make fill_database

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "src/pkg/cjvt-corpusparser"]
+	path = src/pkg/cjvt-corpusparser
+	url = git@gitea.cjvt.si:kristjan/cjvt-corpusparser.git

Makefile

@@ -11,9 +11,9 @@ MAKE_ROOT = $(shell pwd)
 SSJ_FILE = "$(MAKE_ROOT)/data/samples/ssj_example/ssj500k-sl.body.sample.xml"
 KRES_FOLDER = "$(MAKE_ROOT)/data/samples/kres_example"
 KRES_SRL_FOLDER = "$(MAKE_ROOT)/data/kres_srl"
-OUTPUT = "file"
+OUTPUT = "db"
 OUTDIR = "/home/voje/workdir/test_out"
-DBADDR = ""
+DBADDR = "0.0.0.0:27017"  # don't use localhost
 
 DB_ADM_USER = testadmin
 DB_ADM_PASS = testadminpass
@@ -21,25 +21,42 @@ DB_USR_USER = testuser
 DB_USR_PASS = testuserpass
 export
 
-.PHONY: dev-env preflight
+.PHONY: python-env fill_database
 
 all:
 	echo "Select an argument"
 
-# prereq (environment)
+# create database (run from host):
-dev-env:
+# !!! might need to run several times, so the containers come online
-	cd dockerfiles/dev-env; $(MAKE)
+# Successful if you see the lines:
+# Successfully added user: { "user" : "testuser", "roles" : [ "readWrite" ] }
+# bye
+database-service:
+	cd dockerfiles/database; $(MAKE) build_run
 
-# run these inside dev-env container
+database-users:
+	cd dockerfiles/database; $(MAKE) create_users
+
+# also useful, if we want to restart the db
+database-clean:
+	cd dockerfiles/database; $(MAKE) clean_stack
+
+# create python-env container
+python-env:
+	cd dockerfiles/python-env; $(MAKE)
+
+# inside the container, install our packages
+python-env-install:
+	pip3 install -e src/pkg/cjvt-corpusparser/.
+
+# from inside python-env container:
 data/samples:
 	cd data; tar xzvf samples.tar.gz
 
-# installs our python code as packages
+# from inside python-env container:
-# when debugging, run this once, then run python3 ... by hand
+fill_database: data/samples
-preflight: data/samples
+	python3 src/pkg/cjvt-corpusparser/corpusparser/main.py --kres-folder $(KRES_FOLDER) \
-	pip3 install -e src/pkg/corpusparser/.
+		--ssj-file $(SSJ_FILE) --kres-srl-folder $(KRES_SRL_FOLDER) \
-	python3 src/pkg/corpusparser/corpusparser/main.py --kres-folder $(KRES_FOLDER) \
+		--output $(OUTPUT) --outdir $(OUTDIR) --dbaddr $(DBADDR) \
-		--ssj-file $(SSJ_FILE) --kres-srl-folder $(KRES_SRL_FOLDER) --output $(OUTPUT) --outdir $(OUTDIR) --dbaddr $(DBADDR)
+		--dbuser $(DB_USR_USER) --dbpass $(DB_USR_PASS)
 
-database:
-	cd dockerfiles/database; $(MAKE)

README.md

@@ -1,23 +1,42 @@
 # cjvt-valency
+Required submodules:
+
+* `https://gitea.cjvt.si/kristjan/cjvt-corpusparser.git`
+
+```bash
+$ git submodule init
+```
 
 ## Components
 
 
 ### Database (2 containers)
-Input:
+Spin up the database service and create users:
+```bash
+# $ make database-clean  # opt
+$ make database-service
+$ make database-users
+```
+
+Populate the database with data form files:  
 
 * ssj500k.xml
 * kres.xml
 * kres_SRL.json
 
-Intermediate:
+Set path to files in `Makefile`.  
+```bash
+# spin up a container with python env
+$ make python-env
 
-* ssj500k.json **HERE HERE**
+# install our packages
-* kres.json
+$ make python-env-install
 
-Output:
+# run the code
+$ make fill_database
+```
 
-* DB containing both corpora (1:1 map of the intermediate json formats)
+If all goes well, we should be able to inspect the database on `0.0.0.0:8087`.  
 
