5it :dZddlmZmZmZmZddlZejeZ e jejddl Z ddl Z ddlZddlZddlZddlZddlZddlZddlZddlZddlZddlZddlmZddlmZddlmZddlmZdd l m!Z!dd l"m#Z#m$Z$m%Z%m&Z&m'Z'm(Z(dd l)m*Z*ddl+Z+dd lm,Z,dd l-m.Z.ejXZ/da0dZ1dZ2e2ddl3m4Z5e5Z6dZ7d\a8a9d\a:a;adZ?dZ@e>aAe?aBe@aCdZDdZEdZFdaGdZHdjee5ej ejZKejZMeKdddd ZNe+jjjeEeE!ZRed"d#ZSe!je!jee!je!jfZXe,ZYdaZd$Z[dCd&Z\dDd'Z]d(Z^ejejejhZbe!jee!jede+jBje!jfZfd)Zgd*Zhd+Zid,ZjdEd-Zkd.Zld/Zmd0ddeEddd%dddeDd%f d1ZnGd2d3Zo dFd4ZpdGd5Zqd6Zrd7Zsd8Ztd9ZudDd:ZvdHd;Zw daxd<Zyd=Zzd>Z{dd?l|m}Z~e~Zdd@lddAlmZddBlmZmZy)Ia When this package is imported, configuration values will be loaded from the following sources in order of decreasing priority: 1. Environment variables 2. Values stored in ``~/.dnanexus_config/environment`` 3. Hardcoded defaults The bindings are configured by the following environment variables: .. envvar:: DX_SECURITY_CONTEXT A JSON hash containing your auth token, typically of the form ``{"auth_token_type": "Bearer", "auth_token": "YOUR_TOKEN"}``. .. envvar:: DX_APISERVER_PROTOCOL Either ``http`` or ``https`` (usually ``https``). .. envvar:: DX_APISERVER_HOST Hostname of the DNAnexus API server. .. envvar:: DX_APISERVER_PORT Port of the DNAnexus API server. .. envvar:: DX_JOB_ID Should only be present if run in an Execution Environment; indicates the ID of the currently running job. .. envvar:: DX_WORKSPACE_ID Should only be present if run in an Execution Environment; indicates the running job's temporary workspace ID. .. envvar:: DX_PROJECT_CONTEXT_ID Indicates either the project context of a running job, or the default project to use for a user accessing the platform from the outside. The following fields can be used to read the current configuration values: .. py:data:: APISERVER_PROTOCOL Protocol being used to access the DNAnexus API server. Either ``http`` or ``https`` (usually ``https``). .. py:data:: APISERVER_HOST Hostname of the DNAnexus API server. .. py:data:: APISERVER_PORT Port of the DNAnexus API server. .. py:data:: JOB_ID Indicates the ID of the currently running job, or None if we are not in an Execution Environment. .. py:data:: WORKSPACE_ID Indicates the temporary workspace ID of the currently running job, or the current project if we are not in an Execution Environment. .. py:data:: PROJECT_CONTEXT_ID Indicates either the project context of a running job, if there is one, or the default project that is being used, for users accessing the platform from the outside. .. py:data:: USER_AGENT The user agent string that dxpy will send to the server with each request. The :func:`dxpy.DXHTTPRequest` function uses the ``DX_SECURITY_CONTEXT`` and ``DX_APISERVER_*`` variables to select an API server and provide appropriate authentication headers to it. (Note: all methods in the :mod:`dxpy.api` module, and by extension any of the bindings methods that make API calls, use this function.) All object handler methods that require a project or data container ID use by default the ``DX_WORKSPACE_ID`` (if running inside an Execution Environment) or ``DX_PROJECT_CONTEXT_ID`` (otherwise). The following functions can be used to override any of the settings obtained from the environment for the duration of the session: * :func:`dxpy.set_security_context`: to specify an authentication token * :func:`dxpy.set_api_server_info`: to specify the API server (host, port, or protocol) * :func:`dxpy.set_workspace_id`: to specify the default data container To pass API server requests through an HTTP(S) proxy, set the following environment variables: .. envvar:: HTTP_PROXY HTTP proxy, in the form 'protocol://hostname:port' (e.g. 