_extractors/js_patterns.py
← Index redb/extractors/js_extractors/js_patterns.py python
"""Canonical, compiled JavaScript regex patterns shared across JS extractors.

All suspicious-API patterns and the few feature-only patterns live here so each
expression is compiled exactly once per Python process and so any pattern that
was previously duplicated across `js_features.py` and `js_suspicious_apis.py`
now resolves to a single shared compiled object.

JavaScript is case-sensitive at runtime, but every suspicious-API pattern matches
either a literal-case identifier (`\\beval\\s*\\(`, `String\\.fromCharCode`, etc.)
or a string-quoted token (`"powershell"`). Compiling them with `re.IGNORECASE`
matches the historical behaviour of `JSSuspiciousAPIsExtractor` and is safe for
the patterns that historically came from `JSFeaturesExtractor` — those literals
are spelled in real-world JS exactly as written.

`scan_source()` is the entry point used by extractors: it walks the source once
per pattern using the pre-compiled regexes and returns a flat
`{name: {"count": N, "lines": [unique_line_numbers_sorted]}}` dict. Both
`JSFeaturesExtractor` and `JSSuspiciousAPIsExtractor` consume the same dict so
the per-pattern × per-line loops they used to run independently collapse to a
single shared scan.
"""

import bisect
import re
from typing import Dict, Iterable, List, Mapping

_FLAGS = re.IGNORECASE

# Canonical compiled patterns, keyed by their human-readable name. The name is
# also the value emitted into `redb_js_suspicious_apis.api_name`.
PATTERNS = {
    # ---- code execution ----
    "eval": re.compile(r"\beval\s*\(", _FLAGS),
    "Function constructor": re.compile(r"\bnew\s+Function\s*\(", _FLAGS),
    "execScript": re.compile(r"\bexecScript\s*\(", _FLAGS),
    "document.write": re.compile(r"\bdocument\.write(?:ln)?\s*\(", _FLAGS),
    "innerHTML assignment": re.compile(r"\.innerHTML\s*=", _FLAGS),
    "outerHTML assignment": re.compile(r"\.outerHTML\s*=", _FLAGS),
    "insertAdjacentHTML": re.compile(r"\.insertAdjacentHTML\s*\(", _FLAGS),
    # ---- network ----
    "XMLHttpRequest": re.compile(r"\bnew\s+XMLHttpRequest\b", _FLAGS),
    "fetch": re.compile(r"\bfetch\s*\(", _FLAGS),
    "WebSocket": re.compile(r"\bnew\s+WebSocket\s*\(", _FLAGS),
    "navigator.sendBeacon": re.compile(r"\bnavigator\.sendBeacon\s*\(", _FLAGS),
    "ActiveXObject XMLHTTP": re.compile(
        r"ActiveXObject\s*\(\s*[\"\'](?:MSXML2\.XMLHTTP|Microsoft\.XMLHTTP)", _FLAGS
    ),
    "require network module": re.compile(
        r"require\s*\(\s*[\"\'](?:http|https|net|dgram)[\"\']", _FLAGS
    ),
    "axios": re.compile(r"\baxios\b", _FLAGS),
    # ---- filesystem ----
    "require fs": re.compile(r"require\s*\(\s*[\"\']fs[\"\']", _FLAGS),
    "require path": re.compile(r"require\s*\(\s*[\"\']path[\"\']", _FLAGS),
    "FileSystemObject": re.compile(r"Scripting\.FileSystemObject", _FLAGS),
    "ADODB.Stream": re.compile(r"ADODB\.Stream", _FLAGS),
    "Shell.Application": re.compile(r"Shell\.Application", _FLAGS),
    "WScript.CreateObject": re.compile(r"WScript\.CreateObject", _FLAGS),
    # ---- process ----
    "require child_process": re.compile(r"require\s*\(\s*[\"\']child_process[\"\']", _FLAGS),
    "child_process exec": re.compile(r"child_process\.(?:exec|spawn|execFile|fork)\s*\(", _FLAGS),
    "WScript.Shell": re.compile(r"WScript\.Shell", _FLAGS),
    "WScript.Shell.Run": re.compile(r"\.Run\s*\(", _FLAGS),
    "WScript.Shell.Exec": re.compile(r"\.Exec\s*\(", _FLAGS),
    "ShellExecute": re.compile(r"\bShellExecute\b", _FLAGS),
    "PowerShell reference": re.compile(r"[\"\']powershell[\"\']", _FLAGS),
    "cmd.exe reference": re.compile(r"[\"\']cmd\.exe[\"\']", _FLAGS),
    "require os": re.compile(r"require\s*\(\s*[\"\']os[\"\']", _FLAGS),
    # ---- registry ----
    "RegRead": re.compile(r"\.RegRead\s*\(", _FLAGS),
    "RegWrite": re.compile(r"\.RegWrite\s*\(", _FLAGS),
    "RegDelete": re.compile(r"\.RegDelete\s*\(", _FLAGS),
    "StdRegProv": re.compile(r"StdRegProv", _FLAGS),
    # ---- crypto / encoding ----
    "atob": re.compile(r"\batob\s*\(", _FLAGS),
    "btoa": re.compile(r"\bbtoa\s*\(", _FLAGS),
    "String.fromCharCode": re.compile(r"String\.fromCharCode\s*\(", _FLAGS),
    "unescape": re.compile(r"\bunescape\s*\(", _FLAGS),
    "decodeURIComponent": re.compile(r"\bdecodeURIComponent\s*\(", _FLAGS),
    "Buffer.from": re.compile(r"Buffer\.from\s*\(", _FLAGS),
    "crypto module": re.compile(r"crypto\.create(?:Cipher|Decipher|Hash|Hmac)", _FLAGS),
    # ---- DOM manipulation ----
    "document.forms": re.compile(r"document\.forms", _FLAGS),
    "document.cookie": re.compile(r"document\.cookie", _FLAGS),
    "querySelector sensitive input": re.compile(
        r"document\.querySelector\s*\([^)]*(?:password|credit|card|cvv|ssn)", _FLAGS
    ),
    "submit event listener": re.compile(r"addEventListener\s*\(\s*[\"\']submit", _FLAGS),
    "createElement script/iframe": re.compile(
        r"\.createElement\s*\(\s*[\"\'](?:script|iframe)", _FLAGS
    ),
    "dynamic script src": re.compile(r"\.src\s*=\s*[\"\'](?:https?://|//)", _FLAGS),
}