 
 ### Flask backend (1 container)

dockerfiles/database/Makefile

@@ -8,10 +8,9 @@ STACKNAME = dbstack
 
 .PHONY: start_db FORCE
 
-all: build_mongo run_stack create_users
+all: build_run create_users
 
-info:
+build_run: build_mongo run_stack
-	echo "[*] RUN THIS A FEW TIMES (THE STACK NEEDS TIME TO CLEAN UP AND TO SPIN UP THE NODES)"
 
 create.js: FORCE
 

dockerfiles/database/mongodb-stack.yml

@@ -5,6 +5,8 @@ services:
   my-mongo:
     image: my-mongo
     restart: always
+    ports:
+      - 27017:27017
     environment:
       MONGO_INITDB_ROOT_USERNAME: ${DB_ADM_USER}
       MONGO_INITDB_ROOT_PASSWORD: ${DB_ADM_PASS}

dockerfiles/python-env/Dockerfile

@@ -12,6 +12,10 @@ RUN pip3 install \
 	pandas \
 	sklearn \
 	argparse \
-	pathlib
+	pathlib \
+	pymongo
+
+RUN apt-get install -y \
+	curl
 
 ENV PYTHONIOENCODING UTF-8

dockerfiles/python-env/Makefile

@@ -1,4 +1,4 @@
-IMAGE_NAME="cjvt-dev-env"
+IMAGE_NAME="cjvt-python-env"
 
 all: build run
 
@@ -14,5 +14,6 @@ run:
 	-v /etc/group:/etc/group \
     -v $(MAKE_ROOT):/project \
 	-w /project \
+	--net host \
 	$(IMAGE_NAME) \
     /bin/bash

