Revert "SCIPROD-432 CAWFR dataset utilities (#786)"

This reverts commit 6ec44f2.

build/Jenkinsfile

@@ -67,6 +67,22 @@ stage 'Build'
                 deleteDir()
             }
         },
+        "centos-amd64" : { 
+            node('master'){
+                deleteDir()
+                sh  """
+                    commit_hash=\"${env.commit_hash}\"
+                    mkdir \$commit_hash
+                    working_dir=\$(pwd)
+                    docker run -v \$working_dir/\$commit_hash:/\$commit_hash --rm dnanexus/dx-toolkit:centos6 \\
+                        /bin/bash -xc \"git clone https://github.com/dnanexus/dx-toolkit.git; \\
+                        cd dx-toolkit; git checkout \$commit_hash; build/package.sh centos-amd64; \\
+                        mv dx-toolkit-*.tar.gz /\$commit_hash/\"
+                    """
+                archive "${env.commit_hash}/dx-toolkit-*.tar.gz"
+                deleteDir()
+            }
+        },
         "xenial-deb" : { 
             node('master'){
                 deleteDir()

debian/rules

@@ -9,6 +9,3 @@ override_dh_auto_install:
 	DESTDIR="$(CURDIR)/debian/dx-java-bindings" PREFIX="/usr" $(MAKE) -C src debian_java_install
 
 override_dh_auto_test:
-
-override_dh_shlibdeps:
-	dh_shlibdeps --exclude=numpy

src/python/dxpy/scripts/dx.py

@@ -41,7 +41,6 @@
 from ..cli import try_call, prompt_for_yn, INTERACTIVE_CLI
 from ..cli import workflow as workflow_cli
 from ..cli.cp import cp
-from ..cli.dataset_utilities import extract_dataset
 from ..cli.download import (download_one_file, download_one_database_file, download)
 from ..cli.parsers import (no_color_arg, delim_arg, env_args, stdout_args, all_arg, json_arg, parser_dataobject_args,
                            parser_single_dataobject_output_args, process_properties_args,
@@ -6015,21 +6014,6 @@ def positive_integer(value):
 parser_unarchive.set_defaults(func=archive, request_mode="unarchival")
 register_parser(parser_unarchive, categories='fs')
 
-#####################################
-# extract_dataset
-#####################################
-parser_extract_dataset = subparsers.add_parser('extract_dataset', help="Retrieves the data or generates SQL to retrieve the data from a dataset or cohort for a set of entity.fields. Additionally, the dataset's dictionary can be extracted independently or in conjunction with data.",
-                                   description="Retrieves the data or generates SQL to retrieve the data from a dataset or cohort for a set of entity.fields. Additionally, the dataset's dictionary can be extracted independently or in conjunction with data.",
-                                   prog='dx extract_dataset')
-parser_extract_dataset.add_argument('path', help='v3.0 Dataset or Cohort object ID (project-id:record-id where "record-id" indicates the record ID in the currently selected project) or name')
-parser_extract_dataset.add_argument('-ddd', '--dump-dataset-dictionary', action="store_true", default=False, help='If provided, the three dictionary files, <record_name>.data_dictionary.csv, <record_name>.entity_dictionary.csv, and <record_name>.codings.csv will be generated. Files will be comma delimited and written to the local working directory, unless otherwise specified using --delimiter and --output arguments. If any of the three dictionary files does not contain data (i.e. the dictionary is empty), then that particular file will not be created.')
-parser_extract_dataset.add_argument('--fields', nargs='+', help='A comma-separated string where each value is the phenotypic entity name and field name, separated by a dot.  For example: "<entity_name>.<field_name>,<entity_name>.<field_name>". If multiple entities are provided, field values will be automatically inner joined. If only the --fields argument is provided, data will be retrieved and returned. If both --fields and --sql arguments are provided, a SQL statement to retrieve the specified field data will be automatically generated and returned.')
-parser_extract_dataset.add_argument('--sql', action="store_true", default=False, help='If provided, a SQL statement (string) will be returned to query the set of entity.fields, instead of returning stored values from the set of entity.fields')
-parser_extract_dataset.add_argument('--delim', '--delimiter', nargs='?', const=',', default=',', help='Always use exactly one of DELIMITER to separate fields to be printed; if no delimiter is provided with this flag, COMMA will be used')
-parser_extract_dataset.add_argument('-o', '--output', help='Local filename or directory to be used ("-" indicates stdout output). If not supplied, output will create a file with a default name in the current folder')
-parser_extract_dataset.set_defaults(func=extract_dataset)
-register_parser(parser_extract_dataset)
-
 #####################################
 # help
 #####################################

src/python/requirements.txt

@@ -9,6 +9,3 @@ cryptography>=3.4.2,<37; python_version > "3.5"
 gnureadline==8.0.0; sys_platform == "darwin" and python_version < "3.9" and platform_machine == "x86_64"
 pyreadline==2.1; sys_platform == "win32"  and python_version < "3.10"
 colorama==0.4.4; sys_platform == "win32"
-pandas==1.3.5; python_version>="3.7"
-pandas>=0.23.3,<=0.25.3; python_version>="3.5.3" and python_version<"3.7"
-pandas>=0.23.3,< 0.25.0; python_version<"3.5.3"

src/python/requirements_setuptools.txt

@@ -1,3 +1,3 @@
-pip==20.3.4
+pip==19.2
 setuptools==41.4.0
 wheel==0.33.4