# Pattern name -> category (one of code_execution / network / filesystem /
# process / registry / crypto_encoding / dom_manipulation).
CATEGORIES = {
    "eval": "code_execution",
    "Function constructor": "code_execution",
    "execScript": "code_execution",
    "document.write": "code_execution",
    "innerHTML assignment": "code_execution",
    "outerHTML assignment": "code_execution",
    "insertAdjacentHTML": "code_execution",
    "XMLHttpRequest": "network",
    "fetch": "network",
    "WebSocket": "network",
    "navigator.sendBeacon": "network",
    "ActiveXObject XMLHTTP": "network",
    "require network module": "network",
    "axios": "network",
    "require fs": "filesystem",
    "require path": "filesystem",
    "FileSystemObject": "filesystem",
    "ADODB.Stream": "filesystem",
    "Shell.Application": "filesystem",
    "WScript.CreateObject": "filesystem",
    "require child_process": "process",
    "child_process exec": "process",
    "WScript.Shell": "process",
    "WScript.Shell.Run": "process",
    "WScript.Shell.Exec": "process",
    "ShellExecute": "process",
    "PowerShell reference": "process",
    "cmd.exe reference": "process",
    "require os": "process",
    "RegRead": "registry",
    "RegWrite": "registry",
    "RegDelete": "registry",
    "StdRegProv": "registry",
    "atob": "crypto_encoding",
    "btoa": "crypto_encoding",
    "String.fromCharCode": "crypto_encoding",
    "unescape": "crypto_encoding",
    "decodeURIComponent": "crypto_encoding",
    "Buffer.from": "crypto_encoding",
    "crypto module": "crypto_encoding",
    "document.forms": "dom_manipulation",
    "document.cookie": "dom_manipulation",
    "querySelector sensitive input": "dom_manipulation",
    "submit event listener": "dom_manipulation",
    "createElement script/iframe": "dom_manipulation",
    "dynamic script src": "dom_manipulation",
}