src/pkg/cjvt-corpusparser

@@ -0,0 +1 @@
+Subproject commit e599740ac940be1b150d653dfbf66d0551ece3a3

src/pkg/corpusparser/corpusparser/Parser.py

@@ -1,196 +0,0 @@
-from pathlib import Path
-import re
-import json
-from lxml import etree
-import logging
-
-logging.basicConfig(level=logging.INFO)
-
-# Read input file(.xml, .json; kres or ssj500k).  
-# Create an iterator that outputs resulting sentences (python dict format).  
-class Parser():
-
-    def __init__(self, corpus, infiles, logger=None):
-
-        if corpus == "kres":
-            self.kres_folder = Path(infiles[0])
-            self.kres_srl_folder = Path(infiles[1])
-        elif corpus == "ssj":
-            self.ssj_file = Path(infiles[0])
-        else:
-            raise ValueError("Argument corpus should be 'ssj' or 'kres'.")
-
-        self.corpus = corpus
-        self.W_TAGS = ['w']
-        self.C_TAGS = ['c']
-        self.S_TAGS = ['S', 'pc']
-        self.logger = logger or logging.getLogger(__name__)
-        self.stats = {
-            "parsed_count": 0,
-            "missing_srl": []
-        }
-
-    def parse_jos_links(self, sent_el):
-        if self.corpus == "kres":
-            return self.parse_jos_links_kres(sent_el)
-        else:
-            # 'syntax' is the linkgroup we're looking for
-            return self.parse_any_links_ssj(sent_el, "syntax")
-
-    def parse_jos_links_kres(self, sent_el):
-        lgrps = sent_el.findall(".//links")
-        if len(lgrps) < 1:
-            raise IOError("Can't find links.")
-        res_links = []
-        for link in lgrps[0]:
-            res_links += [{
-                "from": int(link.get("from").split(".")[-1]),
-                "afun": link.get("afun"),
-                "to": int(link.get("dep").split(".")[-1]),
-            }]
-        return res_links
-
-    def parse_ssj_target_arg(self, text):
-        # from: 0, to: 6
-        # <link ana="syn:modra" target="#ssj1.1.3 #ssj1.1.3.t6"/>
-        # from: 6, to: 7
-        # <link ana="syn:dol" target="#ssj1.1.3.t6 #ssj1.1.3.t7"/>
-        lst = [x.split(".")[-1] for x in text.split(" ")]
-        return [int(x[1:] if x[0] == "t" else 0) for x in lst]
-
-    def parse_any_links_ssj(self, sent_el, links_type):
-        lgrps = sent_el.findall(".//linkGrp")
-        links = [x for x in lgrps if x.get("type") == links_type][0]
-        res_links = []
-        for link in links:
-            tar = self.parse_ssj_target_arg(link.get("target"))
-            res_links += [{
-                "from": tar[0],
-                "afun": link.get("ana").split(":")[1],
-                "to": tar[1],
-            }]
-        return res_links
-
-    def parse_srl_links(self, sent_el, sent_srl_links=None):
-        if self.corpus == "kres":
-            return self.parse_srl_links_kres(sent_el, sent_srl_links)
-        else:
-            return self.parse_any_links_ssj(sent_el, "SRL")
-
-    def parse_srl_links_kres(self, sent_el, sent_srl_links):
-        res_links = []
-        for link in sent_srl_links:
-            res_links += [{
-                "from": int(link["from"]),
-                "afun": link["arg"],
-                "to": int(link["dep"]),
-            }]
-        # find the correspointing json file with srl links
-        return res_links
-
-    def sentence_generator(self):
-        # Using generators so we don't copy a whole corpu around in memory.
-        if self.corpus == "kres":
-            for xml_file in self.kres_folder.iterdir():
-                # self.parse_xml_file(xml_file)
-                yield from self.parse_xml_file(xml_file)
-        else:
-            yield from self.parse_xml_file(self.ssj_file)
-
-    def parse_xml_file(self, xml_file):
-        srl_from_json = {}
-        if self.corpus == "kres":  
-            # in case of kres, read the SRL links form a separate json file
-            file_id = xml_file.name.split(".")[0]
-            json_file = self.kres_srl_folder / Path(file_id).with_suffix(".srl.json")
-            with json_file.open("r") as fp:
-                srl_from_json = json.loads(fp.read())
-
-        with xml_file.open("rb") as fp:
-            # remove namespaces
-            bstr = fp.read()
-
-        utf8str = bstr.decode("utf-8")
-        utf8str = re.sub('\\sxmlns="[^"]+"', '', utf8str, count=1)
-        utf8str = re.sub(' xml:', ' ', utf8str)
-
-        root = etree.XML(utf8str.encode("utf-8"))
-
-        divs = []  # in ssj, there are divs, in Kres, there are separate files
-        if self.corpus == "kres":
-            divs = [root]
-        else:
-            divs = root.findall(".//div")
-
-        res_dict = {}
-
-        # parse divs
-        for div in divs:
-            f_id = div.get("id")
-
-            # parse paragraphs
-            for p in div.findall(".//p"):
-                p_id = p.get("id").split(".")[-1]
-
-                # parse sentences
-                for s in p.findall(".//s"):
-                    s_id = s.get("id").split(".")[-1]
-                    sentence_text = ""
-                    sentence_tokens = []
-
-                    # parse tokens
-                    for el in s.iter():
-                        if el.tag in self.W_TAGS:
-                            el_id = el.get("id").split(".")[-1]
-                            if el_id[0] == 't':
-                                el_id = el_id[1:]  # ssj W_TAG ids start with t
-                            sentence_text += el.text
-                            sentence_tokens += [{
-                                "word": True,
-                                "tid": int(el_id),
-                                "text": el.text,
-                                "lemma": el.get("lemma"),
-                                "msd": (el.get("msd") if self.corpus == "kres"
-                                    else el.get("ana").split(":")[-1]),
-                            }]
-                        elif el.tag in self.C_TAGS:
-                            # only Kres' C_TAGS have ids
-                            el_id = el.get("id") or "none"
-                            el_id = el_id.split(".")[-1]
-                            sentence_text += el.text
-                            sentence_tokens += [{
-                                "word": False,
-                                "tid": (int(el_id) if self.corpus == "kres" else -1),
-                                "text": el.text,
-                            }]
-                        elif el.tag in self.S_TAGS:
-                            # Kres' <S /> doesn't contain .text
-                            sentence_text += " "
-                        else:
-                            # pass links and linkGroups
-                            pass
-                    sentence_id = "{}.{}.{}".format(f_id, p_id, s_id)
-
-                    jos_links = self.parse_jos_links(s)
-
-                    if self.corpus == "kres":
-                        srl_links_raw = srl_from_json.get(sentence_id)
-                        if srl_links_raw is None:
-                            srl_links_parsed = None
-                            self.stats["missing_srl"] += [(sentence_id, sentence_text)]
-                        else:
-                            srl_links_parsed = self.parse_srl_links(s, srl_links_raw)
-                    else:
-                        srl_links_parsed = self.parse_srl_links(s)
-                        if len(srl_links_parsed) == 0:
-                            self.stats["missing_srl"] += [(sentence_id, sentence_text)]
-
-                    sentence_entry = {
-                        "sid": sentence_id,
-                        "text": sentence_text,
-                        "tokens": sentence_tokens,
-                        "jos_links": jos_links,
-                        "srl_links": srl_links_parsed
-                    }
-                    self.stats["parsed_count"] += 1
-                    yield (xml_file, sentence_entry)