'http://10.10.1.10:3128') .. envvar:: HTTPS_PROXY HTTPS proxy, in the form 'protocol://hostname:port' )print_functionunicode_literalsdivisionabsolute_importN) namedtuple) BadStatusLine)StringIO)Repr) exceptions)BOLDBLUEYELLOWGREENREDWHITE)randint)Lock)urlsplitc\t5t}tdz a|cdddS#1swYyxYw)Nr )sequence_number_mutexcounter)retvals o/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/__init__.py_get_sequence_numberrs+ 1 s"+ctjtjjt j dj tjy)N)categoryzurllib3.connectionpool)urllib3disable_warningsr InsecurePlatformWarninglogging getLoggersetLevelERRORrconfigure_urllib3r's: g&8&8&P&PQ ./88Gr&)versionz1.0.0)NN)NNNNhttpsapi.dnanexus.com443iTz5{name}/{version} ({platform}) Python/{python_version})namer(platformpython_versionz gzip, deflatez*/*z keep-alive) User-AgentzAccept-EncodingAccept Connection)connectread_RequestForAuthzmethod url headersci}t|}|jr|j|jjddzd}dj |j ||d<|j r'dj |j|j }n |j}tj||d<|S||d<|S)N@r z {0}://{1} proxy_urlz{0}:{1})proxy_basic_auth proxy_headers) rusernamenetlocfindformatschemepasswordr make_headers)url proxy_infourl_info proxy_auths r_get_proxy_inforGsJ}Hoohoo22379:;"-"4"4X__c"J ;   "))(*;*;X=N=NOJ!**J&-&:&:J&W ?# #& ; r&Fcd}d}|D](}|tjvstj|}*|r"tdd|dtj|S)N) http_proxy HTTP_PROXY https_proxy HTTPS_PROXYzUsing env variable =z as proxyfile)osenvironprintsysstderr) print_proxy proxy_tupleproxy env_proxys r_get_env_var_proxyrYsUJ+ %$iBJJjj#e$ 5 Azz ,r&c tdtjtt}dt j vr|jt||dt j vrwt5t[trrindentz Range z%s [%f] %s %s%s => %s z>%d)rOendz%s [%f] %s %s => %s )rstr_DEBUGjsondumpsUnicodeDecodeError TypeErrorrRrr rrSrTr repr) debug_levelseq_num time_startedr~rCr^ jsonify_datarformatted_dataprintable_headerss r_debug_print_requestrsEa4yA~!%!83s4y>!IC!O 1Q;%)ZZQ%?N%)ZZ%5N g  #djj'77;K1L&M M  '6$uw2G+H+7+/<+.+<+9 +;; ::  q %UW_0E)F)5)-f),)-T): )<< ::   ' 2 1!0 1s6D22EEc l|dkDr.|re|dk\r+dtj|djddz} nS|dk(rtj|} n8tj |} nt |dkDrdt |znd} t tj|z d z} d |cxkrd kr nntnt} td ttd |zzd|zt|||d| t|ttd| z| t j" yy)Nrrz rr z (%d bytes)rii,z z<%dz[%f]z<=z(%dms)rN)rrreplacer rrrtimerrrRrr rrrrSrT) rrrreq_idresponse_statusresponse_was_jsonr~rCcontentcontent_to_printt code_formats r_debug_print_responsers Q a#)DJJwq,I,Q,QRVX^,_#_ !#'::g#6 #'6;;w#7 >A'lQ>N|c'l:TV  |+t3 4 # < |4fz}5n d?|4|d1z| fz}5d@tjVdA|dB|dC|/dD|5dB|, }6t|.t8jlr|6dE|.jzz }6tLj|6tj|4|d1z }||jTd=vr|d1z }Yd}.~.|s |d kDs tLjOd!tjV||| t|.t8jfsbd@tjVdA|dB|dC|/dF }6t|.t8jlr|6dE|.jzz }6tLj|6t|.t6j8jrdG|/vrt9j|/d}.~.wwxYw#|r2|d kDr,tLjOd!tjV|||wwwxYw)Ka :param resource: API server route, e.g. "/record/new". If *prepend_srv* is False, a fully qualified URL is expected. If this argument is a callable, it will be called just before each request attempt, and expected to return a tuple (URL, headers). Headers returned by the callback are updated with *headers* (including headers set by this method). :type resource: string :param data: Content of the request body :type data: list or dict, if *jsonify_data* is True; or string or file-like object, otherwise :param headers: Names and values of HTTP headers to submit with the request (in addition to those needed for authentication, compression, or other options specified with the call). :type headers: dict :param auth: Controls the ``Authentication`` header or other means of authentication supplied with the request. If ``True`` (default), a token is obtained from the ``DX_SECURITY_CONTEXT``. If the value evaluates to false, no action is taken to prepare authentication for the request. Otherwise, the value is assumed to be callable, and called with three arguments (method, url, headers) and expected to prepare the authentication headers by reference. :type auth: tuple, object, True (default), or None :param timeout: HTTP request timeout, in seconds :type timeout: float :param use_compression: Deprecated :type use_compression: string or None :param jsonify_data: If True, *data* is converted from a Python list or dict to a JSON string :type jsonify_data: boolean :param want_full_response: If True, the full :class:`urllib3.response.HTTPResponse` object is returned (otherwise, only the content of the response body is returned) :type want_full_response: boolean :param decode_response_body: If True (and *want_full_response* is False), the response body is decoded and, if it is a JSON string, deserialized. Otherwise, the response body is uncompressed if transport compression is on, and returned raw. :type decode_response_body: boolean :param prepend_srv: If True, prepends the API server location to the URL :type prepend_srv: boolean :param session_handler: Deprecated. :param max_retries: Maximum number of retries to perform for a request. A "failed" request is retried if any of the following is true: - A response is received from the server, and the content length received does not match the "Content-Length" header. - A response is received from the server, and the response has an HTTP status code in 5xx range. - A response is received from the server, the "Content-Length" header is not set, and the response JSON cannot be parsed. - No response is received from the server, and either *always_retry* is True or the request *method* is "GET". :type max_retries: int :param always_retry: If True, indicates that it is safe to retry a request on failure - Note: It is not guaranteed that the request will *always* be retried on failure; rather, this is an indication to the function that it would be safe to do so. :type always_retry: boolean :returns: Response from API server in the format indicated by *want_full_response* and *decode_response_body*. :raises: :exc:`exceptions.DXAPIError` or a subclass if the server returned a non-200 status code; :exc:`urllib3.exceptions.HTTPError` if an invalid response was received from the server; or :exc:`urllib3.exceptions.ConnectionError` if a connection cannot be established. Wrapper around :meth:`urllib3.request()` that makes an HTTP request, inserting authentication headers and (by default) converting *data* to JSON. .. note:: Bindings methods that make API calls make the underlying HTTP request(s) using :func:`DXHTTPRequest`, and most of them will pass any unrecognized keyword arguments you have supplied through to :func:`DXHTTPRequest`. NT)rvrcrdre_test_retry_http_requestFz Content-Typerzapplication/jsonseektellr)TNr1z DNAnexus-APIcHt|ts|jd}|S)Nascii)rbytesencode)is r ensure_asciiz#DXHTTPRequest..ensure_asciiUs%a/HHW-Hr&shostscontent-lengthsContent-Lengthr)r^bodyr_retriesClosedPoolErrorz x-request-id unavailablezx-upgrade-inforz!A recommended update is available _ARGCOMPLETEadrLocationz'Location not found in redirect responsez&[%s] %s %s: Recovered after %d retriesz content-typezutf-8zContent is nonez!Invalid JSON received from serverrtypez0Appropriate error class not found. 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