# Patterns consumed only by JSFeaturesExtractor (no category, never surfaced as
# a suspicious-API row). Kept here so every JS regex is compiled in one place.
FEATURE_PATTERNS = {
    "hex_escape": re.compile(r"\\x[0-9a-fA-F]{2}"),
    "unicode_escape": re.compile(r"\\u[0-9a-fA-F]{4}"),
    "base64_string": re.compile(r"[A-Za-z0-9+/]{40,}={0,2}"),
    # decodeURI matches BOTH decodeURI and decodeURIComponent. The latter is also
    # a suspicious-API pattern in PATTERNS; this broader form is what the
    # `decodeuri_count` feature column has historically counted.
    "decodeURI": re.compile(r"\b(?:decodeURI|decodeURIComponent)\s*\(", _FLAGS),
    "settimeout_setinterval": re.compile(r"\b(?:setTimeout|setInterval)\s*\(", _FLAGS),
    "function_decl": re.compile(r"\bfunction\s+\w+\s*\(|\bfunction\s*\("),
    "var_decl": re.compile(r"\b(?:var|let|const)\s+"),
    "string_concat": re.compile(r"[\"\'][\s]*\+[\s]*[\"\']"),
    "comment": re.compile(r"//.*?$|/\*[\s\S]*?\*/", re.MULTILINE),
    "long_string": re.compile(r"[\"\']([^\"\']{256,})[\"\']"),
    "array_function_call": re.compile(r"\[(?:0x[0-9a-f]+|[\d]+)\]\s*\(", _FLAGS),
}

# Patterns consumed only by JSStringsExtractor for encoded-string discovery.
# Scoped to *hidden* strings only — patterns whose decoded form is not visible
# to a substring search over the raw text. Plain long literals are not
# extracted here because they're already preserved in code_text_content and
# scraped by the IOC pipeline over text_raw / text_normalized.
#
# Distinct from FEATURE_PATTERNS even where the names rhyme:
#   FEATURE_PATTERNS["hex_escape"] / ["unicode_escape"]   -> single escape
#   STRING_PATTERNS["hex_escape_seq"] / ["unicode_escape_seq"] -> 4+ / 3+ in a row
#   FEATURE_PATTERNS["base64_string"]                     -> bare base64 token
#   STRING_PATTERNS["base64_quoted"]                      -> base64 inside JS quotes
# These do not share match objects with the suspicious-API or feature scans, so
# they are not folded into JSContext.scan; the strings extractor walks them
# itself (one finditer per pattern, with shared line-offset bisect in #4b).
STRING_PATTERNS = {
    "hex_escape_seq": re.compile(r"(?:\\x[0-9a-fA-F]{2}){4,}"),
    "unicode_escape_seq": re.compile(r"(?:\\u[0-9a-fA-F]{4}){3,}"),
    "charcode_call": re.compile(r"String\.fromCharCode\s*\(\s*([\d,\s]+)\s*\)"),
    "base64_quoted": re.compile(r"[\"\']([A-Za-z0-9+/]{40,}={0,2})[\"\']"),
    "concat_chain": re.compile(r"(?:[\"\'][^\"\']+[\"\']\s*\+\s*){3,}[\"\'][^\"\']+[\"\']"),
}


def line_offsets(source: str) -> List[int]:
    """Sorted list of byte offsets for every newline in `source`, plus a final
    sentinel of len(source). Used to translate match offsets into 1-indexed
    line numbers via bisect.
    """
    offsets = [-1]  # so that bisect_right of offset 0 returns line 1
    push = offsets.append
    idx = source.find("\n")
    while idx != -1:
        push(idx)
        idx = source.find("\n", idx + 1)
    return offsets


def _scan_one(
    pattern: "re.Pattern[str]", source: str, offsets: List[int]
) -> Dict[str, object]:
    """Run a single compiled pattern over `source` and return count + unique lines."""
    count = 0
    seen_lines: "set[int]" = set()
    for m in pattern.finditer(source):
        count += 1
        seen_lines.add(bisect.bisect_right(offsets, m.start()))
    if not count:
        return None  # type: ignore[return-value]
    return {"count": count, "lines": sorted(seen_lines)}


def scan_source(
    source: str,
    patterns: Iterable[Mapping[str, "re.Pattern[str]"]] = (PATTERNS, FEATURE_PATTERNS),
) -> Dict[str, Dict[str, object]]:
    """Scan `source` against every compiled pattern in `patterns`.

    Returns a dict keyed by pattern name. Each entry has:
        "count": total number of matches in the source
        "lines": sorted list of unique 1-indexed line numbers where the pattern
                 matched (deduplicated — multiple matches on the same line
                 collapse to one entry, preserving the historical
                 line-set semantics of JSSuspiciousAPIsExtractor)
    Patterns with zero matches are absent from the dict; callers should default
    to {"count": 0, "lines": []}.
    """
    if not source:
        return {}
    offsets = line_offsets(source)
    results: Dict[str, Dict[str, object]] = {}
    for table in patterns:
        for name, pat in table.items():
            entry = _scan_one(pat, source, offsets)
            if entry is not None:
                results[name] = entry
    return results