src/pkg/corpusparser/corpusparser/README.md

@@ -1,38 +0,0 @@
-# corpusparser
-A tool for parsing ssj500k and Kres into a unified .json format. 
-
-## Input:
-### ssj500k
-To parse ssj500k, point to the monolythic `ssj500k-sl.body.xml` file (tested on ssj500k 2.1).  
-
-### Kres
-To parse Kres, point to folders:
-* Kres folder, containig several (around 20K) .xml files (`F00XXXXX.xml.parsed.xml`).  
-* Kres SRL folder, containing SRL links for the corresponding F00...xml files (`F00XXXXX.srl.json`).  
-
-## Internal data format
-This is the internal python dict data format. It can be stored to file as `.json` or stored into a database for application usage.  
-```python
-{
-	'sid': 'F0034713.5.0',
-	'text': 'Mednarodni denarni sklad je odobril 30 milijard evrov vredno posojilo Grčiji. ',
-	'tokens': [
-		{'text': 'Mednarodni', 'lemma': 'mednaroden', 'msd': 'Ppnmeid', 'word': True, 'tid': 1},
-		{'text': 'denarni', 'lemma': 'denaren', 'msd': 'Ppnmeid', 'word': True, 'tid': 2},
-		{'text': 'sklad', 'lemma': 'sklad', 'msd': 'Somei', 'word': True, 'tid': 3},
-		{'text': 'je', 'lemma': 'biti', 'msd': 'Gp-ste-n', 'word': True, 'tid': 4},
-		{'text': 'odobril', 'lemma': 'odobriti', 'msd': 'Ggdd-em', 'word': True, 'tid': 5},
-		{'text': '30', 'lemma': '30', 'msd': 'Kag', 'word': True, 'tid': 6},
-		{'text': 'milijard', 'lemma': 'milijarda', 'msd': 'Sozmr', 'word': True, 'tid': 7}, # ... 
-	]
-	'jos_links': [
-		{'to': 1, 'from': 3, 'afun': 'dol'},
-		{'to': 2, 'from': 3, 'afun': 'dol'},
-		{'to': 3, 'from': 5, 'afun': 'ena'}, # ...
-	]
-	'srl_links': [
-		{'to': 3, 'from': 5, 'afun': 'ACT'},
-		{'to': 7, 'from': 5, 'afun': 'PAT'}
-	]
-}
-```

src/pkg/corpusparser/corpusparser/__init__.py

@@ -1 +0,0 @@
-from corpusparser.Parser import Parser

src/pkg/corpusparser/corpusparser/main.py

@@ -1,102 +0,0 @@
-from pathlib import Path
-from corpusparser import Parser 
-import argparse
-import logging
-import json
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-## Main handles command line arguments and writing to files / DB.  
-
-def ssj_to_json_file(sentence_generator, outfolder):
-    # this funciton is based on the fact that files are parsed sequentially
-    outfolder = Path(outfolder)
-    outfolder.mkdir(parents=True, exist_ok=True)
-    outfile = outfolder / "ssj500k.json"
-
-    data_buffer = []
-    for s in sentence_generator:
-        sdata = s[1]
-        data_buffer += [sdata]
-
-    # outfile = Path(outfile)
-    with outfile.open("w") as fp:
-        logger.info("Writing to {}".format(outfile))
-        json.dump(data_buffer, fp)
-
-def kres_to_json_files(sentence_generator, outfolder):
-    outfolder = Path(outfolder) / "kres_json"
-    outfolder.mkdir(parents=True, exist_ok=True)
-
-    def write_buffer_to_file(outfile, outfile_buffer):
-        logger.info("Writing file: {}".format(outfile))
-        with outfile.open("w") as fp:
-            json.dump(outfile_buffer, fp)
-
-    outfile_buffer = None
-    current_outfile = None
-    for s in sentence_generator:
-        infile = s[0]
-        outfile = outfolder / Path(infile.name.split(".")[0]).with_suffix(".json")
-
-        # parser sequentially parses files; when we're done with a file, write it out
-        if current_outfile is None:
-            current_outfile = outfile
-            outfile_buffer = [] 
-        elif outfile != current_outfile:
-            write_buffer_to_file(current_outfile, outfile_buffer)
-            current_outfile = outfile
-            outfile_buffer = []
-
-        # update buffer
-        sdata = s[1]
-        outfile_buffer += [sdata]
-    write_buffer_to_file(current_outfile, outfile_buffer)
-
-
-
-def to_db():
-    return "TODO"
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Parsing corpora kres and ssj500k.")
-    parser.add_argument('--kres-folder', required=True)
-    parser.add_argument('--kres-srl-folder', required=True)
-    parser.add_argument('--ssj-file', required=True)
-    parser.add_argument('--output', required=False, default=None)
-    parser.add_argument('--outdir', required=False, default=None)
-    parser.add_argument('--dbaddr', required=False, default=None)
-    args = parser.parse_args()
-
-    # parse ssj
-    logger.info("Parsing ssj500k: {}".format(args.ssj_file))
-    ssj_parser = Parser(
-        corpus="ssj",
-        infiles=[args.ssj_file],
-    )
-    # res = [x[1]["sid"] for x in ssj_parser.sentence_generator()]
-    # logger.info("Parsed {} sentences (ssj500k)".format(len(res)))
-
-    # ssj to json
-    ssj_to_json_file(ssj_parser.sentence_generator(), args.outdir)
-
-    # parse kres
-    logger.info("Parsing Kres: {}".format(args.ssj_file))
-    kres_parser = Parser(
-        corpus="kres",
-        infiles=[args.kres_folder, args.kres_srl_folder],
-    )
-    # res = [x[1]["sid"] for x in kres_parser.sentence_generator()]
-    # logger.info("Parsed {} sentences (kres)".format(len(res)))
-
-    # kres to json
-    kres_to_json_files(kres_parser.sentence_generator(), args.outdir)
-
-
-## Handling output is situational --- implement it outside of Parser.
-## Parser returns tuples (orig_file, element)
-# 1. parse per-file and output to file (JSON)
-# 2. parse and save to DB
-
-# TODO

src/pkg/corpusparser/setup.py

@@ -1,10 +0,0 @@
-from setuptools import setup
-
-setup(name='corpusparser',
-  version='0.0.1',
-  description=u"Parser for kres and ssj500k",
-  author=u"Kristjan Voje",
-  author_email='kristjan.voje@gmail.com',
-  license='MIT',
-  zip_safe=False,
-)